diff --git a/NAMESPACE b/NAMESPACE index 9edf6375..2e884319 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,12 +1,27 @@ # Generated by roxygen2: do not edit by hand -S3method(ATSB,null) -S3method(BedNets,lemenach) -S3method(BedNets,null) +S3method(Abiotic,forced) +S3method(Abiotic,null) +S3method(AreaSpray,null) +S3method(AreaSprayEffectSizes,null) +S3method(AreaSprayEffects,null) +S3method(BedNetEffectSizes,lemenach) +S3method(BedNetEffectSizes,null) +S3method(BedNetEffects,null) +S3method(Behavior,forced) +S3method(Behavior,null) S3method(Births,numeric) S3method(Births,static) -S3method(ExogenousForcing,forced) -S3method(ExogenousForcing,null) +S3method(CareSeeking,null) +S3method(Civil,forced) +S3method(Civil,null) +S3method(Clinic,null) +S3method(Control,forced) +S3method(Control,null) +S3method(Control,static) +S3method(Development,null) +S3method(DistributeBedNets,null) +S3method(EIP,static) S3method(F_H,dynamic) S3method(F_H,static) S3method(F_X,SIP) @@ -15,6 +30,10 @@ S3method(F_X,hMoI) S3method(F_X,trace) S3method(F_alpha,basic) S3method(F_alpha,trace) +S3method(F_b,SIP) +S3method(F_b,SIS) +S3method(F_b,hMoI) +S3method(F_b,trace) S3method(F_births,constant) S3method(F_births,exp) S3method(F_births,forced) @@ -24,7 +43,6 @@ S3method(F_eggs,Gtrace) S3method(F_eggs,RM) S3method(F_eggs,Ztrace) S3method(F_eggs,basicM) -S3method(F_eip,static) S3method(F_f,static) S3method(F_f,type2) S3method(F_foi,nb) @@ -34,42 +52,63 @@ S3method(F_fqZ,Gtrace) S3method(F_fqZ,RM) S3method(F_fqZ,Ztrace) S3method(F_g,static) -S3method(F_habitats,forced) -S3method(F_habitats,null) -S3method(F_habitats,static) S3method(F_nu,static) S3method(F_nu,type2) -S3method(F_otherblood,forced) -S3method(F_otherblood,null) -S3method(F_otherblood,static) S3method(F_q,dynamic) S3method(F_q,static) S3method(F_sigma,BQS) S3method(F_sigma,static) -S3method(F_sugar,forced) -S3method(F_sugar,null) -S3method(F_sugar,static) S3method(HTC,SIP) S3method(HTC,SIS) S3method(HTC,hMoI) -S3method(HumanBehavior,null) +S3method(HabitatAvailability,forced) +S3method(HabitatAvailability,null) +S3method(HabitatDynamics,null) +S3method(HumanAvailability,forced) +S3method(HumanAvailability,null) S3method(Hydrology,null) -S3method(IRS,null) -S3method(LSM,null) -S3method(MosquitoBehavior,GeRM) -S3method(MosquitoBehavior,Gtrace) -S3method(MosquitoBehavior,RM) -S3method(MosquitoBehavior,Ztrace) -S3method(MosquitoBehavior,basicM) -S3method(Resources,GeRM) -S3method(Resources,dynamic) +S3method(IRSeffectSizes,null) +S3method(IRSeffects,null) +S3method(LBionomics,basic) +S3method(LBionomics,trace) +S3method(LSMeffectSizes,null) +S3method(LSMeffects,null) +S3method(MBionomics,GeRM) +S3method(MBionomics,Gtrace) +S3method(MBionomics,RM) +S3method(MBionomics,Ztrace) +S3method(MBionomics,basicM) +S3method(MassMedical,forced) +S3method(MassMedical,null) +S3method(OtherBloodHosts,null) +S3method(OviTraps,null) +S3method(OwnBedNet,null) +S3method(Resources,forced) S3method(Resources,null) -S3method(Resources,static) +S3method(Shock,null) +S3method(SprayHouses,null) +S3method(Sugar,null) +S3method(SugarAvailability,forced) +S3method(SugarAvailability,null) +S3method(SugarBaitEffectSizes,null) +S3method(SugarBaitEffects,null) +S3method(SugarBaits,null) +S3method(TreatHabitats,null) +S3method(UseBedNet,null) S3method(VectorControl,control) S3method(VectorControl,null) +S3method(VectorControlEffectSizes,control) +S3method(VectorControlEffectSizes,null) +S3method(VectorControlEffects,control) +S3method(VectorControlEffects,null) S3method(Visitors,basic) S3method(Visitors,null) +S3method(Weather,forced) S3method(Weather,null) +S3method(check_abiotic,forced) +S3method(check_abiotic,null) +S3method(check_civil,forced) +S3method(check_civil,null) S3method(dHdt,numeric) S3method(dHdt,static) S3method(dLdt,basic) @@ -147,65 +186,88 @@ S3method(setup_X,SIP) S3method(setup_X,SIS) S3method(setup_X,hMoI) S3method(setup_X,trace) +S3method(setup_behavior,forced) +S3method(setup_behavior,null) +S3method(setup_control,forced) +S3method(setup_control,null) S3method(travel_malaria,eir) S3method(travel_malaria,foi) S3method(travel_malaria,null) -S3method(update_BloodFeeding,dynamic) -S3method(update_BloodFeeding,static) -S3method(update_EggLaying,dynamic) -S3method(update_EggLaying,static) -S3method(update_O,dynamic) -S3method(update_O,static) -S3method(update_S,dynamic) -S3method(update_S,static) -S3method(update_W,dynamic) -S3method(update_W,static) S3method(xde_solve,aqua) S3method(xde_solve,aqua_dde) +S3method(xde_solve,cohort) S3method(xde_solve,dde) S3method(xde_solve,human) S3method(xde_solve,mosy) S3method(xde_solve,mosy_dde) S3method(xde_solve,ode) -export(ATSB) -export(BedNets) +export(Abiotic) +export(AreaSpray) +export(AreaSprayEffectSizes) +export(AreaSprayEffects) +export(BedNetEffectSizes) +export(BedNetEffects) +export(Behavior) export(Births) -export(ExogenousForcing) +export(CareSeeking) +export(Civil) +export(Clinic) +export(Control) +export(Development) +export(DistributeBedNets) +export(EIP) +export(Exposure) export(F_EIR) export(F_H) export(F_X) export(F_alpha) +export(F_b) export(F_beta) export(F_births) export(F_eggs) -export(F_eip) export(F_f) export(F_foi) export(F_fqZ) export(F_g) -export(F_habitats) export(F_kappa) export(F_nu) -export(F_otherblood) export(F_q) export(F_sigma) -export(F_sugar) export(F_tau) export(HTC) -export(HumanBehavior) +export(HabitatAvailability) +export(HabitatDynamics) +export(HumanAvailability) export(Hydrology) -export(IRS) -export(LSM) -export(MosquitoBehavior) +export(IRSeffectSizes) +export(IRSeffects) +export(LBionomics) +export(LSMeffectSizes) +export(LSMeffects) +export(MBionomics) +export(MassMedical) +export(OtherBloodHosts) +export(OviTraps) +export(OwnBedNet) export(Resources) +export(Shock) +export(SprayHouses) +export(Sugar) +export(SugarAvailability) +export(SugarBaitEffectSizes) +export(SugarBaitEffects) +export(SugarBaits) +export(TreatHabitats) +export(UseBedNet) export(VectorControl) +export(VectorControlEffectSizes) +export(VectorControlEffects) export(Visitors) export(Weather) export(approx_equal) export(checkIt) -export(compute_B) -export(compute_Q) -export(compute_W) +export(check_abiotic) +export(check_civil) export(compute_beta) export(compute_local_frac) export(dHdt) @@ -290,25 +352,42 @@ export(setup_Hpar) export(setup_L) export(setup_MYZ) export(setup_X) -export(setup_atsb_null) -export(setup_exogenous_forced) -export(setup_exogenous_null) +export(setup_abiotic_forced) +export(setup_abiotic_null) +export(setup_area_spray_null) +export(setup_behavior) +export(setup_behavior_forced) +export(setup_behavior_null) +export(setup_care_seeking_null) +export(setup_civil_forced) +export(setup_civil_null) +export(setup_clinic_forced) +export(setup_clinic_null) +export(setup_control) +export(setup_control_forced) +export(setup_control_null) +export(setup_development_null) +export(setup_eip_static) export(setup_exposure_nb) export(setup_exposure_pois) -export(setup_forcing_MYZ_GeRM_basic) -export(setup_habitats_forced) -export(setup_habitats_null) -export(setup_habitats_static) -export(setup_humanbehavior_null) +export(setup_habitat_dynamics_null) export(setup_hydrology_null) export(setup_irs_null) export(setup_itn_lemenach) export(setup_itn_null) export(setup_lsm_null) -export(setup_otherblood_forced) +export(setup_mass_medical_forced) +export(setup_mass_medical_null) +export(setup_other_blood_hosts_null) +export(setup_ovitraps_null) +export(setup_rainfall_null) +export(setup_relative_humidity_null) +export(setup_resources_forced) export(setup_resources_null) -export(setup_resources_static) -export(setup_sugar_forced) +export(setup_shock_null) +export(setup_sugar_baits_null) +export(setup_sugar_null) +export(setup_temperature_null) export(setup_travel_eir) export(setup_travel_foi) export(setup_travel_null) @@ -316,13 +395,9 @@ export(setup_vc_control) export(setup_vc_null) export(setup_visitors_basic) export(setup_visitors_null) +export(setup_weather_forced) export(setup_weather_null) export(travel_malaria) -export(update_BloodFeeding) -export(update_EggLaying) -export(update_O) -export(update_S) -export(update_W) export(xDE_diffeqn) export(xDE_diffeqn_aquatic) export(xDE_diffeqn_cohort) @@ -330,6 +405,7 @@ export(xDE_diffeqn_human) export(xDE_diffeqn_mosy) export(xde_setup) export(xde_setup_aquatic) +export(xde_setup_cohort) export(xde_setup_human) export(xde_setup_mosy) export(xde_solve) diff --git a/R/abiotic.R b/R/abiotic.R new file mode 100644 index 00000000..e3ec5373 --- /dev/null +++ b/R/abiotic.R @@ -0,0 +1,77 @@ +# generic methods for exogenous forcing by abiotic factors + +#' @title Set up exogenous variables for abiotic forcing +#' @description This method dispatches on the type of `pars$ABIOTIC`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +Abiotic <- function(t, pars) { + UseMethod("Abiotic", pars$ABIOTIC) +} + +#' @title Set up exogenous variables for abiotic forcing +#' @description Implements [Abiotic] for the null model of exogenous forcing (do nothing) +#' @inheritParams Abiotic +#' @return [list] +#' @export +Abiotic.null <- function(t, pars) {pars} + +#' @title Set up the null model for exogenous forcing (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_abiotic_null <- function(pars) { + ABIOTIC <- list() + class(ABIOTIC) <- 'null' + pars$ABIOTIC <- ABIOTIC + return(pars) +} + +#' @title Set up exogenous variables for abiotic forcing +#' @description Implements [Abiotic] for abiotic forcing +#' @param t current simulation time +#' @param pars a [list] +#' @return pars a [list] +#' @export +Abiotic.forced <- function(t, pars) { + pars = Weather(t, pars) + pars = Hydrology(t, pars) + return(pars) +} + +#' @title Make parameters for the null model of abiotic forcing (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_abiotic_forced <- function(pars) { + ABIOTIC <- list() + class(ABIOTIC) <- 'forced' + pars$ABIOTIC <- ABIOTIC + pars = setup_weather_null(pars) + pars = setup_hydrology_null(pars) + return(pars) +} + +#' @title Check abiotic +#' @param pars a [list] +#' @return [list] +#' @export +check_abiotic <- function(pars) { + UseMethod("check_abiotic", pars$EfSz) +} + +#' @title Check abiotic +#' @param pars a [list] +#' @return [list] +#' @export +check_abiotic.null <- function(pars) { + setup_abiotic_forced(pars) +} + +#' @title Check abiotic +#' @param pars a [list] +#' @return [list] +#' @export +check_abiotic.forced<- function(pars) {pars} + diff --git a/R/adult-GeRM.R b/R/adult-GeRM.R index 95169e9b..c36ab42b 100644 --- a/R/adult-GeRM.R +++ b/R/adult-GeRM.R @@ -1,37 +1,21 @@ # specialized methods for the adult mosquito GeRM model -#' @title Set the availability of resources -#' @description Implements [Resources] for the GeRM model -#' @inheritParams Resources -#' @return a named [list] -#' @export -Resources.GeRM <- function(t, y, pars) { - pars$O = F_otherblood(t, pars) - pars$S = F_sugar(t, pars) - pars$Q = compute_Q(pars) - pars$W = compute_W(t, y, pars) - pars$B = compute_B( pars) - pars$local_frac = with(pars, W/(W + Visitors)) - return(pars) -} - - #' @title Reset bloodfeeding and mortality rates to baseline -#' @description Implements [MosquitoBehavior] for the GeRM model -#' @inheritParams MosquitoBehavior +#' @description Implements [MBionomics] for the GeRM model +#' @inheritParams MBionomics #' @return a named [list] #' @export -MosquitoBehavior.GeRM <- function(t, y, pars) { +MBionomics.GeRM <- function(t, y, pars) { with(pars,{ pars$MYZpar$f = F_f(t, pars) pars$MYZpar$q = F_q(t, pars) pars$MYZpar$g = F_g(t, pars) pars$MYZpar$sigma = F_sigma(t, pars) pars$MYZpar$nu = F_nu(t, pars) - pars$MYZpar$eip = F_eip(t, pars) return(pars) })} + #' @title Blood feeding rate of the infective mosquito population #' @description Implements [F_fqZ] for the GeRM model. #' @inheritParams F_fqZ @@ -228,18 +212,14 @@ make_MYZpar_GeRM = function(pars, MYZopts=list(), calK, MYZpar$nu0 <- checkIt(nu, pars$nPatches) } else MYZpar$nu_par= setup_Fx(setup_Fnu) - if(length(setup_Feip) == 0){ - MYZpar$eip_par <- list() - class(MYZpar$eip_par) <- "static" - MYZpar$eip <- eip - } else MYZpar$eip_par = setup_Fx(setup_Feip) + MYZpar$eip <- eip MYZpar$eggsPerBatch <- eggsPerBatch MYZpar$calK <- calK pars$MYZpar = MYZpar - pars = MosquitoBehavior(0, 0, pars) + pars = MBionomics(0, 0, pars) return(pars) })} @@ -389,50 +369,10 @@ make_parameters_MYZ_GeRM_static <- function(pars, g, sigma, f, q, nu, eggsPerBat MYZpar$calK <- calK pars$MYZpar <- MYZpar - pars = MosquitoBehavior(0, 0, pars) + pars = MBionomics(0, 0, pars) return(pars) } -#' @title Set up a static exogenous forcing for the GeRM ODE adult mosquito model -#' @param pars a [list] -#' @param other is the availability of other blood hosts -#' @param zeta is a shape parameter -#' @param sugar is sugar availability -#' @return none -#' @export -setup_forcing_MYZ_GeRM_basic <- function(pars, other, sugar, zeta) { - - RApar = list() - class(RApar) = "GeRM" - pars$RApar = RApar - - Wpar = list() - class(Wpar) <- "static" - pars$Wpar = Wpar - pars$W = compute_W(0, 0, pars) - - OBHpar = list() - class(OBHpar) <- "static" - OBHpar$other = other - OBHpar$zeta = zeta - pars$OBHpar = OBHpar - pars$OtherBloodHosts = other^zeta - - SGRpar = list() - class(SGRpar) <- "static" - pars$SGRpar = SGRpar - pars$sugar = sugar - - Qpar = list() - class(Qpar) <- "static" - pars$Qpar = Qpar - pars$Q = compute_Q(pars) - - pars = Resources(0, 0, pars) - return(pars) -} - - #' @title Make inits for GeRM adult mosquito model #' @param pars a [list] #' @param M0 total mosquito density at each patch diff --git a/R/adult-Gtrace.R b/R/adult-Gtrace.R index ef3934ac..b65db93d 100644 --- a/R/adult-Gtrace.R +++ b/R/adult-Gtrace.R @@ -1,11 +1,11 @@ # specialized methods for the adult mosquito Gtrace model #' @title Compute bloodfeeding and mortality rates -#' @description Implements [MosquitoBehavior] for the Gtrace model. -#' @inheritParams MosquitoBehavior +#' @description Implements [MBionomics] for the Gtrace model. +#' @inheritParams MBionomics #' @return a named [list] #' @export -MosquitoBehavior.Gtrace <- function(t, y, pars) { +MBionomics.Gtrace <- function(t, y, pars) { return(pars) } @@ -113,7 +113,7 @@ make_parameters_MYZ_Gtrace <- function(pars, Gm, Gf) { MYZpar$Gm <- Gm MYZpar$Gf = Gf pars$MYZpar <- MYZpar - pars = MosquitoBehavior(pars) + pars = MBionomics(pars) return(pars) } diff --git a/R/adult-RM.R b/R/adult-RM.R index 1f128835..4ef12f04 100644 --- a/R/adult-RM.R +++ b/R/adult-RM.R @@ -1,11 +1,11 @@ # specialized methods for the adult mosquito RM model #' @title Reset bloodfeeding and mortality rates to baseline -#' @description Implements [MosquitoBehavior] for the RM model -#' @inheritParams MosquitoBehavior +#' @description Implements [MBionomics] for the RM model +#' @inheritParams MBionomics #' @return a named [list] #' @export -MosquitoBehavior.RM <- function(t, y, pars) { +MBionomics.RM <- function(t, y, pars) { pars$MYZpar$f <- pars$MYZpar$f0 pars$MYZpar$q <- pars$MYZpar$q0 @@ -180,7 +180,7 @@ make_MYZpar_RM = function(pars, MYZopts=list(), calK, MYZpar$calK <- calK pars$MYZpar = MYZpar - pars = MosquitoBehavior(0, 0, pars) + pars = MBionomics.RM(0, 0, pars) return(pars) })} @@ -298,7 +298,7 @@ make_parameters_MYZ_RM <- function(pars, g, sigma, f, q, nu, eggsPerBatch, eip, MYZpar$calK <- calK pars$MYZpar <- MYZpar - pars = MosquitoBehavior.RM(0, 0, pars) + pars = MBionomics.RM(0, 0, pars) return(pars) } diff --git a/R/adult-Ztrace.R b/R/adult-Ztrace.R index ea97ba53..a8bfae0c 100644 --- a/R/adult-Ztrace.R +++ b/R/adult-Ztrace.R @@ -1,11 +1,11 @@ # specialized methods for the adult mosquito Ztrace model #' @title Compute bloodfeeding and mortality rates -#' @description Implements [MosquitoBehavior] for the Ztrace model. -#' @inheritParams MosquitoBehavior +#' @description Implements [MBionomics] for the Ztrace model. +#' @inheritParams MBionomics #' @return a named [list] #' @export -MosquitoBehavior.Ztrace <- function(t, y, pars) { +MBionomics.Ztrace <- function(t, y, pars) { pars$MYZpar$f <- pars$MYZpar$f0 pars$MYZpar$q <- pars$MYZpar$q0 return(pars) @@ -89,7 +89,7 @@ make_MYZpar_Ztrace = function(pars, MYZopts, MYZpar$Zf <- Zf pars$MYZpar = MYZpar - pars = MosquitoBehavior(0, 0, pars) + pars = MBionomics(0, 0, pars) return(pars) })} @@ -124,7 +124,7 @@ make_parameters_MYZ_Ztrace <- function(pars, Zm, f, q, Zf) { MYZpar$q0 <- q MYZpar$Zf = Zf pars$MYZpar <- MYZpar - pars = MosquitoBehavior(0, 0, pars) + pars = MBionomics(0, 0, pars) return(pars) } diff --git a/R/adult-basicM.R b/R/adult-basicM.R index 10786441..ab74422e 100644 --- a/R/adult-basicM.R +++ b/R/adult-basicM.R @@ -1,11 +1,11 @@ # specialized methods for a basic adult mosquito model #' @title Set bionomic parameters to baseline -#' @description Implements [MosquitoBehavior] for the basicM model -#' @inheritParams MosquitoBehavior +#' @description Implements [MBionomics] for the basicM model +#' @inheritParams MBionomics #' @return a named [list] #' @export -MosquitoBehavior.basicM <- function(t, y, pars) { +MBionomics.basicM <- function(t, y, pars) { pars$MYZpar$f <- pars$MYZpar$f0 pars$MYZpar$q <- pars$MYZpar$q0 @@ -109,7 +109,7 @@ make_MYZpar_basicM = function(pars, MYZopts=list(), calK, MYZpar$calK <- calK pars$MYZpar = MYZpar - pars = MosquitoBehavior(0, 0, pars) + pars = MBionomics(0, 0, pars) return(pars) })} @@ -186,7 +186,7 @@ make_parameters_MYZ_basicM <- function(pars, g, sigma, f, q, nu, eggsPerBatch, c MYZpar$calK <- calK pars$MYZpar <- MYZpar - pars = MosquitoBehavior(0, 0, pars) + pars = MBionomics(0, 0, pars) return(pars) } diff --git a/R/bionomics.R b/R/adult-bionomics.R similarity index 87% rename from R/bionomics.R rename to R/adult-bionomics.R index d65f2d02..8baffe7e 100644 --- a/R/bionomics.R +++ b/R/adult-bionomics.R @@ -25,7 +25,7 @@ F_f.static <- function(t, pars){ #' @return a [numeric] vector of length `nPatches` #' @export F_f.type2 <- function(t, pars){ - B = pars$B + B = with(pars, W + Visitors + O) with(pars$MYZpar$f_par,{ return(fx*sf*B/(1+sf*B)) }) @@ -58,7 +58,7 @@ F_q.static <- function(t, pars){ #' @export F_q.dynamic <- function(t, pars){ with(pars,{ - return((W+Visitors)/B) + return((W+Visitors)/(W + Visitors + O)) }) } @@ -140,28 +140,7 @@ F_nu.static <- function(t, pars){ #' @return a [numeric] vector of length `nPatches` #' @export F_nu.type2 <- function(t, pars){ - Q = pars$Q with(pars$MYZpar$nu_par,{ return(nux*snu*Q/(1+snu*Q)) }) } - -#' @title Compute the eip -#' @description This method dispatches on the type of `pars$MYZpar$eip_par`. It should -#' set the values of the eip -#' @param t current simulation time -#' @param pars a [list] -#' @return a [numeric] vector of length `nPatches` -#' @export -F_eip <- function(t, pars) { - UseMethod("F_eip", pars$MYZpar$eip_par) -} - -#' @title Static model for human blood fraction -#' @description Implements [F_eip] for a static model -#' @inheritParams F_eip -#' @return a [numeric] vector of length `nPatches` -#' @export -F_eip.static <- function(t, pars){ - pars$MYZpar$eip -} diff --git a/R/adult-interface.R b/R/adult-interface.R index 181444a0..aea3b7c2 100644 --- a/R/adult-interface.R +++ b/R/adult-interface.R @@ -8,8 +8,8 @@ #' @param pars a [list] #' @return a [list] #' @export -MosquitoBehavior <- function(t, y, pars) { - UseMethod("MosquitoBehavior", pars$MYZpar) +MBionomics <- function(t, y, pars) { + UseMethod("MBionomics", pars$MYZpar) } #' @title Time spent host seeking/feeding and resting/ovipositing diff --git a/R/aquatic-basic.R b/R/aquatic-basic.R index a9008990..3047c3c4 100644 --- a/R/aquatic-basic.R +++ b/R/aquatic-basic.R @@ -1,5 +1,18 @@ # specialized methods for the aquatic mosquito basic competition model +#' @title Reset aquatic parameters to baseline +#' @description Implements [LBionomics] for the RM model +#' @inheritParams LBionomics +#' @return a named [list] +#' @export +LBionomics.basic <- function(t, y, pars) { + pars$Lpar$psi <- pars$Lpar$psi0 + pars$Lpar$phi <- pars$Lpar$phi0 + pars$Lpar$theta <- pars$Lpar$theta0 + return(pars) +} + + #' @title Number of newly emerging adults from each larval habitat #' @description Implements [F_alpha] for the basic competition model. #' @inheritParams F_alpha @@ -43,8 +56,9 @@ setup_L.basic = function(pars, Lname, with(Lopts,{ - pars = make_Lpar_basic(pars, Lopts) - pars = make_Linits_basic(pars, Lopts) + pars <- make_Lpar_basic(pars, Lopts) + pars <- LBionomics.basic(0, 0, pars) + pars <- make_Linits_basic(pars, Lopts) return(pars) })} @@ -60,9 +74,9 @@ setup_L.basic = function(pars, Lname, make_Lpar_basic = function(pars, Lopts=list(), psi=1/8, phi=1/8, theta=1/100){with(Lopts,{ Lpar = list() class(Lpar) <- "basic" - Lpar$psi = checkIt(psi, pars$nHabitats) - Lpar$phi = checkIt(phi, pars$nHabitats) - Lpar$theta = checkIt(theta, pars$nHabitats) + Lpar$psi0 = checkIt(psi, pars$nHabitats) + Lpar$phi0 = checkIt(phi, pars$nHabitats) + Lpar$theta0 = checkIt(theta, pars$nHabitats) pars$Lpar = Lpar return(pars) @@ -115,10 +129,11 @@ make_parameters_L_basic <- function(pars, psi, phi, theta) { stopifnot(is.numeric(psi), is.numeric(phi), is.numeric(theta)) Lpar <- list() class(Lpar) <- 'basic' - Lpar$psi <- psi - Lpar$phi <- phi - Lpar$theta <- theta + Lpar$psi0 <- psi + Lpar$phi0 <- phi + Lpar$theta0 <- theta pars$Lpar <- Lpar + pars <- LBionomics.basic(0, 0, pars) return(pars) } diff --git a/R/aquatic-interface.R b/R/aquatic-interface.R index b4c76241..01f9ae68 100644 --- a/R/aquatic-interface.R +++ b/R/aquatic-interface.R @@ -1,5 +1,19 @@ # generic methods for aquatic component + +#' @title Set aquatic bionomic parameter rates relative to baseline +#' @description This method dispatches on the type of `pars$Lpar`. It should +#' compute the values of parameters as a function of exogenous variables +#' or reset the values of the bionomic parameters to baseline values. +#' @param t current simulation time +#' @param y state vector +#' @param pars a [list] +#' @return a [list] +#' @export +LBionomics <- function(t, y, pars) { + UseMethod("LBionomics", pars$Lpar) +} + #' @title Number of newly emerging adults from each larval habitat #' @description This method dispatches on the type of `pars$Lpar`. #' @param t current simulation time diff --git a/R/aquatic-trace.R b/R/aquatic-trace.R index 96cf7c77..e83faf03 100644 --- a/R/aquatic-trace.R +++ b/R/aquatic-trace.R @@ -1,5 +1,14 @@ # specialized methods for the aquatic mosquito trace model +#' @title Reset aquatic parameters to baseline +#' @description Implements [LBionomics] for the RM model +#' @inheritParams LBionomics +#' @return a named [list] +#' @export +LBionomics.trace <- function(t, y, pars) { + return(pars) +} + #' @title Number of newly emerging adults from each larval habitat #' @description Implements [F_alpha] for the trace (forced emergence) model. #' @inheritParams F_alpha diff --git a/R/area_spray.R b/R/area_spray.R new file mode 100644 index 00000000..e9b842ac --- /dev/null +++ b/R/area_spray.R @@ -0,0 +1,71 @@ +# generic methods for mass spraying + +#' @title Methods for mass spraying +#' @description This method dispatches on the type of `pars$AREA_SPRAY`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +AreaSpray <- function(t, pars) { + UseMethod("AreaSpray", pars$AREA_SPRAY) +} + +#' @title Methods for mass spraying +#' @description This method dispatches on the type of `pars$AREA_SPRAY`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +AreaSprayEffects <- function(t, pars) { + UseMethod("AreaSprayEffects", pars$AREA_SPRAY) +} + +#' @title Methods for mass spraying +#' @description This method dispatches on the type of `pars$AREA_SPRAY`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +AreaSprayEffectSizes <- function(t, pars) { + UseMethod("AreaSprayEffectSizes", pars$AREA_SPRAY) +} + + +#' @title Set up mass spraying +#' @description Implements [AreaSpray] for the null model (do nothing) +#' @inheritParams AreaSpray +#' @return [list] +#' @export +AreaSpray.null <- function(t, pars) { + return(pars) +} + +#' @title Set up mass spraying +#' @description Implements [AreaSprayEffects] for the null model (do nothing) +#' @inheritParams AreaSprayEffects +#' @return [list] +#' @export +AreaSprayEffects.null <- function(t, pars) { + return(pars) +} + +#' @title Set up mass spraying +#' @description Implements [AreaSprayEffectSizes] for the null model (do nothing) +#' @inheritParams AreaSprayEffectSizes +#' @return [list] +#' @export +AreaSprayEffectSizes.null <- function(t, pars) { + return(pars) +} + +#' @title Set up the null model for area spraying (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_area_spray_null <- function(pars) { + pars = setup_vc_control(pars) + AREA_SPRAY <- list() + class(AREA_SPRAY) <- 'null' + pars$AREA_SPRAY <- AREA_SPRAY + return(pars) +} diff --git a/R/atsb-interface.R b/R/atsb-interface.R deleted file mode 100644 index 0c54fe06..00000000 --- a/R/atsb-interface.R +++ /dev/null @@ -1,11 +0,0 @@ -# generic methods for ATSB - -#' @title Modify baseline bionomic values due to ATSB -#' @description This method dispatches on the type of `pars$ATSBpar`. -#' @param t current simulation time -#' @param pars a [list] -#' @return a [list] -#' @export -ATSB <- function(t, pars) { - UseMethod("ATSB", pars$ATSBpar) -} diff --git a/R/atsb-null.R b/R/atsb-null.R deleted file mode 100644 index 8ff2684e..00000000 --- a/R/atsb-null.R +++ /dev/null @@ -1,21 +0,0 @@ -# specialized methods for the null model of ATSB - -#' @title Modify baseline values due to ATSB -#' @description Implements [ATSB] for the null model of ATSB (do nothing) -#' @inheritParams ATSB -#' @return a [list] -#' @export -ATSB.null <- function(t, pars) { - return(pars) -} - -#' @title Make parameters for the null model of ATSB (do nothing) -#' @param pars a [list] -#' @return a [list] -#' @export -setup_atsb_null <- function(pars) { - ATSBpar <- list() - class(ATSBpar) <- 'null' - pars$ATSBpar <- ATSBpar - return(pars) -} diff --git a/R/bednet-interface.R b/R/bednet-interface.R index 8e3d4802..dac44f16 100644 --- a/R/bednet-interface.R +++ b/R/bednet-interface.R @@ -1,11 +1,53 @@ -# generic methods for vector control component +# generic methods for bed nets -#' @title Modify baseline bionomic values due to bed nets -#' @description This method dispatches on the type of `pars$ITNpar`. +#' @title Distribute bed nets, called from Control(VectorControl) +#' @description This method dispatches on the type of `pars$ITNdist`. #' @param t current simulation time #' @param pars a [list] #' @return a [list] #' @export -BedNets <- function(t, pars) { - UseMethod("BedNets", pars$ITNpar) +DistributeBedNets<- function(t, pars) { + UseMethod("DistributeBedNets", pars$ITNdist) +} + +#' @title Model bed net loss, called from Control(VectorControl) +#' @description This method dispatches on the type of `pars$ITNown`. +#' @param t current simulation time +#' @param y vector of state variables +#' @param pars a [list] +#' @return a [list] +#' @export +OwnBedNet <- function(t, y, pars) { + UseMethod("OwnBedNet", pars$ITNown) +} + +#' @title Model bed net usage, called from Behavior +#' @description This method dispatches on the type of `pars$ITNuse`. +#' @param t current simulation time +#' @param y vector of state variables +#' @param pars a [list] +#' @return a [list] +#' @export +UseBedNet <- function(t, y, pars) { + UseMethod("UseBedNets", pars$ITNuse) +} + +#' @title Modify variables or parameters, called from VectorControlEffects +#' @description This method dispatches on the type of `pars$ITNeff`. +#' @param t current simulation time +#' @param pars a [list] +#' @return a [list] +#' @export +BedNetEffects <- function(t, pars) { + UseMethod("BedNetEffects", pars$ITNeff) +} + +#' @title Modify baseline bionomic parameters, called from VectorControlEffectSizes +#' @description This method dispatches on the type of `pars$ITNefsz`. +#' @param t current simulation time +#' @param pars a [list] +#' @return a [list] +#' @export +BedNetEffectSizes <- function(t, pars) { + UseMethod("BedNetEffectSizes", pars$ITNefsz) } diff --git a/R/bednet-lemenach.R b/R/bednet-lemenach.R index 4d7a8a71..2f014ab2 100644 --- a/R/bednet-lemenach.R +++ b/R/bednet-lemenach.R @@ -2,12 +2,12 @@ # https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-6-10 #' @title Modify baseline values due to vector control -#' @description Implements [BedNets] for the Le Menach ITN model of vector control -#' @inheritParams BedNets +#' @description Implements [BedNetEffectSizes] for the Le Menach ITN model of vector control +#' @inheritParams BedNetEffectSizes #' @return a named [list] #' @importFrom stats pexp #' @export -BedNets.lemenach <- function(t, pars) { +BedNetEffectSizes.lemenach <- function(t, pars) { n <- length(pars$MYZpar$f) @@ -55,6 +55,7 @@ setup_itn_lemenach <- function(pars, tau0_frac = c(0.68/3, 2.32/3), r = 0.56, s stopifnot(sum(tau0_frac) == 1) stopifnot(phi(0) >= 0) stopifnot(phi(0) <= 1) + ITNpar <- list() class(ITNpar) <- 'lemenach' @@ -63,6 +64,6 @@ setup_itn_lemenach <- function(pars, tau0_frac = c(0.68/3, 2.32/3), r = 0.56, s ITNpar$s <- s ITNpar$cover <- phi - pars$ITNpar <- ITNpar + pars$ITNefsz <- ITNpar return(pars) } diff --git a/R/bednet-null.R b/R/bednet-null.R index 87371ed4..a1720085 100644 --- a/R/bednet-null.R +++ b/R/bednet-null.R @@ -1,12 +1,48 @@ # specialized methods for the null model of bed nets -#' @title Modify baseline values due to bed nets -#' @description Implements [BedNets] for the null model of bed nets (do nothing) -#' @inheritParams BedNets +#' @title Distribute bed nets +#' @description Implements [DistributeBedNets] for the null model of bed nets (do nothing) +#' @inheritParams DistributeBedNets #' @return a [list] #' @export -BedNets.null <- function(t, pars) { - return(pars) +DistributeBedNets.null <- function(t, pars) { + pars +} + +#' @title Bed net ownership +#' @description Implements [OwnBedNet] for the null model of bed nets (do nothing) +#' @inheritParams OwnBedNet +#' @return a [list] +#' @export +OwnBedNet.null <- function(t, y, pars) { + pars +} + +#' @title Bed net ownership +#' @description Implements [UseBedNet] for the null model of bed nets (do nothing) +#' @inheritParams UseBedNet +#' @return a [list] +#' @export +UseBedNet.null <- function(t, y, pars) { + pars +} + +#' @title Bed net ownership +#' @description Implements [BedNetEffects] for the null model of bed nets (do nothing) +#' @inheritParams BedNetEffects +#' @return a [list] +#' @export +BedNetEffects.null <- function(t, pars) { + pars +} + +#' @title Bed net ownership +#' @description Implements [BedNetEffectSizes] for the null model of bed nets (do nothing) +#' @inheritParams BedNetEffectSizes +#' @return a [list] +#' @export +BedNetEffectSizes.null <- function(t, pars) { + pars } #' @title Make parameters for the null model of bed nets (do nothing) @@ -14,8 +50,12 @@ BedNets.null <- function(t, pars) { #' @return a [list] #' @export setup_itn_null <- function(pars) { - ITNpar <- list() - class(ITNpar) <- 'null' - pars$ITNpar <- ITNpar + ITN<- list() + class(ITN) <- 'null' + pars$ITNdist<- ITN + pars$ITNown<- ITN + pars$ITNuse<- ITN + pars$ITNeff<- ITN + pars$ITNefsz<- ITN return(pars) } diff --git a/R/behavior.R b/R/behavior.R new file mode 100644 index 00000000..e6ada455 --- /dev/null +++ b/R/behavior.R @@ -0,0 +1,83 @@ +# human and mosquito behaviors + +#' @title Methods for dynamic human and mosquito behaviors +#' @description This method dispatches on the type of `pars$BEHAVIOR`. +#' @param t current simulation time +#' @param y state variables +#' @param pars a [list] +#' @return [list] +#' @export +Behavior <- function(t, y, pars) { + UseMethod("Behavior", pars$BEHAVIOR) +} + +#' @title Methods for dynamic human and mosquito behaviors +#' @description Implements [Behavior] for the null model (no changes) +#' @inheritParams Behavior +#' @return [list] +#' @export +Behavior.null <- function(t, y, pars) { + return(pars) +} + +#' @title Make parameters for the null model for resource availability (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_behavior_null<- function(pars) { + BEHAVIOR <- list() + class(BEHAVIOR) <- 'null' + pars$BEHAVIOR <- BEHAVIOR + return(pars) +} + +#' @title Setup behavior +#' @param pars a [list] +#' @return [list] +#' @export +setup_behavior <- function(pars) { + UseMethod("setup_behavior", pars$BEHAVIOR) +} + +#' @title Setup behavior +#' @param pars a [list] +#' @return [list] +#' @export +setup_behavior.null <- function(pars) { + setup_behavior_forced(pars) +} + +#' @title Setup behavior +#' @param pars a [list] +#' @return [list] +#' @export +setup_behavior.forced<- function(pars) {pars} + +#' @title Methods for dynamic human and mosquito behaviors +#' @description Implements [Behavior] for the forced model (no changes) +#' @inheritParams Behavior +#' @return [list] +#' @export +Behavior.forced <- function(t, y, pars) { + pars = UseBedNet(t, y, pars) + pars = CareSeeking(t, y, pars) +# pars = Protect(t, y, pars) +# pars = Mobility(t, y, pars) +# pars = MozySearch(t, y, pars) + return(pars) +} + +#' @title Make parameters for the forced model for resource availability (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_behavior_forced<- function(pars) { + BEHAVIOR <- list() + class(BEHAVIOR) <- 'forced' + pars$BEHAVIOR <- BEHAVIOR + pars = setup_care_seeking_null(pars) +# pars = setup_protect_null(t, y, pars) +# pars = setup_mobility_null(t, y, pars) +# pars = setup_mozy_search_null(t, y, pars) + return(pars) +} diff --git a/R/blood_feeding.R b/R/blood_feeding.R new file mode 100644 index 00000000..e69de29b diff --git a/R/care_seeking.R b/R/care_seeking.R new file mode 100644 index 00000000..71360bc6 --- /dev/null +++ b/R/care_seeking.R @@ -0,0 +1,33 @@ +# Methods to set up variables describing exogenous forcing by care seeking + +#' @title Set the values of exogenous variables describing care seeking +#' @description This method dispatches on the type of `pars$CARE_SEEKING`. +#' @param t current simulation time +#' @param y state variables +#' @param pars a [list] +#' @return [list] +#' @export +CareSeeking <- function(t, y, pars) { + UseMethod("CareSeeking", pars$CARE_SEEKING) +} + +#' @title Set the values of exogenous variables describing care seeking +#' @description Implements [CareSeeking] for the null model of care seeking (do nothing) +#' @inheritParams CareSeeking +#' @return [list] +#' @export +CareSeeking.null <- function(t, y, pars) { + return(pars) +} + +#' @title Make parameters for the null model for care seeking (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_care_seeking_null <- function(pars) { + CARE_SEEKING <- list() + class(CARE_SEEKING) <- 'null' + pars$CARE_SEEKING <- CARE_SEEKING + return(pars) +} + diff --git a/R/civil.R b/R/civil.R new file mode 100644 index 00000000..549f73f6 --- /dev/null +++ b/R/civil.R @@ -0,0 +1,77 @@ + # generic methods for exogenous forcing by civil factors + + #' @title Set up exogenous variables for civil forcing + #' @description This method dispatches on the type of `pars$CIVIL`. + #' @param t current simulation time + #' @param pars a [list] + #' @return [list] + #' @export + Civil <- function(t, pars) { + UseMethod("Civil", pars$CIVIL) + } + + #' @title Set up exogenous variables for civil forcing + #' @description Implements [Civil] for the null model of exogenous forcing (do nothing) + #' @inheritParams Civil + #' @return [list] + #' @export + Civil.null <- function(t, pars) {pars} + + #' @title Set up the null model for exogenous forcing (do nothing) + #' @param pars a [list] + #' @return [list] + #' @export + setup_civil_null <- function(pars) { + CIVIL <- list() + class(CIVIL) <- 'null' + pars$CIVIL <- CIVIL + return(pars) + } + + #' @title Set up exogenous variables for civil forcing + #' @description Implements [Civil] for civil forcing + #' @param t current simulation time + #' @param pars a [list] + #' @return pars a [list] + #' @export + Civil.forced <- function(t, pars) { + pars = Weather(t, pars) + pars = Hydrology(t, pars) + return(pars) + } + + #' @title Make parameters for the null model of civil forcing (do nothing) + #' @param pars a [list] + #' @return [list] + #' @export + setup_civil_forced <- function(pars) { + CIVIL <- list() + class(CIVIL) <- 'forced' + pars$CIVIL <- CIVIL + pars = setup_shock_null(pars) + pars = setup_development_null(pars) + return(pars) + } + + #' @title Check civil + #' @param pars a [list] + #' @return [list] + #' @export + check_civil <- function(pars) { + UseMethod("check_civil", pars$EfSz) + } + + #' @title Check civil + #' @param pars a [list] + #' @return [list] + #' @export + check_civil.null <- function(pars) { + setup_civil_forced(pars) + } + + #' @title Check civil + #' @param pars a [list] + #' @return [list] + #' @export + check_civil.forced<- function(pars) {pars} + diff --git a/R/clinic.R b/R/clinic.R new file mode 100644 index 00000000..23522357 --- /dev/null +++ b/R/clinic.R @@ -0,0 +1,45 @@ +# generic methods for distributing interventions at clinics + +#' @title Methods for distributing interventions during clinical visits +#' @description This method dispatches on the type of `pars$CLINIC`. +#' @param t current simulation time +#' @param y state variables +#' @param pars a [list] +#' @return [list] +#' @export +Clinic <- function(t, y, pars) { + UseMethod("Clinic", pars$CLINIC) +} + +#' @title Methods for distributing interventions during clinical visits +#' @description Implements [Clinic] for the null model (do nothing) +#' @inheritParams Clinic +#' @return [list] +#' @export +Clinic.null <- function(t, y, pars) { + return(pars) +} + +#' @title Set up the null model for clinical distribution (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_clinic_null <- function(pars) { + CLINIC <- list() + class(CLINIC) <- 'null' + pars$CLINIC <- CLINIC + return(pars) +} + + +#' @title Set up a model for clinic +#' @param pars a [list] +#' @return [list] +#' @export +setup_clinic_forced <- function(pars) { + pars = setup_control(pars) + CLINIC <- list() + class(CLINIC) <- 'forced' + pars$CLINIC <- CLINIC + return(pars) +} diff --git a/R/control.R b/R/control.R new file mode 100644 index 00000000..fb4ce2d0 --- /dev/null +++ b/R/control.R @@ -0,0 +1,88 @@ +# generic methods for all kinds of disease control measures + +#' @title Modify parameters due to exogenous forcing by all kinds of control +#' @description This method dispatches on the type of `pars$CONTROL`. +#' @param t current simulation time +#' @param y state variables +#' @param pars a [list] +#' @return [list] +#' @export +Control <- function(t, y, pars) { + UseMethod("Control", pars$CONTROL) +} + +#' @title Modify parameters due to exogenous forcing by all kinds of control +#' @description Implements [Control] for the null model (do nothing) +#' @inheritParams Control +#' @return [list] +#' @export +Control.null <- function(t, y, pars) {pars} + +#' @title Modify parameters due to exogenous forcing by all kinds of control +#' @description Implements [Control] for the static model; after setting up, do nothing +#' @inheritParams Control +#' @return [list] +#' @export +Control.static <- function(t, y, pars) {pars} + +#' @title Set up the null model for control forcing (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_control_null <- function(pars) { + CONTROL <- list() + class(CONTROL) <- 'null' + pars$CONTROL <- CONTROL + return(pars) +} + +#' @title Setup CONTROL with forcing +#' @param pars a [list] +#' @return [list] +#' @export +setup_control <- function(pars){ + UseMethod("setup_control", pars$CONTROL) +} + +#' @title Setup control +#' @param pars a [list] +#' @return [list] +#' @export +setup_control.null <- function(pars) { + setup_control_forced(pars) +} + +#' @title Setup control +#' @param pars a [list] +#' @return [list] +#' @export +setup_control.forced<- function(pars) {pars} + +#' @title Modify parameters due to exogenous forcing by all kinds of control +#' @description Implements [Control] for a model with some control +#' @param t current simulation time +#' @param y vector of state variables +#' @param pars a [list] +#' @return pars a [list] +#' @export +Control.forced <- function(t, y, pars) { + pars = MassMedical(t, y, pars) + pars = Clinic(t, y, pars) + pars = VectorControl(t, y, pars) + return(pars) +} + +#' @title Set up a model with some control +#' @param pars a [list] +#' @return [list] +#' @export +setup_control_forced <- function(pars) { + CONTROL <- list() + class(CONTROL) <- 'forced' + pars$CONTROL <- CONTROL + pars = setup_mass_medical_null(pars) + pars = setup_clinic_null(pars) + pars = setup_vc_null(pars) + return(pars) +} + diff --git a/R/development.R b/R/development.R new file mode 100644 index 00000000..4facf17a --- /dev/null +++ b/R/development.R @@ -0,0 +1,31 @@ +# generic methods for developments + +#' @title Set up developments +#' @description This method dispatches on the type of `pars$DEVELOPMENT`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +Development <- function(t, pars) { + UseMethod("Development", pars$DEVELOPMENT) +} + +#' @title Set up developments +#' @description Implements [Development] for the null model (do nothing) +#' @inheritParams Development +#' @return [list] +#' @export +Development.null <- function(t, pars) { + return(pars) +} + +#' @title Set up the null model for developments (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_development_null <- function(pars) { + DEVELOPMENT <- list() + class(DEVELOPMENT) <- 'null' + pars$DEVELOPMENT <- DEVELOPMENT + return(pars) +} diff --git a/R/diffeqn.R b/R/diffeqn.R index c54c8fa2..feb062e6 100644 --- a/R/diffeqn.R +++ b/R/diffeqn.R @@ -12,21 +12,26 @@ xDE_diffeqn <- function(t, y, pars) { # set the values of exogenous forcing variables - pars <- ExogenousForcing(t, pars) + pars <- Abiotic(t, pars) + pars <- Shock(t, pars) + pars <- Control(t, y, pars) + pars <- Behavior(t, y, pars) pars <- Visitors(t, pars) - pars <- HumanBehavior(t, y, pars) + pars <- VectorControlEffects(t, y, pars) pars <- Resources(t, y, pars) - # set and modify the baseline mosquito bionomic parameters - pars <- MosquitoBehavior(t, y, pars) - pars <- VectorControl(t, y, pars) + # set and modify the baseline bionomic parameters + pars <- EIP(t, pars) + pars <- MBionomics(t, y, pars) + pars <- LBionomics(t, y, pars) + pars <- VectorControlEffectSizes(t, y, pars) # eta: egg laying eggs <- F_eggs(t, y, pars) - eta <- pars$calU %*% eggs + eta <- pars$calU %*% eggs # lambda: emergence of adults - alpha <- F_alpha(t, y, pars) + alpha <- F_alpha(t, y, pars) Lambda <- pars$calN %*% alpha # blood feeding & mixing @@ -35,13 +40,16 @@ xDE_diffeqn <- function(t, y, pars) { # EIR: entomological inoculation rate EIR <- F_EIR(t, y, pars, beta) + # FoI: force of infection + FoI <- Exposure(t, y, pars, EIR) + # kappa: net infectiousness of humans kappa <- F_kappa(t, y, pars, beta) # state derivatives dL <- dLdt(t, y, pars, eta) dMYZ <- dMYZdt(t, y, pars, Lambda, kappa) - dX <- dXdt(t, y, pars, EIR) + dX <- dXdt(t, y, pars, FoI) return(list(c(dL, dMYZ, dX))) } @@ -57,14 +65,17 @@ xDE_diffeqn <- function(t, y, pars) { xDE_diffeqn_human <- function(t, y, pars) { # set the values of exogenous forcing variables - pars <- ExogenousForcing(t, pars) - pars <- Visitors(t, pars) - pars <- HumanBehavior(t, y, pars) + pars <- Abiotic(t, pars) + pars <- Shock(t, pars) + pars <- Control(t, y, pars) + pars <- Behavior(t, y, pars) pars <- Resources(t, y, pars) + pars <- EIP(t, pars) # set and modify the baseline mosquito bionomic parameters - pars <- MosquitoBehavior(t, y, pars) - pars <- VectorControl(t, y, pars) + pars <- EIP(t, pars) + pars <- MBionomics(t, y, pars) + pars <- VectorControlEffectSizes(t, y, pars) # blood feeding & mixing beta <- F_beta(t, y, pars) @@ -72,8 +83,11 @@ xDE_diffeqn_human <- function(t, y, pars) { # EIR: entomological inoculation rate EIR <- F_EIR(t, y, pars, beta) + # FoI: force of infection + FoI <- Exposure(t, y, pars, EIR) + # state derivatives - dX <- dXdt(t, y, pars, EIR) + dX <- dXdt(t, y, pars, FoI) return(list(c(dX))) } @@ -92,17 +106,16 @@ xDE_diffeqn_human <- function(t, y, pars) { xDE_diffeqn_mosy <- function(t, y, pars) { # set the values of exogenous forcing variables - pars <- ExogenousForcing(t, pars) - pars <- Visitors(t, pars) - pars <- HumanBehavior(t, y, pars) + pars <- Abiotic(t, pars) + pars <- Shock(t, pars) + pars <- Control(t, y, pars) + pars <- Behavior(t, y, pars) pars <- Resources(t, y, pars) # set baseline mosquito bionomic parameters - pars <- MosquitoBehavior(t, y, pars) - - # modify baseline mosquito bionomic parameters - pars <- VectorControl(t, y, pars) - + pars <- MBionomics(t, y, pars) + pars <- LBionomics(t, y, pars) + pars <- VectorControlEffectSizes(t, y, pars) # eta: egg laying eggs <- F_eggs(t, y, pars) @@ -132,10 +145,13 @@ xDE_diffeqn_mosy <- function(t, y, pars) { xDE_diffeqn_cohort <- function(a, y, pars, F_eir) { # EIR: entomological inoculation rate trace - eir <- F_eir(a, pars) + EIR <- F_eir(a, pars) + + # FoI: force of infection + FoI <- Exposure(t, y, pars, EIR) # state derivatives - dX <- dXdt(a, y, pars, eir) + dX <- dXdt(a, y, pars, FoI) return(list(c(dX))) } @@ -151,11 +167,14 @@ xDE_diffeqn_cohort <- function(a, y, pars, F_eir) { xDE_diffeqn_aquatic <- function(t, y, pars) { # set the values of exogenous forcing variables - pars <- ExogenousForcing(t, pars) + pars <- Abiotic(t, pars) + pars <- Shock(t, pars) + pars <- Control(t, y, pars) pars <- Resources(t, y, pars) # modify baseline mosquito bionomic parameters - pars <- LSM(t, pars) + pars <- LBionomics(t, y, pars) + pars <- VectorControlEffectSizes(t, y, pars) # egg laying eta <- F_eggs(t, y, pars) diff --git a/R/egg_laying.R b/R/egg_laying.R new file mode 100644 index 00000000..e69de29b diff --git a/R/eip.R b/R/eip.R new file mode 100644 index 00000000..98cbccb0 --- /dev/null +++ b/R/eip.R @@ -0,0 +1,29 @@ +# generic methods to compute the extrinsic incubation period (EIP) + +#' @title Compute the EIP +#' @description This method dispatches on the type of `pars$EIPmod`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +EIP <- function(t, pars) { + UseMethod("EIP", pars$EIPmod) +} + +#' @title Modify parameters due to exogenous forcing by all kinds of control +#' @description Implements [EIP] for the static model (the EIP is constant) +#' @inheritParams EIP +#' @return [list] +#' @export +EIP.static <- function(t, pars) {pars} + +#' @title Set up the static model for control forcing (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_eip_static<- function(pars) { + EIPmod <- list() + class(EIPmod) <- 'static' + pars$EIPmod <- EIPmod + return(pars) +} diff --git a/R/exogenous-forced.R b/R/exogenous-forced.R deleted file mode 100644 index 4278809f..00000000 --- a/R/exogenous-forced.R +++ /dev/null @@ -1,26 +0,0 @@ -# specialized methods for a model with exogenous forcing - -#' @title Modify parameters due to exogenous forcing -#' @description Calls functions that set up exogenous variables -#' @param t current simulation time -#' @param pars a [list] -#' @return pars a [list] -#' @export -ExogenousForcing.forced <- function(t, pars) { - pars = Weather(t, pars) - pars = Hydrology(t, pars) - return(pars) -} - -#' @title Make parameters for the null model of exogenous forcing (do nothing) -#' @param pars a [list] -#' @return none -#' @export -setup_exogenous_forced <- function(pars) { - EXOpar <- list() - class(EXOpar) <- 'forced' - pars$EXOpar <- EXOpar - pars = setup_weather_null(pars) - pars = setup_hydrology_null(pars) - return(pars) -} diff --git a/R/exogenous-interface.R b/R/exogenous-interface.R deleted file mode 100644 index 906ca2ae..00000000 --- a/R/exogenous-interface.R +++ /dev/null @@ -1,34 +0,0 @@ -# generic methods for exogenous forcing - -#' @title Modify parameters due to exogenous forcing -#' @description This method dispatches on the type of `pars$EXOpar`. -#' @param t current simulation time -#' @param pars a [list] -#' @return none -#' @export -ExogenousForcing <- function(t, pars) { - UseMethod("ExogenousForcing", pars$EXOpar) -} - -#' @title Set the values of exogenous variables describing weather -#' @description This method dispatches on the type of `pars$WETpar`. -#' @param t current simulation time -#' @param pars a [list] -#' @return none -#' @export -Weather <- function(t, pars) { - UseMethod("Weather", pars$WETpar) -} - -#' @title Set the values of exogenous variables describing hydrology -#' @description This method dispatches on the type of `pars$HYpar`. -#' @param t current simulation time -#' @param pars a [list] -#' @return none -#' @export -Hydrology <- function(t, pars) { - UseMethod("Hydrology", pars$HYpar) -} - - - diff --git a/R/exogenous-null.R b/R/exogenous-null.R deleted file mode 100644 index 284f01e1..00000000 --- a/R/exogenous-null.R +++ /dev/null @@ -1,59 +0,0 @@ -# specialized methods for the null model of exogenous forcing - -#' @title Modify parameters due to exogenous forcing -#' @description Implements [ExogenousForcing] for the null model of exogenous forcing (do nothing) -#' @inheritParams ExogenousForcing -#' @return none -#' @export -ExogenousForcing.null <- function(t, pars) {pars} - -#' @title Set up the null model for exogenous forcing (do nothing) -#' @param pars a [list] -#' @return none -#' @export -setup_exogenous_null <- function(pars) { - EXOpar <- list() - class(EXOpar) <- 'null' - pars$EXOpar <- EXOpar - return(pars) -} - -#' @title Modify exogenous variables describing weather -#' @description Implements [Weather] for the null model (no variables) -#' @inheritParams Weather -#' @return none -#' @export -Weather.null <- function(t, pars) { - return(pars) -} - -#' @title Set up the null model for weather (do nothing) -#' @param pars a [list] -#' @return none -#' @export -setup_weather_null <- function(pars) { - WETpar <- list() - class(WETpar) <- 'null' - pars$WETpar <- WETpar - return(pars) -} - -#' @title Modify parameters due to exogenous forcing -#' @description Implements [Hydrology] for the null model of hydrology (do nothing) -#' @inheritParams Hydrology -#' @return none -#' @export -Hydrology.null <- function(t, pars) { - return(pars) -} - -#' @title Make parameters for the null model for hydrology (do nothing) -#' @param pars a [list] -#' @return none -#' @export -setup_hydrology_null <- function(pars) { - HYpar <- list() - class(HYpar) <- 'null' - pars$HYpar <- HYpar - return(pars) -} diff --git a/R/exposure.R b/R/exposure.R index fa9a5042..50b83af7 100644 --- a/R/exposure.R +++ b/R/exposure.R @@ -1,3 +1,15 @@ +#' @title A model for exposure. The function `F_b` must be define +#' @param t the time +#' @param y the variables +#' @param pars a [list] +#' @param EIR is the daily eir +#' @export +Exposure <- function(t, y, pars, EIR){ + b = F_b(y, pars) + foi = F_foi(EIR, b, pars) + travel_malaria(t, pars) + return(foi) +} + #' @title A model for exposure #' @description This method dispatches on the type of `pars$FOIpar`. #' @param eir the daily eir diff --git a/R/habitat_dynamics.R b/R/habitat_dynamics.R index 53cf7fb9..b3fa7a73 100644 --- a/R/habitat_dynamics.R +++ b/R/habitat_dynamics.R @@ -1,83 +1,31 @@ -#' @title Set the values for habitat -#' @description This method dispatches on the type of `pars$QHABpar`. It should -#' set the values of habitat at time `t` +# Methods to set up variables describing exogenous forcing by habitat_dynamics + +#' @title Set the values of exogenous variables describing habitat_dynamics +#' @description This method dispatches on the type of `pars$HABITAT_DYNAMICS`. #' @param t current simulation time -#' @param y state vector #' @param pars a [list] -#' @return a [list] +#' @return [list] #' @export -F_habitats <- function(t, y, pars) { - UseMethod("F_habitat", pars$QHABpar) +HabitatDynamics <- function(t, pars) { + UseMethod("HabitatDynamics", pars$HABITAT_DYNAMICS) } -#' @title A null model for habitat -#' @description Implements [F_habitats] for a static model -#' @inheritParams F_habitats -#' @return a [list] -#' @export -F_habitats.null <- function(t, y, pars){ - pars -} - -#' @title Set up the null model for habitat dynamics -#' @param pars a [list] -#' @return none +#' @title Set the values of exogenous variables describing habitat dynamics +#' @description Implements [HabitatDynamics] for the null model of habitat_dynamics (do nothing) +#' @inheritParams HabitatDynamics +#' @return [list] #' @export -setup_habitats_null<- function(pars){ - QHABpar <- list() - class(QHABpar) <- 'null' - pars$QHABpar <- QHABpar +HabitatDynamics.null <- function(t, pars) { return(pars) } -#' @title Static model for habitat -#' @description Implements [F_habitats] for a static model -#' @inheritParams F_habitats -#' @return a [list] -#' @export -F_habitats.static <- function(t, y, pars){ - pars -} - -#' @title Set up the static model for habitat dynamics +#' @title Make parameters for the null model for habitat dynamics (do nothing) #' @param pars a [list] -#' @return none +#' @return [list] #' @export -setup_habitats_static<- function(pars){ - QHABpar <- list() - class(QHABpar) <- 'static' - pars$QHABpar <- QHABpar +setup_habitat_dynamics_null <- function(pars) { + HABITAT_DYNAMICS <- list() + class(HABITAT_DYNAMICS) <- 'null' + pars$HABITAT_DYNAMICS <- HABITAT_DYNAMICS return(pars) } - - -#' @title A basic forcing model for habitat availability -#' @description Implements [F_habitats] for a forced model -#' @inheritParams F_habitats -#' @return a [list] -#' @export -F_habitats.forced <- function(t, pars){ - with(pars$QHABpar,{ - return(habitats_scale*habitats_t(t, pars)) - }) -} - -#' @title Set up forcing for the availability of habitats -#' @param pars a [list] -#' @param habitats_Opts a list, overwrites default values -#' @param habitats_scale a non-negative numeric value to scale the mean availability of habitats -#' @param habitats_t a function that specifies the temporal pattern for the availability of habitats -#' @return none -#' @export -setup_habitats_forced <- function(pars, habitats_Opts = list(), habitats_scale=0, habitats_t=NULL) {with(habitats_Opts,{ - - QHABpar <- list() - class(QHABpar) <- 'foi' - pars$QHABpar <- QHABpar - - pars$QHABpar$habitats_scale = habitats_scale - if(is.null(habitats_t)) habitats_t = function(t, pars){1} - pars$QHABpar$habitats_t = habitats_t - - return(pars) -})} diff --git a/R/human-SIP.R b/R/human-SIP.R index c881b8af..b93ee6d9 100644 --- a/R/human-SIP.R +++ b/R/human-SIP.R @@ -9,23 +9,29 @@ F_X.SIP <- function(t, y, pars) { with(pars$Xpar, y[X_ix] * c) } +#' @title Infection blocking pre-erythrocytic immunity +#' @description Implements [F_b] for the SIP model. +#' @inheritParams F_b +#' @return a [numeric] vector of length `nStrata` +#' @export +F_b.SIP <- function(y, pars) { + with(pars$Xpar, b) +} + #' @title Derivatives for human population #' @description Implements [dXdt] for the SIP model. #' @inheritParams dXdt #' @return a [numeric] vector #' @export -dXdt.SIPdX <- function(t, y, pars, EIR) { +dXdt.SIPdX <- function(t, y, pars, FoI) { with(pars$Xpar, { - - foi = F_foi(EIR, b, pars) + travel_malaria(t, pars) - X <- y[X_ix] P <- y[P_ix] H <- F_H(t, y, pars) - dX <- (1-rho)*foi*(H - X - P) - (r+xi)*X - dP <- rho*foi*(H - X - P) + xi*(H-P) - eta*P + dX <- (1-rho)*FoI*(H - X - P) - (r+xi)*X + dP <- rho*FoI*(H - X - P) + xi*(H-P) - eta*P return(c(dX, dP)) }) @@ -48,18 +54,16 @@ HTC.SIP <- function(pars) { #' @inheritParams dXdt #' @return a [numeric] vector #' @export -dXdt.SIPdXdH <- function(t, y, pars, EIR) { +dXdt.SIPdXdH <- function(t, y, pars, FoI) { with(pars$Xpar, { - foi = F_foi(EIR, b, pars) + travel_malaria(t, pars) - X <- y[X_ix] P <- y[P_ix] H <- F_H(t, y, pars) - dX <- (1-rho)*foi*(H - X - P) - (r+xi)*X + dHdt(t, X, pars) - dP <- rho*foi*(H - X - P) + xi*(H-P) - eta*P + dHdt(t, P, pars) + dX <- (1-rho)*FoI*(H - X - P) - (r+xi)*X + dHdt(t, X, pars) + dP <- rho*FoI*(H - X - P) + xi*(H-P) - eta*P + dHdt(t, P, pars) dH <- Births(t, H, pars) + dHdt(t, H, pars) return(c(dX, dP, dH)) diff --git a/R/human-SIS.R b/R/human-SIS.R index 3b403d4d..05c213b3 100644 --- a/R/human-SIS.R +++ b/R/human-SIS.R @@ -9,20 +9,27 @@ F_X.SIS <- function(t, y, pars) { with(pars$Xpar, y[X_ix]*c) } +#' @title Infection blocking pre-erythrocytic immunity +#' @description Implements [F_b] for the SIS model. +#' @inheritParams F_b +#' @return a [numeric] vector of length `nStrata` +#' @export +F_b.SIS <- function(y, pars) { + with(pars$Xpar, b) +} + #' @title Derivatives for human population #' @description Implements [dXdt] for the SIS model, no demography. #' @inheritParams dXdt #' @return a [numeric] vector #' @export -dXdt.SISdX <- function(t, y, pars, EIR) { +dXdt.SISdX <- function(t, y, pars, FoI) { with(pars$Xpar, { - foi = F_foi(EIR, b, pars) + travel_malaria(t, pars) - X <- y[X_ix] H <- F_H(t, y, pars) - dX <- foi*(H - X) - r*X + dX <- FoI*(H - X) - r*X return(c(dX)) }) @@ -33,15 +40,13 @@ dXdt.SISdX <- function(t, y, pars, EIR) { #' @inheritParams dXdt #' @return a [numeric] vector #' @export -dXdt.SISdXdH <- function(t, y, pars, EIR) { +dXdt.SISdXdH <- function(t, y, pars, FoI) { with(pars$Xpar, { - foi = F_foi(EIR, b, pars) + travel_malaria(t, pars) - H <- F_H(t, y, pars) X <- y[X_ix] - dX <- foi*(H - X) - r*X + dHdt(t, X, pars) + dX <- FoI*(H - X) - r*X + dHdt(t, X, pars) dH <- Births(t, H, pars) + dHdt(t, H, pars) return(c(dX, dH)) diff --git a/R/human-hMoI.R b/R/human-hMoI.R index 3614530f..bb63e918 100644 --- a/R/human-hMoI.R +++ b/R/human-hMoI.R @@ -16,17 +16,28 @@ F_X.hMoI <- function(t, y, pars) { }) } + +#' @title Infection blocking pre-erythrocytic immunity +#' @description Implements [F_b] for the hMoI model. +#' @inheritParams F_b +#' @return a [numeric] vector of length `nStrata` +#' @export +F_b.hMoI <- function(y, pars) { + with(pars$Xpar, b) +} + + #' @title Derivatives for human population #' @description Implements [dXdt] for the hybrid MoI model. #' @inheritParams dXdt #' @return a [numeric] vector #' @export -dXdt.hMoI <- function(t, y, pars, EIR) { +dXdt.hMoI <- function(t, y, pars, FoI) { with(pars$Xpar, { m1 <- y[m1_ix] m2 <- y[m2_ix] - dm1dt <- b*EIR - r1*m1 - dm2dt <- b*EIR - r2*m2 + dm1dt <- FoI - r1*m1 + dm2dt <- FoI - r2*m2 return(c(dm1dt, dm2dt)) }) } diff --git a/R/human-interface.R b/R/human-interface.R index 871df750..eb45b924 100644 --- a/R/human-interface.R +++ b/R/human-interface.R @@ -11,15 +11,25 @@ F_X <- function(t, y, pars) { UseMethod("F_X", pars$Xpar) } +#' @title Infection blocking pre-erythrocytic immunity +#' @description This method dispatches on the type of `pars$Xpar`. +#' @param y state vector +#' @param pars a [list] +#' @return a [numeric] vector of length `nStrata` +#' @export +F_b <- function(y, pars) { + UseMethod("F_b", pars$Xpar) +} + #' @title Derivatives for human population #' @description This method dispatches on the type of `pars$Xpar`. #' @param t current simulation time #' @param y state vector #' @param pars a [list] -#' @param EIR vector giving the per-capita entomological inoculation rate for each strata +#' @param FoI vector giving the per-capita force of infection for each strata #' @return a [numeric] vector #' @export -dXdt <- function(t, y, pars, EIR) { +dXdt <- function(t, y, pars, FoI) { UseMethod("dXdt", pars$Xpar) } diff --git a/R/human-trace.R b/R/human-trace.R index ce2f97b7..afded21d 100644 --- a/R/human-trace.R +++ b/R/human-trace.R @@ -9,12 +9,21 @@ F_X.trace <- function(t, y, pars) { with(pars$Xpar, kappa) } +#' @title Infection blocking pre-erythrocytic immunity +#' @description Implements [F_b] for the trace model. +#' @inheritParams F_b +#' @return a [numeric] vector of length `nStrata` +#' @export +F_b.trace <- function(y, pars) { + numeric(0) +} + #' @title Derivatives for human population #' @description Implements [dXdt] for the trace model. #' @inheritParams dXdt #' @return a [numeric] vector #' @export -dXdt.trace <- function(t, y, pars, EIR) { +dXdt.trace <- function(t, y, pars, FoI) { numeric(0) } diff --git a/R/humanbehavior.R b/R/humanbehavior.R deleted file mode 100644 index c682c6f9..00000000 --- a/R/humanbehavior.R +++ /dev/null @@ -1,30 +0,0 @@ -#' @title Simulate Human Behavior -#' @description This method dispatches on the type of `pars$HBpar`. -#' @param t current simulation time -#' @param y state variables -#' @param pars a [list] -#' @return none -#' @export -HumanBehavior <- function(t, y, pars) { - UseMethod("HumanBehavior", pars$HBpar) -} - -#' @title Simulate no human behaviors -#' @description Implements [HumanBehavior] for the null model (do nothing) -#' @inheritParams HumanBehavior -#' @return none -#' @export -HumanBehavior.null <- function(t, y, pars) { - return(pars) -} - -#' @title Make parameters for the null model for resource availability (do nothing) -#' @param pars a [list] -#' @return none -#' @export -setup_humanbehavior_null<- function(pars) { - HBpar <- list() - class(HBpar) <- 'null' - pars$HBpar <- HBpar - return(pars) -} diff --git a/R/hydrology.R b/R/hydrology.R new file mode 100644 index 00000000..f43c85d9 --- /dev/null +++ b/R/hydrology.R @@ -0,0 +1,32 @@ +# Methods to set up variables describing exogenous forcing by hydrology + +#' @title Set the values of exogenous variables describing hydrology +#' @description This method dispatches on the type of `pars$HYDROLOGY`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +Hydrology <- function(t, pars) { + UseMethod("Hydrology", pars$HYDROLOGY) +} + +#' @title Set the values of exogenous variables describing hydrology +#' @description Implements [Hydrology] for the null model of hydrology (do nothing) +#' @inheritParams Hydrology +#' @return [list] +#' @export +Hydrology.null <- function(t, pars) { + return(pars) +} + +#' @title Make parameters for the null model for hydrology (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_hydrology_null <- function(pars) { + HYDROLOGY <- list() + class(HYDROLOGY) <- 'null' + pars$HYDROLOGY <- HYDROLOGY + return(pars) +} + diff --git a/R/irs-interface.R b/R/irs-interface.R index d1b26ab9..0bff36d2 100644 --- a/R/irs-interface.R +++ b/R/irs-interface.R @@ -1,11 +1,31 @@ # generic methods for IRS -#' @title Modify baseline bionomic values due to IRS -#' @description This method dispatches on the type of `pars$IRSpar`. +#' @title Do mass house spraying (IRS) +#' @description This method dispatches on the type of `pars$IRS`. #' @param t current simulation time #' @param pars a [list] #' @return a [list] #' @export -IRS <- function(t, pars) { - UseMethod("IRS", pars$IRSpar) +SprayHouses <- function(t, pars) { + UseMethod("SprayHouses", pars$IRS) +} + +#' @title Model the effects of IRS +#' @description This method dispatches on the type of `pars$IRS`. +#' @param t current simulation time +#' @param pars a [list] +#' @return a [list] +#' @export +IRSeffects <- function(t, pars) { + UseMethod("IRS_effects", pars$IRS) +} + +#' @title Model IRS effect sizes +#' @description This method dispatches on the type of `pars$IRS`. +#' @param t current simulation time +#' @param pars a [list] +#' @return a [list] +#' @export +IRSeffectSizes <- function(t, pars) { + UseMethod("IRSeffectSizes", pars$IRS) } diff --git a/R/irs-null.R b/R/irs-null.R index c83b8ace..9c0d1448 100644 --- a/R/irs-null.R +++ b/R/irs-null.R @@ -1,21 +1,37 @@ # specialized methods for the null model of IRS +# generic methods for IRS -#' @title Modify baseline values due to IRS -#' @description Implements [IRS] for the null model of IRS (do nothing) -#' @inheritParams IRS +#' @title Do mass house spraying (IRS) +#' @description This method dispatches on the type of `pars$IRS`. +#' @param t current simulation time +#' @param pars a [list] #' @return a [list] #' @export -IRS.null <- function(t, pars) { - return(pars) -} +SprayHouses.null <- function(t, pars) {pars} + +#' @title Model the effects of IRS +#' @description This method dispatches on the type of `pars$IRS`. +#' @param t current simulation time +#' @param pars a [list] +#' @return a [list] +#' @export +IRSeffects.null <- function(t, pars){pars} + +#' @title Model IRS effect sizes +#' @description This method dispatches on the type of `pars$IRS`. +#' @param t current simulation time +#' @param pars a [list] +#' @return a [list] +#' @export +IRSeffectSizes.null <- function(t, pars){pars} #' @title Make parameters for the null model of IRS (do nothing) #' @param pars a [list] #' @return a [list] #' @export setup_irs_null <- function(pars) { - IRSpar <- list() - class(IRSpar) <- 'null' - pars$IRSpar <- IRSpar + IRS <- list() + class(IRS) <- 'null' + pars$IRS <- IRS return(pars) } diff --git a/R/lsm-interface.R b/R/lsm-interface.R index 0732708c..dde60f8c 100644 --- a/R/lsm-interface.R +++ b/R/lsm-interface.R @@ -1,11 +1,34 @@ # generic methods for LSM -#' @title Modify values due to LSM -#' @description This method dispatches on the type of `pars$LSMpar`. +#' @title Modify values due to treat habitats as part of LSM, +#' called by Control->VectorControl +#' @description This method dispatches on the type of `pars$LSM`. #' @param t current simulation time #' @param pars a [list] #' @return a [list] #' @export -LSM <- function(t, pars) { - UseMethod("LSM", pars$LSMpar) +TreatHabitats <- function(t, pars) { + UseMethod("TreatHabitats", pars$LSM) +} + +#' @title Modify effects of LSM +#' @description This method dispatches on the type of `pars$LSM`. +#' @param t current simulation time +#' @param y the state of the system +#' @param pars a [list] +#' @return a [list] +#' @export +LSMeffects <- function(t, y, pars) { + UseMethod("LSM_effects", pars$LSM) +} + +#' @title Compute effect sizes of LSM +#' @description This method dispatches on the type of `pars$LSM`. +#' @param t current simulation time +#' @param y the state of the system +#' @param pars a [list] +#' @return a [list] +#' @export +LSMeffectSizes <- function(t, y, pars) { + UseMethod("LSM_effect_size", pars$LSM) } diff --git a/R/lsm-null.R b/R/lsm-null.R index 078d8ad8..15d527f4 100644 --- a/R/lsm-null.R +++ b/R/lsm-null.R @@ -1,12 +1,30 @@ # specialized methods for the null model of LSM -#' @title Modify baseline values due to LSM -#' @description Implements [LSM] for the null model of LSM (do nothing) -#' @inheritParams LSM +#' @title Set up the null model for LSM +#' @description This method dispatches on the type of `pars$LSM` +#' @inheritParams TreatHabitats #' @return a [list] #' @export -LSM.null <- function(t, pars) { - return(pars) +TreatHabitats.null <- function(t, pars) { + pars +} + +#' @title Modify effects of LSM, the null model +#' @description This method dispatches on the type of `pars$LSM` +#' @inheritParams LSMeffects +#' @return a [list] +#' @export +LSMeffects.null <- function(t, y, pars) { + pars +} + +#' @title Modify effects of LSM, the null model +#' @description This method dispatches on the type of `pars$LSM` +#' @inheritParams LSMeffectSizes +#' @return a [list] +#' @export +LSMeffectSizes.null <- function(t, y, pars) { + pars } #' @title Make parameters for the null model of LSM (do nothing) @@ -14,8 +32,7 @@ LSM.null <- function(t, pars) { #' @return a [list] #' @export setup_lsm_null <- function(pars) { - LSMpar <- list() - class(LSMpar) <- 'null' - pars$LSMpar <- LSMpar + LSM <- list() + class(LSM) <- 'null' return(pars) } diff --git a/R/mass_medical.R b/R/mass_medical.R new file mode 100644 index 00000000..dd250a26 --- /dev/null +++ b/R/mass_medical.R @@ -0,0 +1,56 @@ +# generic methods for mass distribution of medical interventions + +#' @title Methods for mass medical interventions +#' @description This method dispatches on the type of `pars$MASS_MED`. +#' @param t current simulation time +#' @param y state variables +#' @param pars a [list] +#' @return [list] +#' @export +MassMedical <- function(t, y, pars) { + UseMethod("MassMedical", pars$MASS_MED) +} + +#' @title Methods for mass medical +#' @description Implements [MassMedical] for the null model (do nothing) +#' @inheritParams MassMedical +#' @return [list] +#' @export +MassMedical.null <- function(t, y, pars) { + return(pars) +} + +#' @title Set up the null model for mass medical (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_mass_medical_null <- function(pars) { + MASS_MED <- list() + class(MASS_MED) <- 'null' + pars$MASS_MED <- MASS_MED + return(pars) +} + +#' @title Methods for mass medical +#' @description Implements [MassMedical] +#' @inheritParams MassMedical +#' @return [list] +#' @export +MassMedical.forced <- function(t, y, pars) { + return(pars) +} + +#' @title Set up a model for mass medical +#' @param pars a [list] +#' @return [list] +#' @export +setup_mass_medical_forced <- function(pars) { + pars = setup_control(pars) + MASS_MED <- list() + class(MASS_MED) <- 'forced' + pars$MASS_MED <- MASS_MED +# pars = setup_mass_treat_null(pars) +# pars = setup_vaccinate_null(pars) +# pars = setup_mAb_null(pars) + return(pars) +} diff --git a/R/other_blood_hosts.R b/R/other_blood_hosts.R index d7e78378..22bd2d90 100644 --- a/R/other_blood_hosts.R +++ b/R/other_blood_hosts.R @@ -1,62 +1,32 @@ +# Methods to set up variables describing exogenous forcing by other blood hosts -#' @title Set the availability of other -#' @description This method dispatches on the type of `pars$OBHpar`. It should -#' set the values of other availability at time `t` +#' @title Set the values of exogenous variables describing other blood hosts +#' @description This method dispatches on the type of `pars$OTHER_BLOOD`. #' @param t current simulation time #' @param pars a [list] -#' @return a [list] +#' @return [list] #' @export -F_otherblood <- function(t, pars) { - UseMethod("F_otherblood", pars$OBHpar) +OtherBloodHosts <- function(t, pars) { + UseMethod("OtherBloodHosts", pars$OTHER_BLOOD) } -#' @title Null model for other blood hosts -#' @description Implements [F_otherblood] for a null model -#' @inheritParams F_otherblood -#' @return a [list] +#' @title Set the values of exogenous variables describing other blood hosts +#' @description Implements [OtherBloodHosts] for the null model of other_blood_hosts (do nothing) +#' @inheritParams OtherBloodHosts +#' @return [list] #' @export -F_otherblood.null <- function(t, pars){ - pars -} - -#' @title Static model for other blood hosts -#' @description Implements [F_otherblood] for a static model -#' @inheritParams F_otherblood -#' @return a [list] -#' @export -F_otherblood.static <- function(t, pars){ - pars -} - -#' @title A basic forcing model for other blood hosts -#' @description Implements [F_otherblood] for a forced model -#' @inheritParams F_otherblood -#' @return a [list] -#' @export -F_otherblood.forced <- function(t, pars){ - with(pars$OBHpar,{ - return(otherblood_scale*otherblood_t(t, pars)) - }) +OtherBloodHosts.null <- function(t, pars) { + return(pars) } -#' @title Set up forcing for the availability of other blood hosts +#' @title Make parameters for the null model for other blood hosts (do nothing) #' @param pars a [list] -#' @param otherblood_Opts a list, overwrites default values -#' @param otherblood_scale a non-negative numeric value to scale the mean availability of other blood hosts -#' @param otherblood_t a function that specifies the temporal pattern for the availability of other blood hosts -#' @return none +#' @return [list] #' @export -setup_otherblood_forced <- function(pars, otherblood_Opts = list(), otherblood_scale=0, otherblood_t=NULL) {with(otherblood_Opts,{ - - OBHpar <- list() - class(OBHpar) <- 'foi' - pars$OBHpar <- OBHpar - - pars$OBHpar$otherblood_scale = otherblood_scale - if(is.null(otherblood_t)) otherblood_t = function(t, pars){1} - pars$OBHpar$otherblood_t = otherblood_t - +setup_other_blood_hosts_null <- function(pars) { + OTHER_BLOOD <- list() + class(OTHER_BLOOD) <- 'null' + pars$OTHER_BLOOD <- OTHER_BLOOD return(pars) -})} - +} diff --git a/R/ovitrap.R b/R/ovitrap.R new file mode 100644 index 00000000..89ec044b --- /dev/null +++ b/R/ovitrap.R @@ -0,0 +1,31 @@ +# generic methods for oviposition traps + +#' @title Methods for oviposition traps +#' @description This method dispatches on the type of `pars$OVITRAPS`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +OviTraps <- function(t, pars) { + UseMethod("OviTraps", pars$OVITRAPS) +} + +#' @title Methods for oviposition traps +#' @description Implements [OviTraps] for the null model (do nothing) +#' @inheritParams OviTraps +#' @return [list] +#' @export +OviTraps.null <- function(t, pars) { + return(pars) +} + +#' @title Set up the null model for oviposition traps (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_ovitraps_null <- function(pars) { + OVITRAPS <- list() + class(OVITRAPS) <- 'null' + pars$OVITRAPS <- OVITRAPS + return(pars) +} diff --git a/R/resources-dynamic.R b/R/resources-dynamic.R deleted file mode 100644 index 7d87acea..00000000 --- a/R/resources-dynamic.R +++ /dev/null @@ -1,68 +0,0 @@ -# specialized methods for models with dynamically changing resource availability - -#' @title Modify resources and resource availability dynamically -#' @description Implements [Resources] for the null model of resources (do nothing) -#' @inheritParams Resources -#' @return none -#' @export -Resources.dynamic <- function(t, y, pars) { - pars = update_BloodFeeding(pars) - pars = update_EggLaying(t, y, pars) - pars = update_S(t, pars) - return(pars) -} - -#' @title Update total availability of blood hosts for dynamical models -#' @description Implements [update_BloodFeeding] for a dynamic model -#' @inheritParams update_BloodFeeding -#' @return a [list] -#' @export -update_BloodFeeding.dynamic <- function(t, y, pars){ - pars = update_W(t, y, pars) - pars = update_O(t, pars) - pars$B = compute_B(pars) - pars$local_frac = compute_local_frac(pars) - return(pars) -} - -#' @title Update host availability dynamically -#' @description Implements [update_W] for a static model -#' @inheritParams update_W -#' @return a [list] -#' @export -update_W.dynamic<- function(t, y, pars){ - pars$W = compute_W(t, y, pars) - return(pars) -} - -#' @title Update other host availability dynamically -#' @description Implements [update_O] for a static model -#' @inheritParams update_O -#' @return a [list] -#' @export -update_O.dynamic<- function(t, pars){ - pars$OtherBloodHosts = F_otherblood(t, pars) - return(pars) -} - -#' @title Update the total availability of aquatic habitats and egg laying -#' @description Implements [update_EggLaying] for a dynamic model -#' @inheritParams update_EggLaying -#' @return a [list] -#' @export -update_EggLaying.dynamic <- function(t, y, pars){ - pars = F_habitats(t, pars) - pars$Q = compute_Q(pars) - pars$calU = make_calU(pars$calN, pars$searchQ) - return(pars) -} - -#' @title Dynamically update the total availability of sugar -#' @description Implements [update_S] for a dynamic model -#' @inheritParams update_S -#' @return a [list] -#' @export -update_S.dynamic <- function(t, pars){ - pars$S = F_sugar(t, pars) - return(pars) -} diff --git a/R/resources-forced.R b/R/resources-forced.R new file mode 100644 index 00000000..b6719b2d --- /dev/null +++ b/R/resources-forced.R @@ -0,0 +1,87 @@ +# specialized methods for models with dynamically changing resource availability + +#' @title Methods for resources +#' @description Implements [Resources] +#' @inheritParams Resources +#' @return [list] +#' @export +Resources.forced <- function(t, y, pars) { + + # Availability of Blood Hosts + pars = OtherBloodHosts(t, pars) + pars = HumanAvailability(t, y, pars) + + # Availability of Blood Hosts + pars = HabitatDynamics(t, pars) + pars = HabitatAvailability(pars) + + # Availability of Blood Hosts + pars = Sugar(t, pars) + pars = SugarAvailability(pars) + + pars$local_frac = compute_local_frac(pars) + + return(pars) +} + + +#' @title Compute availability of local humans for blood feeding +#' @description Compute the availability for the pathogen's hosts for blood feeding +#' @param t current simulation time +#' @param y state vector +#' @param pars a [list] +#' @return a [numeric] vector of length `nPatches` +#' @export +HumanAvailability.forced <- function(t, y, pars){ + H = F_H(t, y, pars) + pars$W = with(pars$Hpar, TaR %*% (wts_f*H)) + return(pars) +} + +#' @title Compute total availability of aquatic habitats +#' @description Computes the availability of aquatic habitats +#' @param pars a [list] +#' @return a [numeric] vector of length `nPatches` +#' @export +HabitatAvailability.forced <- function(pars){ + habitats = with(pars, calN %*% searchQ) + pars$Q = habitats + pars$ovitraps + pars$non_habitats + pars$eggs_laid = habitats/pars$Q + pars$calU = make_calU(pars$calN, pars$searchQ) + return(pars) +} + +#' @title Compute total availability of sugar +#' @description Computes the availability of sugar +#' @param pars a [list] +#' @return a [numeric] vector of length `nPatches` +#' @export +SugarAvailability.forced <- function(pars){ + pars$S = pars$nectar + pars$sugar_baits + return(pars) +} + +#' @title Set up a model for mass medical +#' @param pars a [list] +#' @return [list] +#' @export +setup_resources_forced <- function(pars) { + pars = setup_control(pars) + RESOURCES <- list() + class(RESOURCES) <- 'forced' + pars$RESOURCES <- RESOURCES + pars = setup_habitat_dynamics_null(pars) + pars = setup_sugar_null(pars) + pars = setup_other_blood_hosts_null(pars) + return(pars) +} + +#' @title Compute the local fraction +#' @description Compute the availability for the pathogen's hosts for blood feeding +#' @param pars a [list] +#' @return pars a [list] +#' @export +compute_local_frac <- function(pars){ + pars$local_frac = with(pars, W/(W+Visitors)) + return(pars) +} diff --git a/R/resources-functions.R b/R/resources-functions.R deleted file mode 100644 index 381fa151..00000000 --- a/R/resources-functions.R +++ /dev/null @@ -1,46 +0,0 @@ -# Functions that exogenously force the availability of resources - -#' @title Compute host availability -#' @description Compute the availability for the pathogen's hosts for blood feeding -#' @param t current simulation time -#' @param y state vector -#' @param pars a [list] -#' @return a [numeric] vector of length `nPatches` -#' @export -compute_W <- function(t, y, pars){ - H = F_H(t, y, pars) - W = with(pars$Hpar, TaR %*% (wts_f*H)) - return(W) -} - -#' @title Compute total availability of aquatic habitats -#' @description Computes the availability of aquatic habitats -#' @param pars a [list] -#' @return a [numeric] vector of length `nPatches` -#' @export -compute_Q <- function(pars){ - with(pars, - return(calN %*% searchQ) -)} - -#' @title Compute the total availability of blood hosts -#' @description Compute the availability for the pathogen's hosts for blood feeding -#' @param pars a [list] -#' @return a [numeric] vector of length `nPatches` -#' @export -compute_B <- function(pars){ - B = with(pars, W + OtherBloodHosts + Visitors) - return(B) -} - -#' @title Compute the fraction of bites occurring on local hosts -#' @description Computes the local_frac -#' @param pars a [list] -#' @return a [numeric] vector of length `nPatches` -#' @export -compute_local_frac <- function(pars){ - with(pars, - return(W/(W+Visitors)) -)} - - diff --git a/R/resources-interface.R b/R/resources-interface.R index 01b2418a..0bf49212 100644 --- a/R/resources-interface.R +++ b/R/resources-interface.R @@ -1,70 +1,40 @@ #' @title Set the values of exogenous variables describing available mosquito resources -#' @description This method dispatches on the type of `pars$RApar`. +#' @description This method dispatches on the type of `pars$RESOURCES`. #' @param t current simulation time -#' @param y state variables +#' @param y vector of state variables #' @param pars a [list] #' @return none #' @export Resources <- function(t, y, pars) { - UseMethod("Resources", pars$RApar) + UseMethod("Resources", pars$RESOURCES) } #' @title Update the availability of blood hosts -#' @description This method dispatches on the type of `pars$B`. It -#' computes availability of all blood hosts at time `t` +#' @description This method dispatches on the type of `pars$RESOURCES`. #' @param t current simulation time -#' @param y state variables +#' @param y vector of state variables #' @param pars an [list] #' @return a [list] #' @export -update_BloodFeeding <- function(t, y, pars) { - UseMethod("update_BloodFeeding", pars$B) +HumanAvailability <- function(t, y, pars) { + UseMethod("HumanAvailability", pars$RESOURCES) } -#' @title Update the availability of habitats and egg laying -#' @description This method dispatches on the type of `pars$Q`. It -#' computes availability of all blood hosts at time `t` -#' @param t current simulation time -#' @param y state variables -#' @param pars an [list] -#' @return a [list] -#' @export -update_EggLaying <- function(t, y, pars) { - UseMethod("update_EggLaying", pars$Q) -} - -#' @title Update host availability -#' @description This method dispatches on the type of `pars$W`. It should -#' update the availability of the pathogen's hosts for blood feeding at time `t` -#' @param t current simulation time -#' @param y state vector -#' @param pars a [list] -#' @return a [list] -#' @export -update_W <- function(t, y, pars) { - UseMethod("update_W", pars$W) -} - -#' @title Update the availability of other blood hosts -#' @description This method dispatches on the type of `pars$O`. It -#' computes availability of blood hosts at time `t`. Other blood hosts -#' include any vertebrate host that does not serve as a host for the pathogen. -#' @param t current simulation time +#' @title Update the availability of aquatic habitats +#' @description This method dispatches on the type of `pars$RESOURCES`. #' @param pars an [list] #' @return a [list] #' @export -update_O <- function(t, pars) { - UseMethod("update_O", pars$O) +HabitatAvailability <- function(pars) { + UseMethod("HabitatAvailability", pars$RESOURCES) } -#' @title Update the total availability of sugar -#' @description This method dispatches on the type of `pars$S`. It should -#' update, and if necessary compute, the availability of sugar at time `t` -#' @param t current simulation time +#' @title Update the availability of sugar +#' @description This method dispatches on the type of `pars$RESOURCES`. #' @param pars an [list] #' @return a [list] #' @export -update_S <- function(t, pars) { - UseMethod("update_S", pars$S) +SugarAvailability <- function(pars) { + UseMethod("SugarAvailability", pars$RESOURCES) } diff --git a/R/resources-null.R b/R/resources-null.R index 8a7d5223..d9f2d311 100644 --- a/R/resources-null.R +++ b/R/resources-null.R @@ -7,13 +7,42 @@ Resources.null <- function(t, y, pars) { return(pars) } +#' @title Compute availability of local humans for blood feeding +#' @description Compute the availability for the pathogen's hosts for blood feeding +#' @param t current simulation time +#' @param y state vector +#' @param pars a [list] +#' @return a [numeric] vector of length `nPatches` +#' @export +HumanAvailability.null <- function(t, y, pars){ + return(pars) +} + +#' @title Compute total availability of aquatic habitats +#' @description Computes the availability of aquatic habitats for the null model (do nothing) +#' @param pars a [list] +#' @return a [numeric] vector of length `nPatches` +#' @export +HabitatAvailability.null <- function(pars){ + return(pars) +} + +#' @title Compute total availability of sugar +#' @description Computes the availability of sugar for the null model (do nothing) +#' @param pars a [list] +#' @return a [numeric] vector of length `nPatches` +#' @export +SugarAvailability.null <- function(pars){ + return(pars) +} + #' @title Set up parameters for the null model for resource availability #' @param pars a [list] #' @return none #' @export setup_resources_null<- function(pars){ - RApar <- list() - class(RApar) <- 'null' - pars$RApar <- RApar + RESOURCES <- list() + class(RESOURCES) <- 'null' + pars$RESOURCES <- RESOURCES return(pars) } diff --git a/R/resources-static.R b/R/resources-static.R deleted file mode 100644 index 63f9d6a9..00000000 --- a/R/resources-static.R +++ /dev/null @@ -1,88 +0,0 @@ -# specialized methods for when resource availability does not change dynamically - -#' @title Modify resources and resource availability -#' @description Implements [Resources] for static models -#' @inheritParams Resources -#' @return none -#' @export -Resources.static <- function(t, y, pars) { - return(pars) -} - -#' @title Update blood feeding for static models -#' @description Implements [update_BloodFeeding] for a dynamic model -#' @inheritParams update_BloodFeeding -#' @return a [list] -#' @export -update_BloodFeeding.static <- function(t, y, pars){ - return(pars) -} - -#' @title Update blood feeding for static models -#' @description Implements [update_EggLaying] for a dynamic model -#' @inheritParams update_EggLaying -#' @return a [list] -#' @export -update_EggLaying.static <- function(t, y, pars){ - return(pars) -} - -#' @title Update host availability for static models -#' @description Implements [update_W] when pars$W doesn't change -#' @inheritParams update_W -#' @return a [list] -#' @export -update_W.static <- function(t, y, pars){ - return(pars) -} - -#' @title Update other host availability for static models -#' @description Implements [update_O] when pars$O doesn't change -#' @inheritParams update_O -#' @return a [list] -#' @export -update_O.static <- function(t, pars){ - return(pars) -} - -#' @title Update sugar availability for static models -#' @description Implements [update_S] when pars$S doesn't change -#' @inheritParams update_S -#' @return a [list] -#' @export -update_S.static <- function(t, pars){ - return(pars) -} - -#' @title Set up parameters for a static model for resource availability -#' @param pars a [list] -#' @param RAopts a set of options that would override the defaults -#' @param other the availability of other blood hosts -#' @param sugar the availability of sugar -#' @return none -#' @export -setup_resources_static <- function(pars, RAopts, other=0, sugar=0){with(RAopts,{ - RApar <- list() - class(RApar) <- 'static' - pars$RApar <- RApar - - pars$OtherBloodHosts <- other - class(pars$OtherBloodHosts) <- 'static' - - pars$W <- compute_W(0, 0, pars) - class(pars$W) <- 'static' - - pars$local_frac <- compute_local_frac(pars) - - pars$B <- compute_B(pars) - class(pars$B) <- 'static' - - pars$Q <- compute_Q(pars) - class(pars$Q) <- 'static' - - pars$S <- sugar - class(pars$S) <- 'static' - - return(pars) -})} - diff --git a/R/setup.R b/R/setup.R index 587f363a..c7221c3e 100644 --- a/R/setup.R +++ b/R/setup.R @@ -222,3 +222,45 @@ xde_setup_human = function(modelName, return(pars) } +#' @title Set up a model for xde_diffeqn_cohort +#' @param modelName is a name for the model (arbitrary) +#' @param F_eir is a function F_eir(t, pars) that returns the daily FoI +#' @param Xname is a character string defining a X model +#' @param HPop is the number of humans in each patch +#' @param Xopts a list to configure the X model +#' @param Hopts a list to configure the H model +#' @return a [list] +#' @export +xde_setup_cohort = function(modelName, F_eir, + + # Dynamical Components + Xname = "SIS", + + # Model Structure + HPop=1000, + + # Human Strata / Options + Xopts = list(), + Hopts = list() + +){ + + pars = make_parameters_xde() + class(pars$xde) <- "cohort" + pars$modelName = modelName + pars$F_eir = F_eir + + # Structure + nStrata = length(HPop) + pars$nPatches = as.integer(nStrata) + pars$nStrata = nStrata + + pars = setup_Hpar(pars, HPop, 1:nStrata, rep(1, nStrata), Hopts) + + # Dynamics + pars = setup_X(pars, Xname, Xopts) + + pars = make_indices(pars) + + return(pars) +} diff --git a/R/shock.R b/R/shock.R new file mode 100644 index 00000000..7971d85f --- /dev/null +++ b/R/shock.R @@ -0,0 +1,31 @@ +# generic methods for shocks + +#' @title Set up shocks +#' @description This method dispatches on the type of `pars$SHOCK`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +Shock <- function(t, pars) { + UseMethod("Shock", pars$SHOCK) +} + +#' @title Set up shocks +#' @description Implements [Shock] for the null model (do nothing) +#' @inheritParams Shock +#' @return [list] +#' @export +Shock.null <- function(t, pars) { + return(pars) +} + +#' @title Set up the null model for shocks (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_shock_null <- function(pars) { + SHOCK <- list() + class(SHOCK) <- 'null' + pars$SHOCK <- SHOCK + return(pars) +} diff --git a/R/solving.R b/R/solving.R index ec90d07c..0efaf5d4 100644 --- a/R/solving.R +++ b/R/solving.R @@ -93,3 +93,15 @@ xde_solve.human = function(pars, Tmax=365, dt=1){ parse_deout(out, pars) } + +#' @title Solve a system of equations with xDE_diffeqn_cohort +#' @description Implements [xde_solve] for mosquito dynamics (no transmission) +#' @inheritParams xde_solve +#' @return a [matrix] +#' @export +xde_solve.cohort = function(pars, Tmax=365, dt=1){ + tt = seq(0, Tmax, by=dt) + y0 = get_inits(pars) + deSolve::ode(y = y0, times = tt, func = xDE_diffeqn_cohort, parms = pars, F_eir = pars$F_eir, method = "lsoda") -> out + parse_deout(out, pars) +} diff --git a/R/sugar.R b/R/sugar.R index 6464dedb..83c71ee1 100644 --- a/R/sugar.R +++ b/R/sugar.R @@ -1,60 +1,32 @@ +# Methods to set up variables describing exogenous forcing by sugar -#' @title Set the availability of sugar -#' @description This method dispatches on the type of `pars$SGRpar`. It should -#' set the values of sugar availability at time `t` +#' @title Set the values of exogenous variables describing sugar +#' @description This method dispatches on the type of `pars$SUGAR`. #' @param t current simulation time #' @param pars a [list] -#' @return a [numeric] vector of length `nPatches` +#' @return [list] #' @export -F_sugar <- function(t, pars) { - UseMethod("F_sugar", pars$SGRpar) +Sugar <- function(t, pars) { + UseMethod("Sugar", pars$SUGAR) } -#' @title Null model for sugar -#' @description Implements [F_sugar] for a null model -#' @inheritParams F_sugar -#' @return a [numeric] vector of length `nStrata` +#' @title Set the values of exogenous variables describing sugar +#' @description Implements [Sugar] for the null model of sugar (do nothing) +#' @inheritParams Sugar +#' @return [list] #' @export -F_sugar.null <- function(t, pars){ - pars -} - -#' @title Basic model for sugar -#' @description Implements [F_sugar] for a basic model -#' @inheritParams F_sugar -#' @return a [numeric] vector of length `nStrata` -#' @export -F_sugar.static <- function(t, pars){ - pars -} - -#' @title A basic forcing model for sugar -#' @description Implements [F_sugar] for a forced model -#' @inheritParams F_sugar -#' @return a [list] -#' @export -F_sugar.forced <- function(t, pars){ - with(pars$SGRpar,{ - return(sugar_scale*sugar_t(t, pars)) - }) +Sugar.null <- function(t, pars) { + return(pars) } -#' @title Set up forcing for the availability of sugar +#' @title Make parameters for the null model for sugar (do nothing) #' @param pars a [list] -#' @param sugar_Opts a list, overwrites default values -#' @param sugar_scale a non-negative numeric value to scale the mean availability of sugar -#' @param sugar_t a function that specifies the temporal pattern for the availability of sugar -#' @return none +#' @return [list] #' @export -setup_sugar_forced <- function(pars, sugar_Opts = list(), sugar_scale=0, sugar_t=NULL) {with(sugar_Opts,{ - - SGRpar <- list() - class(SGRpar) <- 'foi' - pars$SGRpar <- SGRpar - - pars$SGRpar$sugar_scale = sugar_scale - if(is.null(sugar_t)) sugar_t = function(t, pars){1} - pars$SGRpar$sugar_t = sugar_t - +setup_sugar_null <- function(pars) { + SUGAR <- list() + class(SUGAR) <- 'null' + pars$SUGAR <- SUGAR return(pars) -})} +} + diff --git a/R/sugar_baits-interface.R b/R/sugar_baits-interface.R new file mode 100644 index 00000000..b82d5fcc --- /dev/null +++ b/R/sugar_baits-interface.R @@ -0,0 +1,44 @@ +# methods for sugar baits + +#' @title Methods for distributing sugar baits +#' @description This method dispatches on the type of `pars$SUGAR_BAITS`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +SugarBaits <- function(t, pars) { + UseMethod("SugarBaits", pars$SUGAR_BAITS) +} + +#' @title Methods for the durability and effects of the sugar baits +#' @description This method dispatches on the type of `pars$SUGAR_BAITS`. +#' @param t current simulation time +#' @param y vector of state variables +#' @param pars a [list] +#' @return [list] +#' @export +SugarBaitEffects <- function(t, y, pars) { + UseMethod("SugarBaitEffects", pars$SUGAR_BAITS) +} + +#' @title Methods for the effect sizes of the sugar baits +#' @description This method dispatches on the type of `pars$SUGAR_BAITS`. +#' @param t current simulation time +#' @param y vector of state variables +#' @param pars a [list] +#' @return [list] +#' @export +SugarBaitEffectSizes <- function(t, y, pars) { + UseMethod("SugarBaitEffectSizes", pars$SUGAR_BAITS) +} + +#' @title Set up the null model for sugar baits (do nothing) +#' @param pars a [list] +#' @return [list] +#' @export +setup_sugar_baits_null <- function(pars) { + SUGAR_BAITS <- list() + class(SUGAR_BAITS) <- 'null' + pars$SUGAR_BAITS <- SUGAR_BAITS + return(pars) +} diff --git a/R/sugar_baits-null.R b/R/sugar_baits-null.R new file mode 100644 index 00000000..f372460a --- /dev/null +++ b/R/sugar_baits-null.R @@ -0,0 +1,27 @@ + +#' @title Methods for sugar baits +#' @description Implements [SugarBaits] for the null model (do nothing) +#' @inheritParams SugarBaits +#' @return [list] +#' @export +SugarBaits.null <- function(t, pars) { + return(pars) +} + +#' @title Methods for the effects of the sugar baits +#' @description Implements [SugarBaitEffects] for the null model (do nothing) +#' @inheritParams SugarBaitEffects +#' @return [list] +#' @export +SugarBaitEffects.null <- function(t, y, pars) { + return(pars) +} + +#' @title Methods for the effect sizes of the sugar baits +#' @description This method dispatches on the type of `pars$SUGAR_BAITS`. +#' @inheritParams SugarBaitEffectSizes +#' @return [list] +#' @export +SugarBaitEffectSizes.null <- function(t, y, pars) { + return(pars) +} diff --git a/R/travel_malaria-eir.R b/R/travel_malaria-eir.R index 336bbd6c..79f43823 100644 --- a/R/travel_malaria-eir.R +++ b/R/travel_malaria-eir.R @@ -6,7 +6,7 @@ #' @return a [numeric] #' @export travel_malaria.eir <- function(t, pars) { - with(pars$TRVpar,{ + with(pars$TRAVEL,{ eir = travel_eir_scale*travel_eir_t(t, pars)*frac_time_spent_traveling return(F_foi(pars$MYZpar$b*eir, pars)) })} @@ -21,14 +21,14 @@ travel_malaria.eir <- function(t, pars) { #' @export setup_travel_eir <- function(pars, travel_Opts = list(), frac_time_spent_traveling = 0.01, travel_eir_scale=0, travel_eir_t=NULL) {with(travel_Opts,{ - TRVpar <- list() - class(TRVpar) <- 'eir' - pars$TRVpar <- TRVpar + TRAVEL <- list() + class(TRAVEL) <- 'eir' + pars$TRAVEL <- TRAVEL - pars$TRVpar$travel_eir_scale = travel_eir_scale + pars$TRAVEL$travel_eir_scale = travel_eir_scale if(is.null(travel_eir_t)) travel_eir_t = function(t, pars){1} - pars$TRVpar$travel_eir_t = travel_eir_t - pars$TRVpar$frac_time_spent_traveling = frac_time_spent_traveling + pars$TRAVEL$travel_eir_t = travel_eir_t + pars$TRAVEL$frac_time_spent_traveling = frac_time_spent_traveling return(pars) })} diff --git a/R/travel_malaria-foi.R b/R/travel_malaria-foi.R index 91fc03e1..afda276e 100644 --- a/R/travel_malaria-foi.R +++ b/R/travel_malaria-foi.R @@ -6,7 +6,7 @@ #' @return a [numeric] #' @export travel_malaria.foi <- function(t, pars) { - with(pars$TRVpar,{ + with(pars$TRAVEL,{ return(delta_scale*delta_t(t, pars)) })} @@ -19,13 +19,13 @@ travel_malaria.foi <- function(t, pars) { #' @export setup_travel_foi <- function(pars, travel_Opts = list(), delta_scale=0, delta_t=NULL) {with(travel_Opts,{ - TRVpar <- list() - class(TRVpar) <- 'foi' - pars$TRVpar <- TRVpar + TRAVEL <- list() + class(TRAVEL) <- 'foi' + pars$TRAVEL <- TRAVEL - pars$TRVpar$delta_scale = delta_scale + pars$TRAVEL$delta_scale = delta_scale if(is.null(delta_t)) delta_t = function(t, pars){1} - pars$TRVpar$delta_t = delta_t + pars$TRAVEL$delta_t = delta_t return(pars) })} diff --git a/R/travel_malaria-interface.R b/R/travel_malaria-interface.R index 74faf467..23a715e1 100644 --- a/R/travel_malaria-interface.R +++ b/R/travel_malaria-interface.R @@ -1,12 +1,12 @@ # generic methods for a model of travel malaria #' @title Simulate travel malaria -#' @description This method dispatches on the type of `pars$TRVpar`. +#' @description This method dispatches on the type of `pars$TRAVEL`. #' @param t current simulation time #' @param pars a [list] #' @return a [numeric] value #' @export travel_malaria <- function(t, pars) { - UseMethod("travel_malaria", pars$TRVpar) + UseMethod("travel_malaria", pars$TRAVEL) } diff --git a/R/travel_malaria-null.R b/R/travel_malaria-null.R index 2e109a0a..a22785d9 100644 --- a/R/travel_malaria-null.R +++ b/R/travel_malaria-null.R @@ -16,9 +16,9 @@ travel_malaria.null <- function(t, pars) { #' @export setup_travel_null = function(pars){ - TRVpar <- list() - class(TRVpar) <- 'null' - pars$TRVpar <- TRVpar + TRAVEL <- list() + class(TRAVEL) <- 'null' + pars$TRAVEL <- TRAVEL return(pars) } diff --git a/R/utils.R b/R/utils.R index 56690cc4..b5161a76 100644 --- a/R/utils.R +++ b/R/utils.R @@ -10,11 +10,14 @@ make_parameters_xde = function(solve_as='ode'){ class(xde) <- xde pars$xde = xde - pars <- setup_exogenous_null(pars) - pars <- setup_humanbehavior_null(pars) - pars <- setup_resources_null(pars) + pars <- setup_abiotic_null(pars) + pars <- setup_shock_null(pars) + pars <- setup_control_null(pars) pars <- setup_vc_null(pars) + pars <- setup_behavior_null(pars) pars <- setup_visitors_null(pars) + pars <- setup_resources_null(pars) + pars <- setup_eip_static(pars) pars <- setup_travel_null(pars) pars <- setup_exposure_pois(pars) diff --git a/R/vector_control-control.R b/R/vector_control-control.R new file mode 100644 index 00000000..e6d4f460 --- /dev/null +++ b/R/vector_control-control.R @@ -0,0 +1,60 @@ + +# specialized methods for the control model of vector control + +#' @title Distribute vector control, the null model +#' @description Implements [VectorControl] for the control model of vector control (do nothing) +#' @inheritParams VectorControl +#' @return a named [list] +#' @export +VectorControl.control <- function(t, y, pars) { + pars = DistributeBedNets(t, pars) + pars = OwnBedNet(t, y, pars) + pars = AreaSpray(t, pars) + pars = SprayHouses(t, pars) + pars = SugarBaits(t, pars) + pars = TreatHabitats(t, pars) + return(pars) +} + +#' @title Vector control durability and effects +#' @description Implements [VectorControlEffects] for the control model of vector control (do nothing) +#' @inheritParams VectorControlEffects +#' @return a named [list] +#' @export +VectorControlEffects.control <- function(t, y, pars) { + pars = BedNetEffects(t, pars) + pars = AreaSprayEffects(t, pars) + pars = IRSeffects(t, pars) + pars = SugarBaitEffects(t, pars) + pars = LSMeffects(t, pars) + return(pars) +} + +#' @title Distribute vector control, the null model +#' @description Implements [VectorControlEffectSizes] for the control model of vector control (do nothing) +#' @inheritParams VectorControlEffectSizes +#' @return a named [list] +#' @export +VectorControlEffectSizes.control <- function(t, y, pars) { + pars = BedNetEffectSizes(t, pars) + pars = AreaSprayEffectSizes(t, pars) + pars = IRSeffectSizes(t, pars) + pars = SugarBaitEffectSizes(t, pars) + pars = LSMeffectSizes(t, pars) + return(pars) +} + +#' @title Make parameters for the control model of vector control (do nothing) +#' @param pars a [list] +#' @return none +#' @export +setup_vc_control <- function(pars) { + pars = setup_control(pars) + class(pars$VECTOR_CONTROL) <- 'control' + pars <- setup_itn_null(pars) + pars <- setup_area_spray_null(pars) + pars <- setup_irs_null(pars) + pars <- setup_sugar_baits_null(pars) + pars <- setup_lsm_null(pars) + return(pars) +} diff --git a/R/vector_control-interface.R b/R/vector_control-interface.R new file mode 100644 index 00000000..96b2f577 --- /dev/null +++ b/R/vector_control-interface.R @@ -0,0 +1,34 @@ +# generic methods for vector control component + +#' @title Distribute vector control +#' @description This method dispatches on the type of `pars$VECTOR_CONTROL`. +#' @param t current simulation time +#' @param y state vector +#' @param pars a [list] +#' @return a [list] +#' @export +VectorControl <- function(t, y, pars) { + UseMethod("VectorControl", pars$VECTOR_CONTROL) +} + +#' @title Vector control: durability & effects +#' @description This method dispatches on the type of `pars$VECTOR_CONTROL`. +#' @param t current simulation time +#' @param y state vector +#' @param pars a [list] +#' @return a [list] +#' @export +VectorControlEffects <- function(t, y, pars) { + UseMethod("VectorControlEffectSizes", pars$VECTOR_CONTROL) +} + +#' @title Vector control effect sizes +#' @description This method dispatches on the type of `pars$VECTOR_CONTROL`. +#' @param t current simulation time +#' @param y state vector +#' @param pars a [list] +#' @return a [list] +#' @export +VectorControlEffectSizes <- function(t, y, pars) { + UseMethod("VectorControlEffectSizes", pars$VECTOR_CONTROL) +} diff --git a/R/vector_control-null.R b/R/vector_control-null.R new file mode 100644 index 00000000..b549f064 --- /dev/null +++ b/R/vector_control-null.R @@ -0,0 +1,39 @@ +# specialized methods for the null model of vector control + +#' @title Distribute vector control +#' @description Implements [VectorControl] for the null model of vector control (do nothing) +#' @inheritParams VectorControl +#' @return a named [list] +#' @export +VectorControl.null <- function(t, y, pars) { + return(pars) +} + +#' @title Vector control: durability & effects +#' @description Implements [VectorControlEffects] for the null model of vector control (do nothing) +#' @inheritParams VectorControlEffects +#' @return a named [list] +#' @export +VectorControlEffects.null <- function(t, y, pars) { + return(pars) +} + +#' @title Vector control effect sizes +#' @description Implements [VectorControlEffectSizes] for the null model of vector control (do nothing) +#' @inheritParams VectorControlEffectSizes +#' @return a named [list] +#' @export +VectorControlEffectSizes.null <- function(t, y, pars) { + return(pars) +} + +#' @title Distribute vector control, the null model +#' @param pars a [list] +#' @return none +#' @export +setup_vc_null <- function(pars) { + VECTOR_CONTROL <- list() + class(VECTOR_CONTROL) <- 'null' + pars$VECTOR_CONTROL <- VECTOR_CONTROL + return(pars) +} diff --git a/R/vectorcontrol-control.R b/R/vectorcontrol-control.R deleted file mode 100644 index fe424c6a..00000000 --- a/R/vectorcontrol-control.R +++ /dev/null @@ -1,29 +0,0 @@ -# specialized methods for the control model of vector control - -#' @title Modify baseline values due to vector control -#' @description Implements [VectorControl] for the control model of vector control (do nothing) -#' @inheritParams VectorControl -#' @return a named [list] -#' @export -VectorControl.control <- function(t, y, pars) { - pars = BedNets(t, pars) - pars = IRS(t, pars) - pars = ATSB(t, pars) - pars = LSM(t, pars) - return(pars) -} - -#' @title Make parameters for the control model of vector control (do nothing) -#' @param pars a [list] -#' @return none -#' @export -setup_vc_control <- function(pars) { - VCpar <- list() - class(VCpar) <- 'control' - pars$VCpar <- VCpar - pars <- setup_itn_null(pars) - pars <- setup_irs_null(pars) - pars <- setup_atsb_null(pars) - pars <- setup_lsm_null(pars) - return(pars) -} diff --git a/R/vectorcontrol-interface.R b/R/vectorcontrol-interface.R deleted file mode 100644 index 0be4d88f..00000000 --- a/R/vectorcontrol-interface.R +++ /dev/null @@ -1,13 +0,0 @@ -# generic methods for vector control component - -#' @title Modify baseline values due to vector control -#' @description This method dispatches on the type of `pars$VCpar`. -#' @param t current simulation time -#' @param pars a [list] -#' @param y state vector -#' @return a [list] -#' @export -VectorControl <- function(t, y, pars) { - UseMethod("VectorControl", pars$VCpar) -} - diff --git a/R/vectorcontrol-null.R b/R/vectorcontrol-null.R deleted file mode 100644 index 2ded5b28..00000000 --- a/R/vectorcontrol-null.R +++ /dev/null @@ -1,21 +0,0 @@ -# specialized methods for the null model of vector control - -#' @title Modify baseline values due to vector control -#' @description Implements [VectorControl] for the null model of vector control (do nothing) -#' @inheritParams VectorControl -#' @return a named [list] -#' @export -VectorControl.null <- function(t, y, pars) { - return(pars) -} - -#' @title Set up the vector control null model (do nothing) -#' @param pars a [list] -#' @return none -#' @export -setup_vc_null <- function(pars) { - VCpar <- list() - class(VCpar) <- 'null' - pars$VCpar <- VCpar - return(pars) -} diff --git a/R/visitors-basic.R b/R/visitors-basic.R deleted file mode 100644 index 57f764a2..00000000 --- a/R/visitors-basic.R +++ /dev/null @@ -1,34 +0,0 @@ -# specialized methods for a basic visitors model - -#' @title Visitors, the basic model -#' @description Implements [Visitors] for the basic model for Visitors -#' @inheritParams Visitors -#' @return a named [list] -#' @export -Visitors.basic <- function(t, pars) { - pars$x_visitors = with(pars$Ipar, x_scale*xt(t, pars)) - pars$Visitors = with(pars$Ipar, V_scale*Vt(t, pars)) - return(pars) -} - -#' @title Make parameters and functions for the basic model for visitors -#' @param pars a [list] -#' @param IMopts a [list] -#' @param x_scale a non-negative numeric value to set the mean for x_visitors -#' @param xt a function to change the pattern for x_visitors over time -#' @param V_scale a non-negative numeric value to set the mean availability of Visitors -#' @param Vt a function to set the temporal pattern for availability of Visitors -#' @return none -#' @export -setup_visitors_basic <- function(pars, IMopts, x_scale = 0, xt = NULL, V_scale = 0, Vt = NULL) {with(IMopts,{ - - pars$Ipar$x_scale = x_scale - if(is.null(xt)) xt = function(t, pars){1} - pars$Ipar$xt = xt - - pars$Ipar$V_scale = V_scale - if(is.null(Vt)) Vt = function(t, pars){1} - pars$Ipar$Vt = Vt - - return(pars) -})} diff --git a/R/visitors-null.R b/R/visitors-null.R deleted file mode 100644 index 294236fb..00000000 --- a/R/visitors-null.R +++ /dev/null @@ -1,27 +0,0 @@ -# specialized methods for the visitors null - -#' @title Visitors, a null model -#' @description Implements [Visitors] for the null model (do nothing) -#' @inheritParams Visitors -#' @return a named [list] -#' @export -Visitors.null <- function(t, pars) { - return(pars) -} - -#' @title Make parameters for the null model visitors (no visitors) -#' @param pars a [list] -#' @return none -#' @export -setup_visitors_null <- function(pars) { - - Ipar <- list() - class(Ipar) <- 'null' - pars$Ipar <- Ipar - - pars$local_frac = 1 - pars$Visitors = 0 - pars$x_visitors = 0 - - return(pars) -} diff --git a/R/visitors.R b/R/visitors.R index 86d21f4d..6fe26295 100644 --- a/R/visitors.R +++ b/R/visitors.R @@ -1,12 +1,71 @@ # generic methods for parasite / pathogen importation by visitors #' @title Visitors -#' @description This method dispatches on the type of `pars$Ipar`. +#' @description This method dispatches on the type of `pars$VISITORS`. #' @param t current simulation time #' @param pars a [list] -#' @return pars a [list] +#' @return a [list] #' @export Visitors <- function(t, pars) { - UseMethod("Visitors", pars$Ipar) + UseMethod("Visitors", pars$VISITORS) } +#' @title Visitors, a null model +#' @description Implements [Visitors] for the null model (do nothing) +#' @inheritParams Visitors +#' @return a [list] +#' @export +Visitors.null <- function(t, pars) { + return(pars) +} + +#' @title Make parameters for the null model visitors (no visitors) +#' @param pars a [list] +#' @return [list] +#' @export +setup_visitors_null <- function(pars) { + + VISITORS <- list() + class(VISITORS) <- 'null' + pars$VISITORS <- VISITORS + + pars$local_frac = 1 + pars$Visitors = 0 + pars$x_visitors = 0 + + return(pars) +} + + +#' @title Visitors, the basic model +#' @description Implements [Visitors] for the basic model for Visitors +#' @inheritParams Visitors +#' @return a [list] +#' @export +Visitors.basic <- function(t, pars) { + pars$x_visitors = with(pars$VISITORS, x_scale*xt(t, pars)) + pars$Visitors = with(pars$VISITORS, V_scale*Vt(t, pars)) + return(pars) +} + +#' @title Make parameters and functions for the basic model for visitors +#' @param pars a [list] +#' @param IMopts a [list] +#' @param x_scale a non-negative numeric value to set the mean for x_visitors +#' @param xt a function to change the pattern for x_visitors over time +#' @param V_scale a non-negative numeric value to set the mean availability of Visitors +#' @param Vt a function to set the temporal pattern for availability of Visitors +#' @return [list] +#' @export +setup_visitors_basic <- function(pars, IMopts, x_scale = 0, xt = NULL, V_scale = 0, Vt = NULL) {with(IMopts,{ + + pars$VISITORS$x_scale = x_scale + if(is.null(xt)) xt = function(t, pars){1} + pars$VISITORS$xt = xt + + pars$VISITORS$V_scale = V_scale + if(is.null(Vt)) Vt = function(t, pars){1} + pars$VISITORS$Vt = Vt + + return(pars) +})} diff --git a/R/weather.R b/R/weather.R new file mode 100644 index 00000000..cd99c688 --- /dev/null +++ b/R/weather.R @@ -0,0 +1,88 @@ +# generic methods for exogenous forcing by weather + +#' @title Methods for exogenous variables describing weather +#' @description This method dispatches on the type of `pars$WEATHER`. +#' @param t current simulation time +#' @param pars a [list] +#' @return [list] +#' @export +Weather <- function(t, pars) { + UseMethod("Weather", pars$WEATHER) +} + +#' @title Methods for exogenous variables describing weather +#' @description Implements [Weather] for the null model (no variables) +#' @inheritParams Weather +#' @return [list] +#' @export +Weather.null <- function(t, pars) { + return(pars) +} + +#' @title Set up the null model for weather +#' @param pars a [list] +#' @return [list] +#' @export +setup_weather_null <- function(pars) { + WEATHER <- list() + class(WEATHER) <- 'null' + pars$WEATHER <- WEATHER + return(pars) +} + +#' @title Methods for exogenous variables describing weather +#' @description Implements exogenous forcing by [Weather] +#' @inheritParams Weather +#' @return [list] +#' @export +Weather.forced <- function(t, pars) { + return(pars) +} + +#' @title Set up the forced model for weather +#' @param pars a [list] +#' @return [list] +#' @export +setup_weather_forced <- function(pars) { + pars = check_abiotic(pars) + WEATHER <- list() + class(WEATHER) <- 'forced' + pars$WEATHER <- WEATHER + pars = setup_temperature_null(pars) + pars = setup_rainfall_null(pars) + pars = setup_relative_humidity_null(pars) + return(pars) +} + +#' @title Set up the null model for temperature +#' @param pars a [list] +#' @return [list] +#' @export +setup_temperature_null <- function(pars) { + TEMPERATURE <- list() + class(TEMPERATURE) <- 'null' + pars$TEMPERATURE <- TEMPERATURE + return(pars) +} + +#' @title Set up the null model for RAINFALL +#' @param pars a [list] +#' @return [list] +#' @export +setup_rainfall_null <- function(pars) { + RAINFALL <- list() + class(RAINFALL) <- 'null' + pars$RAINFALL <- RAINFALL + return(pars) +} + +#' @title Set up the null model for HUMIDITY +#' @param pars a [list] +#' @return [list] +#' @export +setup_relative_humidity_null <- function(pars) { + HUMIDITY <- list() + class(HUMIDITY) <- 'null' + pars$HUMIDITY <- HUMIDITY + return(pars) +} diff --git a/_pkgdown.yml b/_pkgdown.yml index f9c52353..4bf2c47f 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -68,13 +68,14 @@ reference: - F_EIR - F_kappa - compute_beta + - Exposure - title: Adult Mosquito Dynamics desc: | Generic methods for the adult mosquito dynamics component. contents: - - MosquitoBehavior - - F_tau + - MBionomics - F_fqZ + - F_tau - F_eggs - dMYZdt - setup_MYZ @@ -82,11 +83,18 @@ reference: - parse_deout_MYZ - get_inits_MYZ - make_Omega +- subtitle: EIP + desc: | + Specialized methods for NULL dynamics: a funtion generates values of Z to force human infection dynamics + contents: + - EIP + - EIP.static + - setup_eip_static - subtitle: Ztrace desc: | Specialized methods for NULL dynamics: a funtion generates values of Z to force human infection dynamics contents: - - MosquitoBehavior.Ztrace + - MBionomics.Ztrace - F_fqZ.Ztrace - F_eggs.Ztrace - dMYZdt.Ztrace @@ -101,7 +109,7 @@ reference: desc: | Specialized methods for NULL dynamics: a funtion generates values for eggs laid to aquatic ecology contents: - - MosquitoBehavior.Gtrace + - MBionomics.Gtrace - F_fqZ.Gtrace - F_eggs.Gtrace - dMYZdt.Gtrace @@ -116,7 +124,7 @@ reference: desc: | Specialized methods for basicM, a model of adult mosquito dynamics with no parasite infection dynamics. contents: - - MosquitoBehavior.basicM + - MBionomics.basicM - F_eggs.basicM - dMYZdt.basicM - setup_MYZ.basicM @@ -131,7 +139,7 @@ reference: desc: | Specialized methods for a Ross-Macdonald-style model of adult mosquito dynamics, modified slightly from a model published by Joan Aron & Robert May (1982). contents: - - MosquitoBehavior.RM + - MBionomics.RM - F_fqZ.RM - F_eggs.RM - dMYZdt.RM_ode @@ -151,8 +159,7 @@ reference: desc: | Specialized methods for a generalized Ross-Macdonald model for adult mosquito ecology and parasite infection dynamics, first published by Sean L Wu, et al.(2023). contents: - - MosquitoBehavior.GeRM - - Resources.GeRM + - MBionomics.GeRM - F_fqZ.GeRM - F_eggs.GeRM - dMYZdt.GeRM_ode @@ -168,13 +175,10 @@ reference: - get_inits_MYZ.GeRM_ode - get_inits_MYZ.GeRM_dde - make_parameters_MYZ_GeRM_static - - setup_forcing_MYZ_GeRM_basic - title: Mosquito Bionomic Functional Responses desc: | Compute bionomic parameters as functional responses to resource availability contents: - - F_eip - - F_eip.static - F_sigma - F_sigma.static - F_sigma.BQS @@ -202,6 +206,7 @@ reference: desc: | Generic methods for the aquatic (immature) mosquito component. contents: + - LBionomics - F_alpha - dLdt - setup_L @@ -214,6 +219,7 @@ reference: desc: | Specialized methods for the exogeneously forced trace model of aquatic mosquito dynamics. contents: + - LBionomics.trace - F_alpha.trace - dLdt.trace - setup_L.trace @@ -227,6 +233,7 @@ reference: desc: | Specialized methods for a basic competition model of aquatic mosquito dynamics. contents: + - LBionomics.basic - F_alpha.basic - dLdt.basic - setup_L.basic @@ -242,6 +249,7 @@ reference: Generic methods for the dynamical component that handles human infection dynamics, immunity, disease and transmission contents: - F_X + - F_b - dXdt - setup_X - make_indices_X @@ -253,6 +261,7 @@ reference: Specialized methods for a human trace model to pass kappa as a parameter contents: - F_X.trace + - F_b.trace - dXdt.trace - setup_X.trace - make_Xpar_trace @@ -266,6 +275,7 @@ reference: Specialized methods for a hybrid model of MoI (Multiplicity of Infection) for human infection dynamics. contents: - F_X.hMoI + - F_b.hMoI - dXdt.hMoI - setup_X.hMoI - make_Xpar_hMoI @@ -281,6 +291,7 @@ reference: Specialized methods for the SIS (Susceptible-Infected-Susceptible) model of human dynamics. contents: - F_X.SIS + - F_b.SIS - dXdt.SISdX - dXdt.SISdXdH - setup_X.SIS @@ -297,6 +308,7 @@ reference: Specialized methods for the SIP (Susceptible-Infected-Prophylaxis) model of human dynamics. contents: - F_X.SIP + - F_b.SIP - dXdt.SIPdX - dXdt.SIPdXdH - setup_X.SIP @@ -361,13 +373,25 @@ reference: - make_TaR.as_matrix - make_TaR.xy - make_TaR_xy -- title: Human Behavior +- title: Human and Mosqutio Behaviors desc: | - Methods to implement human behaviors + Methods to implement human and Mosquito Behaviorsbehaviors contents: - - HumanBehavior - - HumanBehavior.null - - setup_humanbehavior_null + - Behavior + - Behavior.null + - Behavior.forced + - setup_behavior_null + - setup_behavior_forced + - setup_behavior + - setup_behavior.null + - setup_behavior.forced +- subtitle: Care Seeking + desc: | + Methods to implement care seeking + contents: + - CareSeeking + - CareSeeking.null + - setup_care_seeking_null - title: Exposure desc: | Methods to implement exposure models (i.e., EIR to FoI) @@ -429,26 +453,66 @@ reference: desc: | Methods to implement exogeneous forcing. contents: - - ExogenousForcing + - Abiotic + - Civil + - Shock + - Control + - Clinic + - Development + - MassMedical - subtitle: null model desc: | Specialized methods the null model (no exogenous forcing) contents: - - ExogenousForcing.null - - setup_exogenous_null + - Abiotic.null + - setup_abiotic_null + - Civil.null + - setup_civil_null + - Shock.null + - setup_shock_null + - Control.null + - Control.static + - setup_control_null + - setup_control + - setup_control.null + - setup_control.forced + - Clinic.null + - setup_clinic_null + - setup_clinic_forced + - Development.null + - setup_development_null + - MassMedical.null + - setup_mass_medical_null - subtitle: forced desc: | Specialized methods to call forcing contents: - - ExogenousForcing.forced - - setup_exogenous_forced + - Abiotic.forced + - setup_abiotic_forced + - check_abiotic + - check_abiotic.null + - check_abiotic.forced + - Civil.forced + - setup_civil_forced + - check_civil + - check_civil.null + - check_civil.forced + - Control.forced + - setup_control_forced + - MassMedical.forced + - setup_mass_medical_forced - subtitle: Weather desc: | Specialized methods for weather contents: - Weather - Weather.null + - Weather.forced - setup_weather_null + - setup_weather_forced + - setup_rainfall_null + - setup_temperature_null + - setup_relative_humidity_null - subtitle: Hydrology desc: | Specialized methods for hydrology @@ -456,119 +520,137 @@ reference: - Hydrology - Hydrology.null - setup_hydrology_null -- title: Resource Availability +- title: Resources and Availability desc: | Methods to implement resource availability contents: - Resources + - HumanAvailability + - HabitatAvailability + - SugarAvailability - Resources.null - - Resources.static - - setup_resources_static - - Resources.dynamic + - HumanAvailability.null + - HabitatAvailability.null + - SugarAvailability.null + - Resources.forced + - HumanAvailability.forced + - HabitatAvailability.forced + - SugarAvailability.forced - setup_resources_null -- subtitle: Blood Feeding - desc: | - Methods to simulate blood feeding rates and habits based on available resources - contents: - - update_BloodFeeding - - update_BloodFeeding.static - - update_BloodFeeding.dynamic - - compute_W - - compute_B - - update_W - - update_W.static - - update_W.dynamic + - setup_resources_forced - compute_local_frac - subtitle: Other Blood Hosts desc: | Methods to simulate availability of other blood hosts contents: - - F_otherblood - - F_otherblood.null - - F_otherblood.static - - F_otherblood.forced - - setup_otherblood_forced - - update_O - - update_O.static - - update_O.dynamic -- subtitle: Egg Laying - desc: | - Methods for the egg laying interface - contents: - - update_EggLaying - - update_EggLaying.static - - update_EggLaying.dynamic + - OtherBloodHosts + - OtherBloodHosts.null + - setup_other_blood_hosts_null - subtitle: Habitat Dynamics desc: | Methods to implement habitat dynamics contents: - - F_habitats - - F_habitats.null - - setup_habitats_null - - F_habitats.static - - setup_habitats_static - - F_habitats.forced - - setup_habitats_forced - - compute_Q + - HabitatDynamics + - HabitatDynamics.null + - setup_habitat_dynamics_null - subtitle: Sugar desc: | Methods to simulate availability of sugar contents: - - update_S - - update_S.static - - update_S.dynamic - - F_sugar - - F_sugar.null - - F_sugar.static - - F_sugar.forced - - setup_sugar_forced + - Sugar + - Sugar.null + - setup_sugar_null - title: Vector Control desc: | Methods to implement vector control. contents: - VectorControl + - VectorControlEffects + - VectorControlEffectSizes - subtitle: null model desc: | Specialized methods for the null model (no vector control) contents: - VectorControl.null + - VectorControlEffects.null + - VectorControlEffectSizes.null - setup_vc_null - subtitle: Implement Control desc: | Specialized methods to implement vector control contents: - VectorControl.control + - VectorControlEffects.control + - VectorControlEffectSizes.control - setup_vc_control - subtitle: Bed Nets desc: | Methods to implement bed nets contents: - - BedNets - - BedNets.null + - DistributeBedNets + - OwnBedNet + - UseBedNet + - BedNetEffects + - BedNetEffectSizes + - DistributeBedNets.null + - OwnBedNet.null + - UseBedNet.null + - BedNetEffects.null + - BedNetEffectSizes.null - setup_itn_null - - BedNets.lemenach + - BedNetEffectSizes.lemenach - setup_itn_lemenach - subtitle: Indoor Residual Spraying desc: | Methods to implement IRS contents: - - IRS - - IRS.null + - SprayHouses + - IRSeffects + - IRSeffectSizes + - SprayHouses.null + - IRSeffects.null + - IRSeffectSizes.null - setup_irs_null -- subtitle: Attractive Toxic Sugar Baits - desc: | - Methods to implement ATSB - contents: - - ATSB - - ATSB.null - - setup_atsb_null +- subtitle: Area Spraying + desc: | + Methods to implement area spraying + contents: + - AreaSpray + - AreaSprayEffects + - AreaSprayEffectSizes + - AreaSpray.null + - AreaSprayEffects.null + - AreaSprayEffectSizes.null + - setup_area_spray_null +- subtitle: Sugar Baits + desc: | + Methods to implement sugar baits + contents: + - SugarBaits + - SugarBaitEffects + - SugarBaitEffectSizes + - SugarBaits.null + - SugarBaitEffects.null + - SugarBaitEffectSizes.null + - setup_sugar_baits_null - subtitle: Larval Source Management desc: | Methods to implement LSM contents: - - LSM - - LSM.null + - TreatHabitats + - LSMeffects + - LSMeffectSizes + - TreatHabitats.null + - LSMeffects.null + - LSMeffectSizes.null - setup_lsm_null +- subtitle: Ovitraps + desc: | + Specialized methods for ovitraps + contents: + - OviTraps + - OviTraps.null + - setup_ovitraps_null - title: Spatial metrics contents: - metric_calV @@ -581,6 +663,7 @@ reference: - xde_setup_aquatic - xde_setup_mosy - xde_setup_human + - xde_setup_cohort - title: Solving contents: - xde_solve @@ -591,6 +674,7 @@ reference: - xde_solve.mosy - xde_solve.mosy_dde - xde_solve.human + - xde_solve.cohort - title: Utilities contents: - make_parameters_xde diff --git a/man/ATSB.Rd b/man/ATSB.Rd deleted file mode 100644 index ad01c0ba..00000000 --- a/man/ATSB.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/atsb-interface.R -\name{ATSB} -\alias{ATSB} -\title{Modify baseline bionomic values due to ATSB} -\usage{ -ATSB(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -This method dispatches on the type of \code{pars$ATSBpar}. -} diff --git a/man/ATSB.null.Rd b/man/ATSB.null.Rd deleted file mode 100644 index 5901f37e..00000000 --- a/man/ATSB.null.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/atsb-null.R -\name{ATSB.null} -\alias{ATSB.null} -\title{Modify baseline values due to ATSB} -\usage{ -\method{ATSB}{null}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{ATSB} for the null model of ATSB (do nothing) -} diff --git a/man/Abiotic.Rd b/man/Abiotic.Rd new file mode 100644 index 00000000..5bddcfee --- /dev/null +++ b/man/Abiotic.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/abiotic.R +\name{Abiotic} +\alias{Abiotic} +\title{Set up exogenous variables for abiotic forcing} +\usage{ +Abiotic(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$ABIOTIC}. +} diff --git a/man/Abiotic.forced.Rd b/man/Abiotic.forced.Rd new file mode 100644 index 00000000..a9cacd8d --- /dev/null +++ b/man/Abiotic.forced.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/abiotic.R +\name{Abiotic.forced} +\alias{Abiotic.forced} +\title{Set up exogenous variables for abiotic forcing} +\usage{ +\method{Abiotic}{forced}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +pars a \link{list} +} +\description{ +Implements \link{Abiotic} for abiotic forcing +} diff --git a/man/Abiotic.null.Rd b/man/Abiotic.null.Rd new file mode 100644 index 00000000..7667bd9e --- /dev/null +++ b/man/Abiotic.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/abiotic.R +\name{Abiotic.null} +\alias{Abiotic.null} +\title{Set up exogenous variables for abiotic forcing} +\usage{ +\method{Abiotic}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Abiotic} for the null model of exogenous forcing (do nothing) +} diff --git a/man/AreaSpray.Rd b/man/AreaSpray.Rd new file mode 100644 index 00000000..9a801d96 --- /dev/null +++ b/man/AreaSpray.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/area_spray.R +\name{AreaSpray} +\alias{AreaSpray} +\title{Methods for mass spraying} +\usage{ +AreaSpray(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$AREA_SPRAY}. +} diff --git a/man/AreaSpray.null.Rd b/man/AreaSpray.null.Rd new file mode 100644 index 00000000..3c51d1a3 --- /dev/null +++ b/man/AreaSpray.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/area_spray.R +\name{AreaSpray.null} +\alias{AreaSpray.null} +\title{Set up mass spraying} +\usage{ +\method{AreaSpray}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{AreaSpray} for the null model (do nothing) +} diff --git a/man/AreaSprayEffectSizes.Rd b/man/AreaSprayEffectSizes.Rd new file mode 100644 index 00000000..1fe79538 --- /dev/null +++ b/man/AreaSprayEffectSizes.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/area_spray.R +\name{AreaSprayEffectSizes} +\alias{AreaSprayEffectSizes} +\title{Methods for mass spraying} +\usage{ +AreaSprayEffectSizes(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$AREA_SPRAY}. +} diff --git a/man/AreaSprayEffectSizes.null.Rd b/man/AreaSprayEffectSizes.null.Rd new file mode 100644 index 00000000..ddbd174b --- /dev/null +++ b/man/AreaSprayEffectSizes.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/area_spray.R +\name{AreaSprayEffectSizes.null} +\alias{AreaSprayEffectSizes.null} +\title{Set up mass spraying} +\usage{ +\method{AreaSprayEffectSizes}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{AreaSprayEffectSizes} for the null model (do nothing) +} diff --git a/man/AreaSprayEffects.Rd b/man/AreaSprayEffects.Rd new file mode 100644 index 00000000..925836b3 --- /dev/null +++ b/man/AreaSprayEffects.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/area_spray.R +\name{AreaSprayEffects} +\alias{AreaSprayEffects} +\title{Methods for mass spraying} +\usage{ +AreaSprayEffects(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$AREA_SPRAY}. +} diff --git a/man/AreaSprayEffects.null.Rd b/man/AreaSprayEffects.null.Rd new file mode 100644 index 00000000..76192fb5 --- /dev/null +++ b/man/AreaSprayEffects.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/area_spray.R +\name{AreaSprayEffects.null} +\alias{AreaSprayEffects.null} +\title{Set up mass spraying} +\usage{ +\method{AreaSprayEffects}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{AreaSprayEffects} for the null model (do nothing) +} diff --git a/man/BedNetEffectSizes.Rd b/man/BedNetEffectSizes.Rd new file mode 100644 index 00000000..e960a08b --- /dev/null +++ b/man/BedNetEffectSizes.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-interface.R +\name{BedNetEffectSizes} +\alias{BedNetEffectSizes} +\title{Modify baseline bionomic parameters, called from VectorControlEffectSizes} +\usage{ +BedNetEffectSizes(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$ITNefsz}. +} diff --git a/man/BedNets.lemenach.Rd b/man/BedNetEffectSizes.lemenach.Rd similarity index 58% rename from man/BedNets.lemenach.Rd rename to man/BedNetEffectSizes.lemenach.Rd index 94fe3083..9eae3879 100644 --- a/man/BedNets.lemenach.Rd +++ b/man/BedNetEffectSizes.lemenach.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/bednet-lemenach.R -\name{BedNets.lemenach} -\alias{BedNets.lemenach} +\name{BedNetEffectSizes.lemenach} +\alias{BedNetEffectSizes.lemenach} \title{Modify baseline values due to vector control} \usage{ -\method{BedNets}{lemenach}(t, pars) +\method{BedNetEffectSizes}{lemenach}(t, pars) } \arguments{ \item{t}{current simulation time} @@ -15,5 +15,5 @@ a named \link{list} } \description{ -Implements \link{BedNets} for the Le Menach ITN model of vector control +Implements \link{BedNetEffectSizes} for the Le Menach ITN model of vector control } diff --git a/man/BedNetEffectSizes.null.Rd b/man/BedNetEffectSizes.null.Rd new file mode 100644 index 00000000..6bfac9c8 --- /dev/null +++ b/man/BedNetEffectSizes.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-null.R +\name{BedNetEffectSizes.null} +\alias{BedNetEffectSizes.null} +\title{Bed net ownership} +\usage{ +\method{BedNetEffectSizes}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +Implements \link{BedNetEffectSizes} for the null model of bed nets (do nothing) +} diff --git a/man/BedNets.Rd b/man/BedNetEffects.Rd similarity index 53% rename from man/BedNets.Rd rename to man/BedNetEffects.Rd index 6a92b4ef..1d5c74c6 100644 --- a/man/BedNets.Rd +++ b/man/BedNetEffects.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/bednet-interface.R -\name{BedNets} -\alias{BedNets} -\title{Modify baseline bionomic values due to bed nets} +\name{BedNetEffects} +\alias{BedNetEffects} +\title{Modify variables or parameters, called from VectorControlEffects} \usage{ -BedNets(t, pars) +BedNetEffects(t, pars) } \arguments{ \item{t}{current simulation time} @@ -15,5 +15,5 @@ BedNets(t, pars) a \link{list} } \description{ -This method dispatches on the type of \code{pars$ITNpar}. +This method dispatches on the type of \code{pars$ITNeff}. } diff --git a/man/BedNets.null.Rd b/man/BedNetEffects.null.Rd similarity index 53% rename from man/BedNets.null.Rd rename to man/BedNetEffects.null.Rd index ef585607..c76316bb 100644 --- a/man/BedNets.null.Rd +++ b/man/BedNetEffects.null.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/bednet-null.R -\name{BedNets.null} -\alias{BedNets.null} -\title{Modify baseline values due to bed nets} +\name{BedNetEffects.null} +\alias{BedNetEffects.null} +\title{Bed net ownership} \usage{ -\method{BedNets}{null}(t, pars) +\method{BedNetEffects}{null}(t, pars) } \arguments{ \item{t}{current simulation time} @@ -15,5 +15,5 @@ a \link{list} } \description{ -Implements \link{BedNets} for the null model of bed nets (do nothing) +Implements \link{BedNetEffects} for the null model of bed nets (do nothing) } diff --git a/man/Behavior.Rd b/man/Behavior.Rd new file mode 100644 index 00000000..fdf3e504 --- /dev/null +++ b/man/Behavior.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/behavior.R +\name{Behavior} +\alias{Behavior} +\title{Methods for dynamic human and mosquito behaviors} +\usage{ +Behavior(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$BEHAVIOR}. +} diff --git a/man/Behavior.forced.Rd b/man/Behavior.forced.Rd new file mode 100644 index 00000000..18a8b120 --- /dev/null +++ b/man/Behavior.forced.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/behavior.R +\name{Behavior.forced} +\alias{Behavior.forced} +\title{Methods for dynamic human and mosquito behaviors} +\usage{ +\method{Behavior}{forced}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Behavior} for the forced model (no changes) +} diff --git a/man/Behavior.null.Rd b/man/Behavior.null.Rd new file mode 100644 index 00000000..8aa20992 --- /dev/null +++ b/man/Behavior.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/behavior.R +\name{Behavior.null} +\alias{Behavior.null} +\title{Methods for dynamic human and mosquito behaviors} +\usage{ +\method{Behavior}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Behavior} for the null model (no changes) +} diff --git a/man/CareSeeking.Rd b/man/CareSeeking.Rd new file mode 100644 index 00000000..0f1b9035 --- /dev/null +++ b/man/CareSeeking.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/care_seeking.R +\name{CareSeeking} +\alias{CareSeeking} +\title{Set the values of exogenous variables describing care seeking} +\usage{ +CareSeeking(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$CARE_SEEKING}. +} diff --git a/man/CareSeeking.null.Rd b/man/CareSeeking.null.Rd new file mode 100644 index 00000000..b2d5655d --- /dev/null +++ b/man/CareSeeking.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/care_seeking.R +\name{CareSeeking.null} +\alias{CareSeeking.null} +\title{Set the values of exogenous variables describing care seeking} +\usage{ +\method{CareSeeking}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{CareSeeking} for the null model of care seeking (do nothing) +} diff --git a/man/Civil.Rd b/man/Civil.Rd new file mode 100644 index 00000000..df7665a7 --- /dev/null +++ b/man/Civil.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{Civil} +\alias{Civil} +\title{Set up exogenous variables for civil forcing} +\usage{ +Civil(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$CIVIL}. +} diff --git a/man/Civil.forced.Rd b/man/Civil.forced.Rd new file mode 100644 index 00000000..6ca1fd6e --- /dev/null +++ b/man/Civil.forced.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{Civil.forced} +\alias{Civil.forced} +\title{Set up exogenous variables for civil forcing} +\usage{ +\method{Civil}{forced}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +pars a \link{list} +} +\description{ +Implements \link{Civil} for civil forcing +} diff --git a/man/Civil.null.Rd b/man/Civil.null.Rd new file mode 100644 index 00000000..b4c7a428 --- /dev/null +++ b/man/Civil.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{Civil.null} +\alias{Civil.null} +\title{Set up exogenous variables for civil forcing} +\usage{ +\method{Civil}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Civil} for the null model of exogenous forcing (do nothing) +} diff --git a/man/Clinic.Rd b/man/Clinic.Rd new file mode 100644 index 00000000..3bbe3486 --- /dev/null +++ b/man/Clinic.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/clinic.R +\name{Clinic} +\alias{Clinic} +\title{Methods for distributing interventions during clinical visits} +\usage{ +Clinic(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$CLINIC}. +} diff --git a/man/Clinic.null.Rd b/man/Clinic.null.Rd new file mode 100644 index 00000000..1ec17bc1 --- /dev/null +++ b/man/Clinic.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/clinic.R +\name{Clinic.null} +\alias{Clinic.null} +\title{Methods for distributing interventions during clinical visits} +\usage{ +\method{Clinic}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Clinic} for the null model (do nothing) +} diff --git a/man/Control.Rd b/man/Control.Rd new file mode 100644 index 00000000..f1b9b08e --- /dev/null +++ b/man/Control.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{Control} +\alias{Control} +\title{Modify parameters due to exogenous forcing by all kinds of control} +\usage{ +Control(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$CONTROL}. +} diff --git a/man/Control.forced.Rd b/man/Control.forced.Rd new file mode 100644 index 00000000..619b46df --- /dev/null +++ b/man/Control.forced.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{Control.forced} +\alias{Control.forced} +\title{Modify parameters due to exogenous forcing by all kinds of control} +\usage{ +\method{Control}{forced}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +pars a \link{list} +} +\description{ +Implements \link{Control} for a model with some control +} diff --git a/man/Control.null.Rd b/man/Control.null.Rd new file mode 100644 index 00000000..9d81ace4 --- /dev/null +++ b/man/Control.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{Control.null} +\alias{Control.null} +\title{Modify parameters due to exogenous forcing by all kinds of control} +\usage{ +\method{Control}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Control} for the null model (do nothing) +} diff --git a/man/Control.static.Rd b/man/Control.static.Rd new file mode 100644 index 00000000..bb33bb26 --- /dev/null +++ b/man/Control.static.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{Control.static} +\alias{Control.static} +\title{Modify parameters due to exogenous forcing by all kinds of control} +\usage{ +\method{Control}{static}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Control} for the static model; after setting up, do nothing +} diff --git a/man/Development.Rd b/man/Development.Rd new file mode 100644 index 00000000..6cc7aa76 --- /dev/null +++ b/man/Development.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/development.R +\name{Development} +\alias{Development} +\title{Set up developments} +\usage{ +Development(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$DEVELOPMENT}. +} diff --git a/man/Development.null.Rd b/man/Development.null.Rd new file mode 100644 index 00000000..4be9bc12 --- /dev/null +++ b/man/Development.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/development.R +\name{Development.null} +\alias{Development.null} +\title{Set up developments} +\usage{ +\method{Development}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Development} for the null model (do nothing) +} diff --git a/man/DistributeBedNets.Rd b/man/DistributeBedNets.Rd new file mode 100644 index 00000000..2b3d287f --- /dev/null +++ b/man/DistributeBedNets.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-interface.R +\name{DistributeBedNets} +\alias{DistributeBedNets} +\title{Distribute bed nets, called from Control(VectorControl)} +\usage{ +DistributeBedNets(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$ITNdist}. +} diff --git a/man/DistributeBedNets.null.Rd b/man/DistributeBedNets.null.Rd new file mode 100644 index 00000000..34271916 --- /dev/null +++ b/man/DistributeBedNets.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-null.R +\name{DistributeBedNets.null} +\alias{DistributeBedNets.null} +\title{Distribute bed nets} +\usage{ +\method{DistributeBedNets}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +Implements \link{DistributeBedNets} for the null model of bed nets (do nothing) +} diff --git a/man/EIP.Rd b/man/EIP.Rd new file mode 100644 index 00000000..80adb309 --- /dev/null +++ b/man/EIP.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/eip.R +\name{EIP} +\alias{EIP} +\title{Compute the EIP} +\usage{ +EIP(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$EIPmod}. +} diff --git a/man/EIP.static.Rd b/man/EIP.static.Rd new file mode 100644 index 00000000..d2a856e7 --- /dev/null +++ b/man/EIP.static.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/eip.R +\name{EIP.static} +\alias{EIP.static} +\title{Modify parameters due to exogenous forcing by all kinds of control} +\usage{ +\method{EIP}{static}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{EIP} for the static model (the EIP is constant) +} diff --git a/man/ExogenousForcing.Rd b/man/ExogenousForcing.Rd deleted file mode 100644 index 7333a9cc..00000000 --- a/man/ExogenousForcing.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-interface.R -\name{ExogenousForcing} -\alias{ExogenousForcing} -\title{Modify parameters due to exogenous forcing} -\usage{ -ExogenousForcing(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -This method dispatches on the type of \code{pars$EXOpar}. -} diff --git a/man/ExogenousForcing.forced.Rd b/man/ExogenousForcing.forced.Rd deleted file mode 100644 index 3f75f700..00000000 --- a/man/ExogenousForcing.forced.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-forced.R -\name{ExogenousForcing.forced} -\alias{ExogenousForcing.forced} -\title{Modify parameters due to exogenous forcing} -\usage{ -\method{ExogenousForcing}{forced}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -pars a \link{list} -} -\description{ -Calls functions that set up exogenous variables -} diff --git a/man/ExogenousForcing.null.Rd b/man/ExogenousForcing.null.Rd deleted file mode 100644 index 83ab974d..00000000 --- a/man/ExogenousForcing.null.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-null.R -\name{ExogenousForcing.null} -\alias{ExogenousForcing.null} -\title{Modify parameters due to exogenous forcing} -\usage{ -\method{ExogenousForcing}{null}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -Implements \link{ExogenousForcing} for the null model of exogenous forcing (do nothing) -} diff --git a/man/Exposure.Rd b/man/Exposure.Rd new file mode 100644 index 00000000..65d7a58d --- /dev/null +++ b/man/Exposure.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/exposure.R +\name{Exposure} +\alias{Exposure} +\title{A model for exposure. The function \code{F_b} must be define} +\usage{ +Exposure(t, y, pars, EIR) +} +\arguments{ +\item{t}{the time} + +\item{y}{the variables} + +\item{pars}{a \link{list}} + +\item{EIR}{is the daily eir} +} +\description{ +A model for exposure. The function \code{F_b} must be define +} diff --git a/man/F_b.Rd b/man/F_b.Rd new file mode 100644 index 00000000..e396abda --- /dev/null +++ b/man/F_b.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/human-interface.R +\name{F_b} +\alias{F_b} +\title{Infection blocking pre-erythrocytic immunity} +\usage{ +F_b(y, pars) +} +\arguments{ +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nStrata} +} +\description{ +This method dispatches on the type of \code{pars$Xpar}. +} diff --git a/man/F_b.SIP.Rd b/man/F_b.SIP.Rd new file mode 100644 index 00000000..1dc302c3 --- /dev/null +++ b/man/F_b.SIP.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/human-SIP.R +\name{F_b.SIP} +\alias{F_b.SIP} +\title{Infection blocking pre-erythrocytic immunity} +\usage{ +\method{F_b}{SIP}(y, pars) +} +\arguments{ +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nStrata} +} +\description{ +Implements \link{F_b} for the SIP model. +} diff --git a/man/F_b.SIS.Rd b/man/F_b.SIS.Rd new file mode 100644 index 00000000..04bb22ef --- /dev/null +++ b/man/F_b.SIS.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/human-SIS.R +\name{F_b.SIS} +\alias{F_b.SIS} +\title{Infection blocking pre-erythrocytic immunity} +\usage{ +\method{F_b}{SIS}(y, pars) +} +\arguments{ +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nStrata} +} +\description{ +Implements \link{F_b} for the SIS model. +} diff --git a/man/F_b.hMoI.Rd b/man/F_b.hMoI.Rd new file mode 100644 index 00000000..4eca8940 --- /dev/null +++ b/man/F_b.hMoI.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/human-hMoI.R +\name{F_b.hMoI} +\alias{F_b.hMoI} +\title{Infection blocking pre-erythrocytic immunity} +\usage{ +\method{F_b}{hMoI}(y, pars) +} +\arguments{ +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nStrata} +} +\description{ +Implements \link{F_b} for the hMoI model. +} diff --git a/man/F_b.trace.Rd b/man/F_b.trace.Rd new file mode 100644 index 00000000..5405c8a2 --- /dev/null +++ b/man/F_b.trace.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/human-trace.R +\name{F_b.trace} +\alias{F_b.trace} +\title{Infection blocking pre-erythrocytic immunity} +\usage{ +\method{F_b}{trace}(y, pars) +} +\arguments{ +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nStrata} +} +\description{ +Implements \link{F_b} for the trace model. +} diff --git a/man/F_eip.Rd b/man/F_eip.Rd deleted file mode 100644 index 87130996..00000000 --- a/man/F_eip.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R -\name{F_eip} -\alias{F_eip} -\title{Compute the eip} -\usage{ -F_eip(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{numeric} vector of length \code{nPatches} -} -\description{ -This method dispatches on the type of \code{pars$MYZpar$eip_par}. It should -set the values of the eip -} diff --git a/man/F_eip.static.Rd b/man/F_eip.static.Rd deleted file mode 100644 index 223247c6..00000000 --- a/man/F_eip.static.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R -\name{F_eip.static} -\alias{F_eip.static} -\title{Static model for human blood fraction} -\usage{ -\method{F_eip}{static}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{numeric} vector of length \code{nPatches} -} -\description{ -Implements \link{F_eip} for a static model -} diff --git a/man/F_f.Rd b/man/F_f.Rd index 40a51c2b..a979952e 100644 --- a/man/F_f.Rd +++ b/man/F_f.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_f} \alias{F_f} \title{Compute the blood feeding rate, f} diff --git a/man/F_f.static.Rd b/man/F_f.static.Rd index bad06411..108e633d 100644 --- a/man/F_f.static.Rd +++ b/man/F_f.static.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_f.static} \alias{F_f.static} \title{Static model for the blood feeding rate} diff --git a/man/F_f.type2.Rd b/man/F_f.type2.Rd index 1f6acc50..56dd1d79 100644 --- a/man/F_f.type2.Rd +++ b/man/F_f.type2.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_f.type2} \alias{F_f.type2} \title{Type 2 functional response for the blood feeding rate} diff --git a/man/F_g.Rd b/man/F_g.Rd index 5b6afada..e0093052 100644 --- a/man/F_g.Rd +++ b/man/F_g.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_g} \alias{F_g} \title{Compute mosguito survival} diff --git a/man/F_g.static.Rd b/man/F_g.static.Rd index d53e4288..e05b89ab 100644 --- a/man/F_g.static.Rd +++ b/man/F_g.static.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_g.static} \alias{F_g.static} \title{Static model for mosquito survival} diff --git a/man/F_habitats.Rd b/man/F_habitats.Rd deleted file mode 100644 index 965969ec..00000000 --- a/man/F_habitats.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/habitat_dynamics.R -\name{F_habitats} -\alias{F_habitats} -\title{Set the values for habitat} -\usage{ -F_habitats(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -This method dispatches on the type of \code{pars$QHABpar}. It should -set the values of habitat at time \code{t} -} diff --git a/man/F_habitats.forced.Rd b/man/F_habitats.forced.Rd deleted file mode 100644 index b21b81f3..00000000 --- a/man/F_habitats.forced.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/habitat_dynamics.R -\name{F_habitats.forced} -\alias{F_habitats.forced} -\title{A basic forcing model for habitat availability} -\usage{ -\method{F_habitats}{forced}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{F_habitats} for a forced model -} diff --git a/man/F_habitats.null.Rd b/man/F_habitats.null.Rd deleted file mode 100644 index 3116138b..00000000 --- a/man/F_habitats.null.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/habitat_dynamics.R -\name{F_habitats.null} -\alias{F_habitats.null} -\title{A null model for habitat} -\usage{ -\method{F_habitats}{null}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{F_habitats} for a static model -} diff --git a/man/F_habitats.static.Rd b/man/F_habitats.static.Rd deleted file mode 100644 index bca8baf8..00000000 --- a/man/F_habitats.static.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/habitat_dynamics.R -\name{F_habitats.static} -\alias{F_habitats.static} -\title{Static model for habitat} -\usage{ -\method{F_habitats}{static}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{F_habitats} for a static model -} diff --git a/man/F_nu.Rd b/man/F_nu.Rd index 39f7d425..e3781952 100644 --- a/man/F_nu.Rd +++ b/man/F_nu.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_nu} \alias{F_nu} \title{Compute the egg laying rate} diff --git a/man/F_nu.static.Rd b/man/F_nu.static.Rd index 3ca56059..77c2dff4 100644 --- a/man/F_nu.static.Rd +++ b/man/F_nu.static.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_nu.static} \alias{F_nu.static} \title{Static model for the egg laying rate} diff --git a/man/F_nu.type2.Rd b/man/F_nu.type2.Rd index 5c60ab0e..bac06e78 100644 --- a/man/F_nu.type2.Rd +++ b/man/F_nu.type2.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_nu.type2} \alias{F_nu.type2} \title{Type 2 functional response for the blood feeding rate} diff --git a/man/F_otherblood.Rd b/man/F_otherblood.Rd deleted file mode 100644 index 34f88e41..00000000 --- a/man/F_otherblood.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/other_blood_hosts.R -\name{F_otherblood} -\alias{F_otherblood} -\title{Set the availability of other} -\usage{ -F_otherblood(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -This method dispatches on the type of \code{pars$OBHpar}. It should -set the values of other availability at time \code{t} -} diff --git a/man/F_otherblood.forced.Rd b/man/F_otherblood.forced.Rd deleted file mode 100644 index e9950e4c..00000000 --- a/man/F_otherblood.forced.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/other_blood_hosts.R -\name{F_otherblood.forced} -\alias{F_otherblood.forced} -\title{A basic forcing model for other blood hosts} -\usage{ -\method{F_otherblood}{forced}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{F_otherblood} for a forced model -} diff --git a/man/F_otherblood.null.Rd b/man/F_otherblood.null.Rd deleted file mode 100644 index 46a5446c..00000000 --- a/man/F_otherblood.null.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/other_blood_hosts.R -\name{F_otherblood.null} -\alias{F_otherblood.null} -\title{Null model for other blood hosts} -\usage{ -\method{F_otherblood}{null}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{F_otherblood} for a null model -} diff --git a/man/F_otherblood.static.Rd b/man/F_otherblood.static.Rd deleted file mode 100644 index d2356dda..00000000 --- a/man/F_otherblood.static.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/other_blood_hosts.R -\name{F_otherblood.static} -\alias{F_otherblood.static} -\title{Static model for other blood hosts} -\usage{ -\method{F_otherblood}{static}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{F_otherblood} for a static model -} diff --git a/man/F_q.Rd b/man/F_q.Rd index f9fbcb79..b9a6743f 100644 --- a/man/F_q.Rd +++ b/man/F_q.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_q} \alias{F_q} \title{Compute the human blood fraction} diff --git a/man/F_q.dynamic.Rd b/man/F_q.dynamic.Rd index bff4842f..d554b769 100644 --- a/man/F_q.dynamic.Rd +++ b/man/F_q.dynamic.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_q.dynamic} \alias{F_q.dynamic} \title{Static model for human blood fraction} diff --git a/man/F_q.static.Rd b/man/F_q.static.Rd index 07c694c5..71c7e3da 100644 --- a/man/F_q.static.Rd +++ b/man/F_q.static.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_q.static} \alias{F_q.static} \title{Static model for human blood fraction} diff --git a/man/F_sigma.BQS.Rd b/man/F_sigma.BQS.Rd index 8776d3b9..fbee9dd4 100644 --- a/man/F_sigma.BQS.Rd +++ b/man/F_sigma.BQS.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_sigma.BQS} \alias{F_sigma.BQS} \title{Model for mosquito emigration based on resource availability} diff --git a/man/F_sigma.Rd b/man/F_sigma.Rd index fa731ae1..1ae85f0b 100644 --- a/man/F_sigma.Rd +++ b/man/F_sigma.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_sigma} \alias{F_sigma} \title{Compute mosquito emigration rates} diff --git a/man/F_sigma.static.Rd b/man/F_sigma.static.Rd index 65836539..613f6f51 100644 --- a/man/F_sigma.static.Rd +++ b/man/F_sigma.static.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R +% Please edit documentation in R/adult-bionomics.R \name{F_sigma.static} \alias{F_sigma.static} \title{Static model for mosquito emigration} diff --git a/man/F_sugar.Rd b/man/F_sugar.Rd deleted file mode 100644 index 346b27ca..00000000 --- a/man/F_sugar.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/sugar.R -\name{F_sugar} -\alias{F_sugar} -\title{Set the availability of sugar} -\usage{ -F_sugar(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{numeric} vector of length \code{nPatches} -} -\description{ -This method dispatches on the type of \code{pars$SGRpar}. It should -set the values of sugar availability at time \code{t} -} diff --git a/man/F_sugar.null.Rd b/man/F_sugar.null.Rd deleted file mode 100644 index ab892502..00000000 --- a/man/F_sugar.null.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/sugar.R -\name{F_sugar.null} -\alias{F_sugar.null} -\title{Null model for sugar} -\usage{ -\method{F_sugar}{null}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{numeric} vector of length \code{nStrata} -} -\description{ -Implements \link{F_sugar} for a null model -} diff --git a/man/F_sugar.static.Rd b/man/F_sugar.static.Rd deleted file mode 100644 index a59640c9..00000000 --- a/man/F_sugar.static.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/sugar.R -\name{F_sugar.static} -\alias{F_sugar.static} -\title{Basic model for sugar} -\usage{ -\method{F_sugar}{static}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{a \link{list}} -} -\value{ -a \link{numeric} vector of length \code{nStrata} -} -\description{ -Implements \link{F_sugar} for a basic model -} diff --git a/man/HabitatAvailability.Rd b/man/HabitatAvailability.Rd new file mode 100644 index 00000000..c68c75b4 --- /dev/null +++ b/man/HabitatAvailability.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-interface.R +\name{HabitatAvailability} +\alias{HabitatAvailability} +\title{Update the availability of aquatic habitats} +\usage{ +HabitatAvailability(pars) +} +\arguments{ +\item{pars}{an \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$RESOURCES}. +} diff --git a/man/compute_Q.Rd b/man/HabitatAvailability.forced.Rd similarity index 62% rename from man/compute_Q.Rd rename to man/HabitatAvailability.forced.Rd index aa4cb62a..7d037878 100644 --- a/man/compute_Q.Rd +++ b/man/HabitatAvailability.forced.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-functions.R -\name{compute_Q} -\alias{compute_Q} +% Please edit documentation in R/resources-forced.R +\name{HabitatAvailability.forced} +\alias{HabitatAvailability.forced} \title{Compute total availability of aquatic habitats} \usage{ -compute_Q(pars) +\method{HabitatAvailability}{forced}(pars) } \arguments{ \item{pars}{a \link{list}} diff --git a/man/HabitatAvailability.null.Rd b/man/HabitatAvailability.null.Rd new file mode 100644 index 00000000..1d94c4d8 --- /dev/null +++ b/man/HabitatAvailability.null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-null.R +\name{HabitatAvailability.null} +\alias{HabitatAvailability.null} +\title{Compute total availability of aquatic habitats} +\usage{ +\method{HabitatAvailability}{null}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nPatches} +} +\description{ +Computes the availability of aquatic habitats for the null model (do nothing) +} diff --git a/man/HabitatDynamics.Rd b/man/HabitatDynamics.Rd new file mode 100644 index 00000000..713e9ff5 --- /dev/null +++ b/man/HabitatDynamics.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/habitat_dynamics.R +\name{HabitatDynamics} +\alias{HabitatDynamics} +\title{Set the values of exogenous variables describing habitat_dynamics} +\usage{ +HabitatDynamics(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$HABITAT_DYNAMICS}. +} diff --git a/man/HabitatDynamics.null.Rd b/man/HabitatDynamics.null.Rd new file mode 100644 index 00000000..0efa4664 --- /dev/null +++ b/man/HabitatDynamics.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/habitat_dynamics.R +\name{HabitatDynamics.null} +\alias{HabitatDynamics.null} +\title{Set the values of exogenous variables describing habitat dynamics} +\usage{ +\method{HabitatDynamics}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{HabitatDynamics} for the null model of habitat_dynamics (do nothing) +} diff --git a/man/update_BloodFeeding.Rd b/man/HumanAvailability.Rd similarity index 54% rename from man/update_BloodFeeding.Rd rename to man/HumanAvailability.Rd index 98030e01..8e3aaaad 100644 --- a/man/update_BloodFeeding.Rd +++ b/man/HumanAvailability.Rd @@ -1,15 +1,15 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/resources-interface.R -\name{update_BloodFeeding} -\alias{update_BloodFeeding} +\name{HumanAvailability} +\alias{HumanAvailability} \title{Update the availability of blood hosts} \usage{ -update_BloodFeeding(t, y, pars) +HumanAvailability(t, y, pars) } \arguments{ \item{t}{current simulation time} -\item{y}{state variables} +\item{y}{vector of state variables} \item{pars}{an \link{list}} } @@ -17,6 +17,5 @@ update_BloodFeeding(t, y, pars) a \link{list} } \description{ -This method dispatches on the type of \code{pars$B}. It -computes availability of all blood hosts at time \code{t} +This method dispatches on the type of \code{pars$RESOURCES}. } diff --git a/man/HumanAvailability.forced.Rd b/man/HumanAvailability.forced.Rd new file mode 100644 index 00000000..09036131 --- /dev/null +++ b/man/HumanAvailability.forced.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-forced.R +\name{HumanAvailability.forced} +\alias{HumanAvailability.forced} +\title{Compute availability of local humans for blood feeding} +\usage{ +\method{HumanAvailability}{forced}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nPatches} +} +\description{ +Compute the availability for the pathogen's hosts for blood feeding +} diff --git a/man/compute_W.Rd b/man/HumanAvailability.null.Rd similarity index 57% rename from man/compute_W.Rd rename to man/HumanAvailability.null.Rd index 218822d5..b80ac704 100644 --- a/man/compute_W.Rd +++ b/man/HumanAvailability.null.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-functions.R -\name{compute_W} -\alias{compute_W} -\title{Compute host availability} +% Please edit documentation in R/resources-null.R +\name{HumanAvailability.null} +\alias{HumanAvailability.null} +\title{Compute availability of local humans for blood feeding} \usage{ -compute_W(t, y, pars) +\method{HumanAvailability}{null}(t, y, pars) } \arguments{ \item{t}{current simulation time} diff --git a/man/HumanBehavior.Rd b/man/HumanBehavior.Rd deleted file mode 100644 index 773aa087..00000000 --- a/man/HumanBehavior.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/humanbehavior.R -\name{HumanBehavior} -\alias{HumanBehavior} -\title{Simulate Human Behavior} -\usage{ -HumanBehavior(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -This method dispatches on the type of \code{pars$HBpar}. -} diff --git a/man/HumanBehavior.null.Rd b/man/HumanBehavior.null.Rd deleted file mode 100644 index 855b4823..00000000 --- a/man/HumanBehavior.null.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/humanbehavior.R -\name{HumanBehavior.null} -\alias{HumanBehavior.null} -\title{Simulate no human behaviors} -\usage{ -\method{HumanBehavior}{null}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -Implements \link{HumanBehavior} for the null model (do nothing) -} diff --git a/man/Hydrology.Rd b/man/Hydrology.Rd index f906abef..6fca07d4 100644 --- a/man/Hydrology.Rd +++ b/man/Hydrology.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-interface.R +% Please edit documentation in R/hydrology.R \name{Hydrology} \alias{Hydrology} \title{Set the values of exogenous variables describing hydrology} @@ -12,8 +12,8 @@ Hydrology(t, pars) \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ -This method dispatches on the type of \code{pars$HYpar}. +This method dispatches on the type of \code{pars$HYDROLOGY}. } diff --git a/man/Hydrology.null.Rd b/man/Hydrology.null.Rd index 0f884297..e3b66eb5 100644 --- a/man/Hydrology.null.Rd +++ b/man/Hydrology.null.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-null.R +% Please edit documentation in R/hydrology.R \name{Hydrology.null} \alias{Hydrology.null} -\title{Modify parameters due to exogenous forcing} +\title{Set the values of exogenous variables describing hydrology} \usage{ \method{Hydrology}{null}(t, pars) } @@ -12,7 +12,7 @@ \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ Implements \link{Hydrology} for the null model of hydrology (do nothing) diff --git a/man/IRSeffectSizes.Rd b/man/IRSeffectSizes.Rd new file mode 100644 index 00000000..f3b70151 --- /dev/null +++ b/man/IRSeffectSizes.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/irs-interface.R +\name{IRSeffectSizes} +\alias{IRSeffectSizes} +\title{Model IRS effect sizes} +\usage{ +IRSeffectSizes(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$IRS}. +} diff --git a/man/IRSeffectSizes.null.Rd b/man/IRSeffectSizes.null.Rd new file mode 100644 index 00000000..7a1e1564 --- /dev/null +++ b/man/IRSeffectSizes.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/irs-null.R +\name{IRSeffectSizes.null} +\alias{IRSeffectSizes.null} +\title{Model IRS effect sizes} +\usage{ +\method{IRSeffectSizes}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$IRS}. +} diff --git a/man/IRS.Rd b/man/IRSeffects.Rd similarity index 60% rename from man/IRS.Rd rename to man/IRSeffects.Rd index 7d60f2d9..6355eb9b 100644 --- a/man/IRS.Rd +++ b/man/IRSeffects.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/irs-interface.R -\name{IRS} -\alias{IRS} -\title{Modify baseline bionomic values due to IRS} +\name{IRSeffects} +\alias{IRSeffects} +\title{Model the effects of IRS} \usage{ -IRS(t, pars) +IRSeffects(t, pars) } \arguments{ \item{t}{current simulation time} @@ -15,5 +15,5 @@ IRS(t, pars) a \link{list} } \description{ -This method dispatches on the type of \code{pars$IRSpar}. +This method dispatches on the type of \code{pars$IRS}. } diff --git a/man/IRS.null.Rd b/man/IRSeffects.null.Rd similarity index 55% rename from man/IRS.null.Rd rename to man/IRSeffects.null.Rd index e31caba4..a6d67eac 100644 --- a/man/IRS.null.Rd +++ b/man/IRSeffects.null.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/irs-null.R -\name{IRS.null} -\alias{IRS.null} -\title{Modify baseline values due to IRS} +\name{IRSeffects.null} +\alias{IRSeffects.null} +\title{Model the effects of IRS} \usage{ -\method{IRS}{null}(t, pars) +\method{IRSeffects}{null}(t, pars) } \arguments{ \item{t}{current simulation time} @@ -15,5 +15,5 @@ a \link{list} } \description{ -Implements \link{IRS} for the null model of IRS (do nothing) +This method dispatches on the type of \code{pars$IRS}. } diff --git a/man/LBionomics.Rd b/man/LBionomics.Rd new file mode 100644 index 00000000..f5927207 --- /dev/null +++ b/man/LBionomics.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/aquatic-interface.R +\name{LBionomics} +\alias{LBionomics} +\title{Set aquatic bionomic parameter rates relative to baseline} +\usage{ +LBionomics(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$Lpar}. It should +compute the values of parameters as a function of exogenous variables +or reset the values of the bionomic parameters to baseline values. +} diff --git a/man/LBionomics.basic.Rd b/man/LBionomics.basic.Rd new file mode 100644 index 00000000..6b56e157 --- /dev/null +++ b/man/LBionomics.basic.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/aquatic-basic.R +\name{LBionomics.basic} +\alias{LBionomics.basic} +\title{Reset aquatic parameters to baseline} +\usage{ +\method{LBionomics}{basic}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a named \link{list} +} +\description{ +Implements \link{LBionomics} for the RM model +} diff --git a/man/LBionomics.trace.Rd b/man/LBionomics.trace.Rd new file mode 100644 index 00000000..32bcef7d --- /dev/null +++ b/man/LBionomics.trace.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/aquatic-trace.R +\name{LBionomics.trace} +\alias{LBionomics.trace} +\title{Reset aquatic parameters to baseline} +\usage{ +\method{LBionomics}{trace}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a named \link{list} +} +\description{ +Implements \link{LBionomics} for the RM model +} diff --git a/man/LSMeffectSizes.Rd b/man/LSMeffectSizes.Rd new file mode 100644 index 00000000..3c28bf73 --- /dev/null +++ b/man/LSMeffectSizes.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/lsm-interface.R +\name{LSMeffectSizes} +\alias{LSMeffectSizes} +\title{Compute effect sizes of LSM} +\usage{ +LSMeffectSizes(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{the state of the system} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$LSM}. +} diff --git a/man/LSMeffectSizes.null.Rd b/man/LSMeffectSizes.null.Rd new file mode 100644 index 00000000..7c740bef --- /dev/null +++ b/man/LSMeffectSizes.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/lsm-null.R +\name{LSMeffectSizes.null} +\alias{LSMeffectSizes.null} +\title{Modify effects of LSM, the null model} +\usage{ +\method{LSMeffectSizes}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{the state of the system} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$LSM} +} diff --git a/man/LSM.Rd b/man/LSMeffects.Rd similarity index 55% rename from man/LSM.Rd rename to man/LSMeffects.Rd index ec7d413f..0e5a8731 100644 --- a/man/LSM.Rd +++ b/man/LSMeffects.Rd @@ -1,19 +1,21 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/lsm-interface.R -\name{LSM} -\alias{LSM} -\title{Modify values due to LSM} +\name{LSMeffects} +\alias{LSMeffects} +\title{Modify effects of LSM} \usage{ -LSM(t, pars) +LSMeffects(t, y, pars) } \arguments{ \item{t}{current simulation time} +\item{y}{the state of the system} + \item{pars}{a \link{list}} } \value{ a \link{list} } \description{ -This method dispatches on the type of \code{pars$LSMpar}. +This method dispatches on the type of \code{pars$LSM}. } diff --git a/man/LSMeffects.null.Rd b/man/LSMeffects.null.Rd new file mode 100644 index 00000000..60f3e2d3 --- /dev/null +++ b/man/LSMeffects.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/lsm-null.R +\name{LSMeffects.null} +\alias{LSMeffects.null} +\title{Modify effects of LSM, the null model} +\usage{ +\method{LSMeffects}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{the state of the system} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$LSM} +} diff --git a/man/MosquitoBehavior.GeRM.Rd b/man/MBionomics.GeRM.Rd similarity index 66% rename from man/MosquitoBehavior.GeRM.Rd rename to man/MBionomics.GeRM.Rd index 50101156..40ac014f 100644 --- a/man/MosquitoBehavior.GeRM.Rd +++ b/man/MBionomics.GeRM.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-GeRM.R -\name{MosquitoBehavior.GeRM} -\alias{MosquitoBehavior.GeRM} +\name{MBionomics.GeRM} +\alias{MBionomics.GeRM} \title{Reset bloodfeeding and mortality rates to baseline} \usage{ -\method{MosquitoBehavior}{GeRM}(t, y, pars) +\method{MBionomics}{GeRM}(t, y, pars) } \arguments{ \item{t}{current simulation time} @@ -17,5 +17,5 @@ a named \link{list} } \description{ -Implements \link{MosquitoBehavior} for the GeRM model +Implements \link{MBionomics} for the GeRM model } diff --git a/man/MosquitoBehavior.Gtrace.Rd b/man/MBionomics.Gtrace.Rd similarity index 64% rename from man/MosquitoBehavior.Gtrace.Rd rename to man/MBionomics.Gtrace.Rd index 743fcc48..617e65f1 100644 --- a/man/MosquitoBehavior.Gtrace.Rd +++ b/man/MBionomics.Gtrace.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-Gtrace.R -\name{MosquitoBehavior.Gtrace} -\alias{MosquitoBehavior.Gtrace} +\name{MBionomics.Gtrace} +\alias{MBionomics.Gtrace} \title{Compute bloodfeeding and mortality rates} \usage{ -\method{MosquitoBehavior}{Gtrace}(t, y, pars) +\method{MBionomics}{Gtrace}(t, y, pars) } \arguments{ \item{t}{current simulation time} @@ -17,5 +17,5 @@ a named \link{list} } \description{ -Implements \link{MosquitoBehavior} for the Gtrace model. +Implements \link{MBionomics} for the Gtrace model. } diff --git a/man/MosquitoBehavior.RM.Rd b/man/MBionomics.RM.Rd similarity index 67% rename from man/MosquitoBehavior.RM.Rd rename to man/MBionomics.RM.Rd index 2666ecd1..377f2c92 100644 --- a/man/MosquitoBehavior.RM.Rd +++ b/man/MBionomics.RM.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-RM.R -\name{MosquitoBehavior.RM} -\alias{MosquitoBehavior.RM} +\name{MBionomics.RM} +\alias{MBionomics.RM} \title{Reset bloodfeeding and mortality rates to baseline} \usage{ -\method{MosquitoBehavior}{RM}(t, y, pars) +\method{MBionomics}{RM}(t, y, pars) } \arguments{ \item{t}{current simulation time} @@ -17,5 +17,5 @@ a named \link{list} } \description{ -Implements \link{MosquitoBehavior} for the RM model +Implements \link{MBionomics} for the RM model } diff --git a/man/MosquitoBehavior.Rd b/man/MBionomics.Rd similarity index 84% rename from man/MosquitoBehavior.Rd rename to man/MBionomics.Rd index 8a260dd1..1d4aa876 100644 --- a/man/MosquitoBehavior.Rd +++ b/man/MBionomics.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-interface.R -\name{MosquitoBehavior} -\alias{MosquitoBehavior} +\name{MBionomics} +\alias{MBionomics} \title{Set bloodfeeding and mortality rates to baseline} \usage{ -MosquitoBehavior(t, y, pars) +MBionomics(t, y, pars) } \arguments{ \item{t}{current simulation time} diff --git a/man/MosquitoBehavior.Ztrace.Rd b/man/MBionomics.Ztrace.Rd similarity index 64% rename from man/MosquitoBehavior.Ztrace.Rd rename to man/MBionomics.Ztrace.Rd index 8cc8f050..deb5d5f6 100644 --- a/man/MosquitoBehavior.Ztrace.Rd +++ b/man/MBionomics.Ztrace.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-Ztrace.R -\name{MosquitoBehavior.Ztrace} -\alias{MosquitoBehavior.Ztrace} +\name{MBionomics.Ztrace} +\alias{MBionomics.Ztrace} \title{Compute bloodfeeding and mortality rates} \usage{ -\method{MosquitoBehavior}{Ztrace}(t, y, pars) +\method{MBionomics}{Ztrace}(t, y, pars) } \arguments{ \item{t}{current simulation time} @@ -17,5 +17,5 @@ a named \link{list} } \description{ -Implements \link{MosquitoBehavior} for the Ztrace model. +Implements \link{MBionomics} for the Ztrace model. } diff --git a/man/MosquitoBehavior.basicM.Rd b/man/MBionomics.basicM.Rd similarity index 52% rename from man/MosquitoBehavior.basicM.Rd rename to man/MBionomics.basicM.Rd index db5e510d..284925f1 100644 --- a/man/MosquitoBehavior.basicM.Rd +++ b/man/MBionomics.basicM.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-basicM.R -\name{MosquitoBehavior.basicM} -\alias{MosquitoBehavior.basicM} -\title{Reset bloodfeeding and mortality rates to baseline} +\name{MBionomics.basicM} +\alias{MBionomics.basicM} +\title{Set bionomic parameters to baseline} \usage{ -\method{MosquitoBehavior}{basicM}(t, y, pars) +\method{MBionomics}{basicM}(t, y, pars) } \arguments{ \item{t}{current simulation time} @@ -17,5 +17,5 @@ a named \link{list} } \description{ -Implements \link{MosquitoBehavior} for the basicM model +Implements \link{MBionomics} for the basicM model } diff --git a/man/MassMedical.Rd b/man/MassMedical.Rd new file mode 100644 index 00000000..df049263 --- /dev/null +++ b/man/MassMedical.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mass_medical.R +\name{MassMedical} +\alias{MassMedical} +\title{Methods for mass medical interventions} +\usage{ +MassMedical(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$MASS_MED}. +} diff --git a/man/MassMedical.forced.Rd b/man/MassMedical.forced.Rd new file mode 100644 index 00000000..f06aa55c --- /dev/null +++ b/man/MassMedical.forced.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mass_medical.R +\name{MassMedical.forced} +\alias{MassMedical.forced} +\title{Methods for mass medical} +\usage{ +\method{MassMedical}{forced}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{MassMedical} +} diff --git a/man/MassMedical.null.Rd b/man/MassMedical.null.Rd new file mode 100644 index 00000000..d9183ee8 --- /dev/null +++ b/man/MassMedical.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mass_medical.R +\name{MassMedical.null} +\alias{MassMedical.null} +\title{Methods for mass medical} +\usage{ +\method{MassMedical}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{MassMedical} for the null model (do nothing) +} diff --git a/man/OtherBloodHosts.Rd b/man/OtherBloodHosts.Rd new file mode 100644 index 00000000..43044475 --- /dev/null +++ b/man/OtherBloodHosts.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/other_blood_hosts.R +\name{OtherBloodHosts} +\alias{OtherBloodHosts} +\title{Set the values of exogenous variables describing other blood hosts} +\usage{ +OtherBloodHosts(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$OTHER_BLOOD}. +} diff --git a/man/OtherBloodHosts.null.Rd b/man/OtherBloodHosts.null.Rd new file mode 100644 index 00000000..1ef0dada --- /dev/null +++ b/man/OtherBloodHosts.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/other_blood_hosts.R +\name{OtherBloodHosts.null} +\alias{OtherBloodHosts.null} +\title{Set the values of exogenous variables describing other blood hosts} +\usage{ +\method{OtherBloodHosts}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{OtherBloodHosts} for the null model of other_blood_hosts (do nothing) +} diff --git a/man/OviTraps.Rd b/man/OviTraps.Rd new file mode 100644 index 00000000..ff6ee7e7 --- /dev/null +++ b/man/OviTraps.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ovitrap.R +\name{OviTraps} +\alias{OviTraps} +\title{Methods for oviposition traps} +\usage{ +OviTraps(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$OVITRAPS}. +} diff --git a/man/OviTraps.null.Rd b/man/OviTraps.null.Rd new file mode 100644 index 00000000..503ddc9c --- /dev/null +++ b/man/OviTraps.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ovitrap.R +\name{OviTraps.null} +\alias{OviTraps.null} +\title{Methods for oviposition traps} +\usage{ +\method{OviTraps}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{OviTraps} for the null model (do nothing) +} diff --git a/man/OwnBedNet.Rd b/man/OwnBedNet.Rd new file mode 100644 index 00000000..c8affaf8 --- /dev/null +++ b/man/OwnBedNet.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-interface.R +\name{OwnBedNet} +\alias{OwnBedNet} +\title{Model bed net loss, called from Control(VectorControl)} +\usage{ +OwnBedNet(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$ITNown}. +} diff --git a/man/OwnBedNet.null.Rd b/man/OwnBedNet.null.Rd new file mode 100644 index 00000000..c8826b56 --- /dev/null +++ b/man/OwnBedNet.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-null.R +\name{OwnBedNet.null} +\alias{OwnBedNet.null} +\title{Bed net ownership} +\usage{ +\method{OwnBedNet}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +Implements \link{OwnBedNet} for the null model of bed nets (do nothing) +} diff --git a/man/Resources.GeRM.Rd b/man/Resources.GeRM.Rd deleted file mode 100644 index 7d07483f..00000000 --- a/man/Resources.GeRM.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/adult-GeRM.R -\name{Resources.GeRM} -\alias{Resources.GeRM} -\title{Set the availability of resources} -\usage{ -\method{Resources}{GeRM}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{a \link{list}} -} -\value{ -a named \link{list} -} -\description{ -Implements \link{Resources} for the GeRM model -} diff --git a/man/Resources.Rd b/man/Resources.Rd index 057ac68d..b3dd48ec 100644 --- a/man/Resources.Rd +++ b/man/Resources.Rd @@ -9,7 +9,7 @@ Resources(t, y, pars) \arguments{ \item{t}{current simulation time} -\item{y}{state variables} +\item{y}{vector of state variables} \item{pars}{a \link{list}} } @@ -17,5 +17,5 @@ Resources(t, y, pars) none } \description{ -This method dispatches on the type of \code{pars$RApar}. +This method dispatches on the type of \code{pars$RESOURCES}. } diff --git a/man/Resources.dynamic.Rd b/man/Resources.dynamic.Rd deleted file mode 100644 index 594b2604..00000000 --- a/man/Resources.dynamic.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-dynamic.R -\name{Resources.dynamic} -\alias{Resources.dynamic} -\title{Modify resources and resource availability dynamically} -\usage{ -\method{Resources}{dynamic}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -Implements \link{Resources} for the null model of resources (do nothing) -} diff --git a/man/Resources.forced.Rd b/man/Resources.forced.Rd new file mode 100644 index 00000000..b1e6dd85 --- /dev/null +++ b/man/Resources.forced.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-forced.R +\name{Resources.forced} +\alias{Resources.forced} +\title{Methods for resources} +\usage{ +\method{Resources}{forced}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Resources} +} diff --git a/man/Resources.null.Rd b/man/Resources.null.Rd index 5ece9129..8041c073 100644 --- a/man/Resources.null.Rd +++ b/man/Resources.null.Rd @@ -9,7 +9,7 @@ \arguments{ \item{t}{current simulation time} -\item{y}{state variables} +\item{y}{vector of state variables} \item{pars}{a \link{list}} } diff --git a/man/Resources.static.Rd b/man/Resources.static.Rd deleted file mode 100644 index 17874873..00000000 --- a/man/Resources.static.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-static.R -\name{Resources.static} -\alias{Resources.static} -\title{Modify resources and resource availability} -\usage{ -\method{Resources}{static}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -Implements \link{Resources} for static models -} diff --git a/man/Shock.Rd b/man/Shock.Rd new file mode 100644 index 00000000..77fc5603 --- /dev/null +++ b/man/Shock.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/shock.R +\name{Shock} +\alias{Shock} +\title{Set up shocks} +\usage{ +Shock(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$SHOCK}. +} diff --git a/man/Shock.null.Rd b/man/Shock.null.Rd new file mode 100644 index 00000000..b2d61e42 --- /dev/null +++ b/man/Shock.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/shock.R +\name{Shock.null} +\alias{Shock.null} +\title{Set up shocks} +\usage{ +\method{Shock}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Shock} for the null model (do nothing) +} diff --git a/man/SprayHouses.Rd b/man/SprayHouses.Rd new file mode 100644 index 00000000..5c622f28 --- /dev/null +++ b/man/SprayHouses.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/irs-interface.R +\name{SprayHouses} +\alias{SprayHouses} +\title{Do mass house spraying (IRS)} +\usage{ +SprayHouses(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$IRS}. +} diff --git a/man/SprayHouses.null.Rd b/man/SprayHouses.null.Rd new file mode 100644 index 00000000..09976eec --- /dev/null +++ b/man/SprayHouses.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/irs-null.R +\name{SprayHouses.null} +\alias{SprayHouses.null} +\title{Do mass house spraying (IRS)} +\usage{ +\method{SprayHouses}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$IRS}. +} diff --git a/man/F_sugar.forced.Rd b/man/Sugar.Rd similarity index 52% rename from man/F_sugar.forced.Rd rename to man/Sugar.Rd index e84cef5c..5594e04d 100644 --- a/man/F_sugar.forced.Rd +++ b/man/Sugar.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/sugar.R -\name{F_sugar.forced} -\alias{F_sugar.forced} -\title{A basic forcing model for sugar} +\name{Sugar} +\alias{Sugar} +\title{Set the values of exogenous variables describing sugar} \usage{ -\method{F_sugar}{forced}(t, pars) +Sugar(t, pars) } \arguments{ \item{t}{current simulation time} @@ -12,8 +12,8 @@ \item{pars}{a \link{list}} } \value{ -a \link{list} +\link{list} } \description{ -Implements \link{F_sugar} for a forced model +This method dispatches on the type of \code{pars$SUGAR}. } diff --git a/man/Sugar.null.Rd b/man/Sugar.null.Rd new file mode 100644 index 00000000..0f63dba6 --- /dev/null +++ b/man/Sugar.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar.R +\name{Sugar.null} +\alias{Sugar.null} +\title{Set the values of exogenous variables describing sugar} +\usage{ +\method{Sugar}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{Sugar} for the null model of sugar (do nothing) +} diff --git a/man/SugarAvailability.Rd b/man/SugarAvailability.Rd new file mode 100644 index 00000000..51a6a397 --- /dev/null +++ b/man/SugarAvailability.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-interface.R +\name{SugarAvailability} +\alias{SugarAvailability} +\title{Update the availability of sugar} +\usage{ +SugarAvailability(pars) +} +\arguments{ +\item{pars}{an \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$RESOURCES}. +} diff --git a/man/SugarAvailability.forced.Rd b/man/SugarAvailability.forced.Rd new file mode 100644 index 00000000..a1b94e35 --- /dev/null +++ b/man/SugarAvailability.forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-forced.R +\name{SugarAvailability.forced} +\alias{SugarAvailability.forced} +\title{Compute total availability of sugar} +\usage{ +\method{SugarAvailability}{forced}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nPatches} +} +\description{ +Computes the availability of sugar +} diff --git a/man/SugarAvailability.null.Rd b/man/SugarAvailability.null.Rd new file mode 100644 index 00000000..012840db --- /dev/null +++ b/man/SugarAvailability.null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-null.R +\name{SugarAvailability.null} +\alias{SugarAvailability.null} +\title{Compute total availability of sugar} +\usage{ +\method{SugarAvailability}{null}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +a \link{numeric} vector of length \code{nPatches} +} +\description{ +Computes the availability of sugar for the null model (do nothing) +} diff --git a/man/SugarBaitEffectSizes.Rd b/man/SugarBaitEffectSizes.Rd new file mode 100644 index 00000000..3d04e24b --- /dev/null +++ b/man/SugarBaitEffectSizes.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar_baits-interface.R +\name{SugarBaitEffectSizes} +\alias{SugarBaitEffectSizes} +\title{Methods for the effect sizes of the sugar baits} +\usage{ +SugarBaitEffectSizes(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$SUGAR_BAITS}. +} diff --git a/man/SugarBaitEffectSizes.null.Rd b/man/SugarBaitEffectSizes.null.Rd new file mode 100644 index 00000000..0e04b4ac --- /dev/null +++ b/man/SugarBaitEffectSizes.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar_baits-null.R +\name{SugarBaitEffectSizes.null} +\alias{SugarBaitEffectSizes.null} +\title{Methods for the effect sizes of the sugar baits} +\usage{ +\method{SugarBaitEffectSizes}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$SUGAR_BAITS}. +} diff --git a/man/SugarBaitEffects.Rd b/man/SugarBaitEffects.Rd new file mode 100644 index 00000000..57fae517 --- /dev/null +++ b/man/SugarBaitEffects.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar_baits-interface.R +\name{SugarBaitEffects} +\alias{SugarBaitEffects} +\title{Methods for the durability and effects of the sugar baits} +\usage{ +SugarBaitEffects(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$SUGAR_BAITS}. +} diff --git a/man/SugarBaitEffects.null.Rd b/man/SugarBaitEffects.null.Rd new file mode 100644 index 00000000..cc64a014 --- /dev/null +++ b/man/SugarBaitEffects.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar_baits-null.R +\name{SugarBaitEffects.null} +\alias{SugarBaitEffects.null} +\title{Methods for the effects of the sugar baits} +\usage{ +\method{SugarBaitEffects}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{SugarBaitEffects} for the null model (do nothing) +} diff --git a/man/SugarBaits.Rd b/man/SugarBaits.Rd new file mode 100644 index 00000000..01d2a13e --- /dev/null +++ b/man/SugarBaits.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar_baits-interface.R +\name{SugarBaits} +\alias{SugarBaits} +\title{Methods for distributing sugar baits} +\usage{ +SugarBaits(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +This method dispatches on the type of \code{pars$SUGAR_BAITS}. +} diff --git a/man/SugarBaits.null.Rd b/man/SugarBaits.null.Rd new file mode 100644 index 00000000..47b5bc58 --- /dev/null +++ b/man/SugarBaits.null.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar_baits-null.R +\name{SugarBaits.null} +\alias{SugarBaits.null} +\title{Methods for sugar baits} +\usage{ +\method{SugarBaits}{null}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements \link{SugarBaits} for the null model (do nothing) +} diff --git a/man/TreatHabitats.Rd b/man/TreatHabitats.Rd new file mode 100644 index 00000000..0a44f1a2 --- /dev/null +++ b/man/TreatHabitats.Rd @@ -0,0 +1,20 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/lsm-interface.R +\name{TreatHabitats} +\alias{TreatHabitats} +\title{Modify values due to treat habitats as part of LSM, +called by Control->VectorControl} +\usage{ +TreatHabitats(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$LSM}. +} diff --git a/man/LSM.null.Rd b/man/TreatHabitats.null.Rd similarity index 54% rename from man/LSM.null.Rd rename to man/TreatHabitats.null.Rd index 5c1ac0bb..b85b1ae2 100644 --- a/man/LSM.null.Rd +++ b/man/TreatHabitats.null.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/lsm-null.R -\name{LSM.null} -\alias{LSM.null} -\title{Modify baseline values due to LSM} +\name{TreatHabitats.null} +\alias{TreatHabitats.null} +\title{Set up the null model for LSM} \usage{ -\method{LSM}{null}(t, pars) +\method{TreatHabitats}{null}(t, pars) } \arguments{ \item{t}{current simulation time} @@ -15,5 +15,5 @@ a \link{list} } \description{ -Implements \link{LSM} for the null model of LSM (do nothing) +This method dispatches on the type of \code{pars$LSM} } diff --git a/man/UseBedNet.Rd b/man/UseBedNet.Rd new file mode 100644 index 00000000..54b0ae0c --- /dev/null +++ b/man/UseBedNet.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-interface.R +\name{UseBedNet} +\alias{UseBedNet} +\title{Model bed net usage, called from Behavior} +\usage{ +UseBedNet(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$ITNuse}. +} diff --git a/man/UseBedNet.null.Rd b/man/UseBedNet.null.Rd new file mode 100644 index 00000000..77b25722 --- /dev/null +++ b/man/UseBedNet.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/bednet-null.R +\name{UseBedNet.null} +\alias{UseBedNet.null} +\title{Bed net ownership} +\usage{ +\method{UseBedNet}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{vector of state variables} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +Implements \link{UseBedNet} for the null model of bed nets (do nothing) +} diff --git a/man/VectorControl.Rd b/man/VectorControl.Rd index af74b7c3..1885023c 100644 --- a/man/VectorControl.Rd +++ b/man/VectorControl.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/vectorcontrol-interface.R +% Please edit documentation in R/vector_control-interface.R \name{VectorControl} \alias{VectorControl} -\title{Modify baseline values due to vector control} +\title{Distribute vector control} \usage{ VectorControl(t, y, pars) } @@ -17,5 +17,5 @@ VectorControl(t, y, pars) a \link{list} } \description{ -This method dispatches on the type of \code{pars$VCpar}. +This method dispatches on the type of \code{pars$VECTOR_CONTROL}. } diff --git a/man/VectorControl.control.Rd b/man/VectorControl.control.Rd index c676e2ad..ed230500 100644 --- a/man/VectorControl.control.Rd +++ b/man/VectorControl.control.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/vectorcontrol-control.R +% Please edit documentation in R/vector_control-control.R \name{VectorControl.control} \alias{VectorControl.control} -\title{Modify baseline values due to vector control} +\title{Distribute vector control, the null model} \usage{ \method{VectorControl}{control}(t, y, pars) } diff --git a/man/VectorControl.null.Rd b/man/VectorControl.null.Rd index 5e7f817f..34d41e45 100644 --- a/man/VectorControl.null.Rd +++ b/man/VectorControl.null.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/vectorcontrol-null.R +% Please edit documentation in R/vector_control-null.R \name{VectorControl.null} \alias{VectorControl.null} -\title{Modify baseline values due to vector control} +\title{Distribute vector control} \usage{ \method{VectorControl}{null}(t, y, pars) } diff --git a/man/VectorControlEffectSizes.Rd b/man/VectorControlEffectSizes.Rd new file mode 100644 index 00000000..4c783de0 --- /dev/null +++ b/man/VectorControlEffectSizes.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vector_control-interface.R +\name{VectorControlEffectSizes} +\alias{VectorControlEffectSizes} +\title{Vector control effect sizes} +\usage{ +VectorControlEffectSizes(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$VECTOR_CONTROL}. +} diff --git a/man/VectorControlEffectSizes.control.Rd b/man/VectorControlEffectSizes.control.Rd new file mode 100644 index 00000000..373d7fdf --- /dev/null +++ b/man/VectorControlEffectSizes.control.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vector_control-control.R +\name{VectorControlEffectSizes.control} +\alias{VectorControlEffectSizes.control} +\title{Distribute vector control, the null model} +\usage{ +\method{VectorControlEffectSizes}{control}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a named \link{list} +} +\description{ +Implements \link{VectorControlEffectSizes} for the control model of vector control (do nothing) +} diff --git a/man/VectorControlEffectSizes.null.Rd b/man/VectorControlEffectSizes.null.Rd new file mode 100644 index 00000000..6fcbd052 --- /dev/null +++ b/man/VectorControlEffectSizes.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vector_control-null.R +\name{VectorControlEffectSizes.null} +\alias{VectorControlEffectSizes.null} +\title{Vector control effect sizes} +\usage{ +\method{VectorControlEffectSizes}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a named \link{list} +} +\description{ +Implements \link{VectorControlEffectSizes} for the null model of vector control (do nothing) +} diff --git a/man/VectorControlEffects.Rd b/man/VectorControlEffects.Rd new file mode 100644 index 00000000..e0860542 --- /dev/null +++ b/man/VectorControlEffects.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vector_control-interface.R +\name{VectorControlEffects} +\alias{VectorControlEffects} +\title{Vector control: durability & effects} +\usage{ +VectorControlEffects(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a \link{list} +} +\description{ +This method dispatches on the type of \code{pars$VECTOR_CONTROL}. +} diff --git a/man/VectorControlEffects.control.Rd b/man/VectorControlEffects.control.Rd new file mode 100644 index 00000000..1c1150bf --- /dev/null +++ b/man/VectorControlEffects.control.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vector_control-control.R +\name{VectorControlEffects.control} +\alias{VectorControlEffects.control} +\title{Vector control durability and effects} +\usage{ +\method{VectorControlEffects}{control}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a named \link{list} +} +\description{ +Implements \link{VectorControlEffects} for the control model of vector control (do nothing) +} diff --git a/man/VectorControlEffects.null.Rd b/man/VectorControlEffects.null.Rd new file mode 100644 index 00000000..9a45d75d --- /dev/null +++ b/man/VectorControlEffects.null.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/vector_control-null.R +\name{VectorControlEffects.null} +\alias{VectorControlEffects.null} +\title{Vector control: durability & effects} +\usage{ +\method{VectorControlEffects}{null}(t, y, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{y}{state vector} + +\item{pars}{a \link{list}} +} +\value{ +a named \link{list} +} +\description{ +Implements \link{VectorControlEffects} for the null model of vector control (do nothing) +} diff --git a/man/Visitors.Rd b/man/Visitors.Rd index 4525b932..14841ede 100644 --- a/man/Visitors.Rd +++ b/man/Visitors.Rd @@ -12,8 +12,8 @@ Visitors(t, pars) \item{pars}{a \link{list}} } \value{ -pars a \link{list} +a \link{list} } \description{ -This method dispatches on the type of \code{pars$Ipar}. +This method dispatches on the type of \code{pars$VISITORS}. } diff --git a/man/Visitors.basic.Rd b/man/Visitors.basic.Rd index 37a0c7cc..6f406b2b 100644 --- a/man/Visitors.basic.Rd +++ b/man/Visitors.basic.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/visitors-basic.R +% Please edit documentation in R/visitors.R \name{Visitors.basic} \alias{Visitors.basic} \title{Visitors, the basic model} @@ -12,7 +12,7 @@ \item{pars}{a \link{list}} } \value{ -a named \link{list} +a \link{list} } \description{ Implements \link{Visitors} for the basic model for Visitors diff --git a/man/Visitors.null.Rd b/man/Visitors.null.Rd index bd03e051..bc64b8ca 100644 --- a/man/Visitors.null.Rd +++ b/man/Visitors.null.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/visitors-null.R +% Please edit documentation in R/visitors.R \name{Visitors.null} \alias{Visitors.null} \title{Visitors, a null model} @@ -12,7 +12,7 @@ \item{pars}{a \link{list}} } \value{ -a named \link{list} +a \link{list} } \description{ Implements \link{Visitors} for the null model (do nothing) diff --git a/man/Weather.Rd b/man/Weather.Rd index 240ba390..1095660e 100644 --- a/man/Weather.Rd +++ b/man/Weather.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-interface.R +% Please edit documentation in R/weather.R \name{Weather} \alias{Weather} -\title{Set the values of exogenous variables describing weather} +\title{Methods for exogenous variables describing weather} \usage{ Weather(t, pars) } @@ -12,8 +12,8 @@ Weather(t, pars) \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ -This method dispatches on the type of \code{pars$WETpar}. +This method dispatches on the type of \code{pars$WEATHER}. } diff --git a/man/Weather.forced.Rd b/man/Weather.forced.Rd new file mode 100644 index 00000000..487113d3 --- /dev/null +++ b/man/Weather.forced.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/weather.R +\name{Weather.forced} +\alias{Weather.forced} +\title{Methods for exogenous variables describing weather} +\usage{ +\method{Weather}{forced}(t, pars) +} +\arguments{ +\item{t}{current simulation time} + +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Implements exogenous forcing by \link{Weather} +} diff --git a/man/Weather.null.Rd b/man/Weather.null.Rd index 35906f58..8e9be1ce 100644 --- a/man/Weather.null.Rd +++ b/man/Weather.null.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-null.R +% Please edit documentation in R/weather.R \name{Weather.null} \alias{Weather.null} -\title{Modify exogenous variables describing weather} +\title{Methods for exogenous variables describing weather} \usage{ \method{Weather}{null}(t, pars) } @@ -12,7 +12,7 @@ \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ Implements \link{Weather} for the null model (no variables) diff --git a/man/check_abiotic.Rd b/man/check_abiotic.Rd new file mode 100644 index 00000000..d552c175 --- /dev/null +++ b/man/check_abiotic.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/abiotic.R +\name{check_abiotic} +\alias{check_abiotic} +\title{Check abiotic} +\usage{ +check_abiotic(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Check abiotic +} diff --git a/man/check_abiotic.forced.Rd b/man/check_abiotic.forced.Rd new file mode 100644 index 00000000..bb2c8e18 --- /dev/null +++ b/man/check_abiotic.forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/abiotic.R +\name{check_abiotic.forced} +\alias{check_abiotic.forced} +\title{Check abiotic} +\usage{ +\method{check_abiotic}{forced}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Check abiotic +} diff --git a/man/check_abiotic.null.Rd b/man/check_abiotic.null.Rd new file mode 100644 index 00000000..04e1feec --- /dev/null +++ b/man/check_abiotic.null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/abiotic.R +\name{check_abiotic.null} +\alias{check_abiotic.null} +\title{Check abiotic} +\usage{ +\method{check_abiotic}{null}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Check abiotic +} diff --git a/man/check_civil.Rd b/man/check_civil.Rd new file mode 100644 index 00000000..c7f69b9e --- /dev/null +++ b/man/check_civil.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{check_civil} +\alias{check_civil} +\title{Check civil} +\usage{ +check_civil(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Check civil +} diff --git a/man/check_civil.forced.Rd b/man/check_civil.forced.Rd new file mode 100644 index 00000000..4f0a7cf2 --- /dev/null +++ b/man/check_civil.forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{check_civil.forced} +\alias{check_civil.forced} +\title{Check civil} +\usage{ +\method{check_civil}{forced}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Check civil +} diff --git a/man/check_civil.null.Rd b/man/check_civil.null.Rd new file mode 100644 index 00000000..50ebff41 --- /dev/null +++ b/man/check_civil.null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{check_civil.null} +\alias{check_civil.null} +\title{Check civil} +\usage{ +\method{check_civil}{null}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Check civil +} diff --git a/man/compute_B.Rd b/man/compute_B.Rd deleted file mode 100644 index ab40431f..00000000 --- a/man/compute_B.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-functions.R -\name{compute_B} -\alias{compute_B} -\title{Compute the total availability of blood hosts} -\usage{ -compute_B(pars) -} -\arguments{ -\item{pars}{a \link{list}} -} -\value{ -a \link{numeric} vector of length \code{nPatches} -} -\description{ -Compute the availability for the pathogen's hosts for blood feeding -} diff --git a/man/compute_local_frac.Rd b/man/compute_local_frac.Rd index df15f291..55406689 100644 --- a/man/compute_local_frac.Rd +++ b/man/compute_local_frac.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-functions.R +% Please edit documentation in R/resources-forced.R \name{compute_local_frac} \alias{compute_local_frac} -\title{Compute the fraction of bites occurring on local hosts} +\title{Compute the local fraction} \usage{ compute_local_frac(pars) } @@ -10,8 +10,8 @@ compute_local_frac(pars) \item{pars}{a \link{list}} } \value{ -a \link{numeric} vector of length \code{nPatches} +pars a \link{list} } \description{ -Computes the local_frac +Compute the availability for the pathogen's hosts for blood feeding } diff --git a/man/dXdt.Rd b/man/dXdt.Rd index ccd9beef..d2029e8e 100644 --- a/man/dXdt.Rd +++ b/man/dXdt.Rd @@ -4,7 +4,7 @@ \alias{dXdt} \title{Derivatives for human population} \usage{ -dXdt(t, y, pars, EIR) +dXdt(t, y, pars, FoI) } \arguments{ \item{t}{current simulation time} @@ -13,7 +13,7 @@ dXdt(t, y, pars, EIR) \item{pars}{a \link{list}} -\item{EIR}{vector giving the per-capita entomological inoculation rate for each strata} +\item{FoI}{vector giving the per-capita force of infection for each strata} } \value{ a \link{numeric} vector diff --git a/man/dXdt.SIPdX.Rd b/man/dXdt.SIPdX.Rd index 61f9ae50..400b6e82 100644 --- a/man/dXdt.SIPdX.Rd +++ b/man/dXdt.SIPdX.Rd @@ -4,7 +4,7 @@ \alias{dXdt.SIPdX} \title{Derivatives for human population} \usage{ -\method{dXdt}{SIPdX}(t, y, pars, EIR) +\method{dXdt}{SIPdX}(t, y, pars, FoI) } \arguments{ \item{t}{current simulation time} @@ -13,7 +13,7 @@ \item{pars}{a \link{list}} -\item{EIR}{vector giving the per-capita entomological inoculation rate for each strata} +\item{FoI}{vector giving the per-capita force of infection for each strata} } \value{ a \link{numeric} vector diff --git a/man/dXdt.SIPdXdH.Rd b/man/dXdt.SIPdXdH.Rd index a8f6e835..fa52fa38 100644 --- a/man/dXdt.SIPdXdH.Rd +++ b/man/dXdt.SIPdXdH.Rd @@ -4,7 +4,7 @@ \alias{dXdt.SIPdXdH} \title{Derivatives for human population} \usage{ -\method{dXdt}{SIPdXdH}(t, y, pars, EIR) +\method{dXdt}{SIPdXdH}(t, y, pars, FoI) } \arguments{ \item{t}{current simulation time} @@ -13,7 +13,7 @@ \item{pars}{a \link{list}} -\item{EIR}{vector giving the per-capita entomological inoculation rate for each strata} +\item{FoI}{vector giving the per-capita force of infection for each strata} } \value{ a \link{numeric} vector diff --git a/man/dXdt.SISdX.Rd b/man/dXdt.SISdX.Rd index 9688835b..1c8b3591 100644 --- a/man/dXdt.SISdX.Rd +++ b/man/dXdt.SISdX.Rd @@ -4,7 +4,7 @@ \alias{dXdt.SISdX} \title{Derivatives for human population} \usage{ -\method{dXdt}{SISdX}(t, y, pars, EIR) +\method{dXdt}{SISdX}(t, y, pars, FoI) } \arguments{ \item{t}{current simulation time} @@ -13,7 +13,7 @@ \item{pars}{a \link{list}} -\item{EIR}{vector giving the per-capita entomological inoculation rate for each strata} +\item{FoI}{vector giving the per-capita force of infection for each strata} } \value{ a \link{numeric} vector diff --git a/man/dXdt.SISdXdH.Rd b/man/dXdt.SISdXdH.Rd index 2a8b4350..7016cbc4 100644 --- a/man/dXdt.SISdXdH.Rd +++ b/man/dXdt.SISdXdH.Rd @@ -4,7 +4,7 @@ \alias{dXdt.SISdXdH} \title{Derivatives for human population} \usage{ -\method{dXdt}{SISdXdH}(t, y, pars, EIR) +\method{dXdt}{SISdXdH}(t, y, pars, FoI) } \arguments{ \item{t}{current simulation time} @@ -13,7 +13,7 @@ \item{pars}{a \link{list}} -\item{EIR}{vector giving the per-capita entomological inoculation rate for each strata} +\item{FoI}{vector giving the per-capita force of infection for each strata} } \value{ a \link{numeric} vector diff --git a/man/dXdt.hMoI.Rd b/man/dXdt.hMoI.Rd index 030d3ddf..d542d245 100644 --- a/man/dXdt.hMoI.Rd +++ b/man/dXdt.hMoI.Rd @@ -4,7 +4,7 @@ \alias{dXdt.hMoI} \title{Derivatives for human population} \usage{ -\method{dXdt}{hMoI}(t, y, pars, EIR) +\method{dXdt}{hMoI}(t, y, pars, FoI) } \arguments{ \item{t}{current simulation time} @@ -13,7 +13,7 @@ \item{pars}{a \link{list}} -\item{EIR}{vector giving the per-capita entomological inoculation rate for each strata} +\item{FoI}{vector giving the per-capita force of infection for each strata} } \value{ a \link{numeric} vector diff --git a/man/dXdt.trace.Rd b/man/dXdt.trace.Rd index 75aed296..09b905ac 100644 --- a/man/dXdt.trace.Rd +++ b/man/dXdt.trace.Rd @@ -4,7 +4,7 @@ \alias{dXdt.trace} \title{Derivatives for human population} \usage{ -\method{dXdt}{trace}(t, y, pars, EIR) +\method{dXdt}{trace}(t, y, pars, FoI) } \arguments{ \item{t}{current simulation time} @@ -13,7 +13,7 @@ \item{pars}{a \link{list}} -\item{EIR}{vector giving the per-capita entomological inoculation rate for each strata} +\item{FoI}{vector giving the per-capita force of infection for each strata} } \value{ a \link{numeric} vector diff --git a/man/setup_abiotic_forced.Rd b/man/setup_abiotic_forced.Rd new file mode 100644 index 00000000..435f0e67 --- /dev/null +++ b/man/setup_abiotic_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/abiotic.R +\name{setup_abiotic_forced} +\alias{setup_abiotic_forced} +\title{Make parameters for the null model of abiotic forcing (do nothing)} +\usage{ +setup_abiotic_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Make parameters for the null model of abiotic forcing (do nothing) +} diff --git a/man/setup_exogenous_null.Rd b/man/setup_abiotic_null.Rd similarity index 63% rename from man/setup_exogenous_null.Rd rename to man/setup_abiotic_null.Rd index 3e8e0feb..06bfdb8f 100644 --- a/man/setup_exogenous_null.Rd +++ b/man/setup_abiotic_null.Rd @@ -1,16 +1,16 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-null.R -\name{setup_exogenous_null} -\alias{setup_exogenous_null} +% Please edit documentation in R/abiotic.R +\name{setup_abiotic_null} +\alias{setup_abiotic_null} \title{Set up the null model for exogenous forcing (do nothing)} \usage{ -setup_exogenous_null(pars) +setup_abiotic_null(pars) } \arguments{ \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ Set up the null model for exogenous forcing (do nothing) diff --git a/man/setup_area_spray_null.Rd b/man/setup_area_spray_null.Rd new file mode 100644 index 00000000..352a217c --- /dev/null +++ b/man/setup_area_spray_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/area_spray.R +\name{setup_area_spray_null} +\alias{setup_area_spray_null} +\title{Set up the null model for area spraying (do nothing)} +\usage{ +setup_area_spray_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for area spraying (do nothing) +} diff --git a/man/setup_atsb_null.Rd b/man/setup_atsb_null.Rd deleted file mode 100644 index 2c9c622d..00000000 --- a/man/setup_atsb_null.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/atsb-null.R -\name{setup_atsb_null} -\alias{setup_atsb_null} -\title{Make parameters for the null model of ATSB (do nothing)} -\usage{ -setup_atsb_null(pars) -} -\arguments{ -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Make parameters for the null model of ATSB (do nothing) -} diff --git a/man/setup_behavior.Rd b/man/setup_behavior.Rd new file mode 100644 index 00000000..597ddc43 --- /dev/null +++ b/man/setup_behavior.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/behavior.R +\name{setup_behavior} +\alias{setup_behavior} +\title{Setup behavior} +\usage{ +setup_behavior(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Setup behavior +} diff --git a/man/setup_behavior.forced.Rd b/man/setup_behavior.forced.Rd new file mode 100644 index 00000000..ceca1b1e --- /dev/null +++ b/man/setup_behavior.forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/behavior.R +\name{setup_behavior.forced} +\alias{setup_behavior.forced} +\title{Setup behavior} +\usage{ +\method{setup_behavior}{forced}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Setup behavior +} diff --git a/man/setup_behavior.null.Rd b/man/setup_behavior.null.Rd new file mode 100644 index 00000000..2351116e --- /dev/null +++ b/man/setup_behavior.null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/behavior.R +\name{setup_behavior.null} +\alias{setup_behavior.null} +\title{Setup behavior} +\usage{ +\method{setup_behavior}{null}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Setup behavior +} diff --git a/man/setup_behavior_forced.Rd b/man/setup_behavior_forced.Rd new file mode 100644 index 00000000..a06272bd --- /dev/null +++ b/man/setup_behavior_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/behavior.R +\name{setup_behavior_forced} +\alias{setup_behavior_forced} +\title{Make parameters for the forced model for resource availability (do nothing)} +\usage{ +setup_behavior_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Make parameters for the forced model for resource availability (do nothing) +} diff --git a/man/setup_humanbehavior_null.Rd b/man/setup_behavior_null.Rd similarity index 64% rename from man/setup_humanbehavior_null.Rd rename to man/setup_behavior_null.Rd index 73d85dff..71379e66 100644 --- a/man/setup_humanbehavior_null.Rd +++ b/man/setup_behavior_null.Rd @@ -1,16 +1,16 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/humanbehavior.R -\name{setup_humanbehavior_null} -\alias{setup_humanbehavior_null} +% Please edit documentation in R/behavior.R +\name{setup_behavior_null} +\alias{setup_behavior_null} \title{Make parameters for the null model for resource availability (do nothing)} \usage{ -setup_humanbehavior_null(pars) +setup_behavior_null(pars) } \arguments{ \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ Make parameters for the null model for resource availability (do nothing) diff --git a/man/setup_care_seeking_null.Rd b/man/setup_care_seeking_null.Rd new file mode 100644 index 00000000..f04ca511 --- /dev/null +++ b/man/setup_care_seeking_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/care_seeking.R +\name{setup_care_seeking_null} +\alias{setup_care_seeking_null} +\title{Make parameters for the null model for care seeking (do nothing)} +\usage{ +setup_care_seeking_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Make parameters for the null model for care seeking (do nothing) +} diff --git a/man/setup_civil_forced.Rd b/man/setup_civil_forced.Rd new file mode 100644 index 00000000..2c1bd292 --- /dev/null +++ b/man/setup_civil_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{setup_civil_forced} +\alias{setup_civil_forced} +\title{Make parameters for the null model of civil forcing (do nothing)} +\usage{ +setup_civil_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Make parameters for the null model of civil forcing (do nothing) +} diff --git a/man/setup_civil_null.Rd b/man/setup_civil_null.Rd new file mode 100644 index 00000000..0f277f91 --- /dev/null +++ b/man/setup_civil_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/civil.R +\name{setup_civil_null} +\alias{setup_civil_null} +\title{Set up the null model for exogenous forcing (do nothing)} +\usage{ +setup_civil_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for exogenous forcing (do nothing) +} diff --git a/man/setup_clinic_forced.Rd b/man/setup_clinic_forced.Rd new file mode 100644 index 00000000..3675364c --- /dev/null +++ b/man/setup_clinic_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/clinic.R +\name{setup_clinic_forced} +\alias{setup_clinic_forced} +\title{Set up a model for clinic} +\usage{ +setup_clinic_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up a model for clinic +} diff --git a/man/setup_clinic_null.Rd b/man/setup_clinic_null.Rd new file mode 100644 index 00000000..bc4796e6 --- /dev/null +++ b/man/setup_clinic_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/clinic.R +\name{setup_clinic_null} +\alias{setup_clinic_null} +\title{Set up the null model for clinical distribution (do nothing)} +\usage{ +setup_clinic_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for clinical distribution (do nothing) +} diff --git a/man/setup_control.Rd b/man/setup_control.Rd new file mode 100644 index 00000000..10919490 --- /dev/null +++ b/man/setup_control.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{setup_control} +\alias{setup_control} +\title{Setup CONTROL with forcing} +\usage{ +setup_control(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Setup CONTROL with forcing +} diff --git a/man/setup_control.forced.Rd b/man/setup_control.forced.Rd new file mode 100644 index 00000000..9ebc1e17 --- /dev/null +++ b/man/setup_control.forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{setup_control.forced} +\alias{setup_control.forced} +\title{Setup control} +\usage{ +\method{setup_control}{forced}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Setup control +} diff --git a/man/setup_control.null.Rd b/man/setup_control.null.Rd new file mode 100644 index 00000000..f427f173 --- /dev/null +++ b/man/setup_control.null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{setup_control.null} +\alias{setup_control.null} +\title{Setup control} +\usage{ +\method{setup_control}{null}(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Setup control +} diff --git a/man/setup_control_forced.Rd b/man/setup_control_forced.Rd new file mode 100644 index 00000000..537ea018 --- /dev/null +++ b/man/setup_control_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{setup_control_forced} +\alias{setup_control_forced} +\title{Set up a model with some control} +\usage{ +setup_control_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up a model with some control +} diff --git a/man/setup_control_null.Rd b/man/setup_control_null.Rd new file mode 100644 index 00000000..48236259 --- /dev/null +++ b/man/setup_control_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/control.R +\name{setup_control_null} +\alias{setup_control_null} +\title{Set up the null model for control forcing (do nothing)} +\usage{ +setup_control_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for control forcing (do nothing) +} diff --git a/man/setup_development_null.Rd b/man/setup_development_null.Rd new file mode 100644 index 00000000..7bb08c5e --- /dev/null +++ b/man/setup_development_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/development.R +\name{setup_development_null} +\alias{setup_development_null} +\title{Set up the null model for developments (do nothing)} +\usage{ +setup_development_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for developments (do nothing) +} diff --git a/man/setup_eip_static.Rd b/man/setup_eip_static.Rd new file mode 100644 index 00000000..bb03a6f0 --- /dev/null +++ b/man/setup_eip_static.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/eip.R +\name{setup_eip_static} +\alias{setup_eip_static} +\title{Set up the static model for control forcing (do nothing)} +\usage{ +setup_eip_static(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the static model for control forcing (do nothing) +} diff --git a/man/setup_exogenous_forced.Rd b/man/setup_exogenous_forced.Rd deleted file mode 100644 index 43d789ee..00000000 --- a/man/setup_exogenous_forced.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-forced.R -\name{setup_exogenous_forced} -\alias{setup_exogenous_forced} -\title{Make parameters for the null model of exogenous forcing (do nothing)} -\usage{ -setup_exogenous_forced(pars) -} -\arguments{ -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -Make parameters for the null model of exogenous forcing (do nothing) -} diff --git a/man/setup_forcing_MYZ_GeRM_basic.Rd b/man/setup_forcing_MYZ_GeRM_basic.Rd deleted file mode 100644 index 72349c85..00000000 --- a/man/setup_forcing_MYZ_GeRM_basic.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/adult-GeRM.R -\name{setup_forcing_MYZ_GeRM_basic} -\alias{setup_forcing_MYZ_GeRM_basic} -\title{Set up a static exogenous forcing for the GeRM ODE adult mosquito model} -\usage{ -setup_forcing_MYZ_GeRM_basic(pars, other, sugar, zeta) -} -\arguments{ -\item{pars}{a \link{list}} - -\item{other}{is the availability of other blood hosts} - -\item{sugar}{is sugar availability} - -\item{zeta}{is a shape parameter} -} -\value{ -none -} -\description{ -Set up a static exogenous forcing for the GeRM ODE adult mosquito model -} diff --git a/man/setup_habitat_dynamics_null.Rd b/man/setup_habitat_dynamics_null.Rd new file mode 100644 index 00000000..1a1c84b8 --- /dev/null +++ b/man/setup_habitat_dynamics_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/habitat_dynamics.R +\name{setup_habitat_dynamics_null} +\alias{setup_habitat_dynamics_null} +\title{Make parameters for the null model for habitat dynamics (do nothing)} +\usage{ +setup_habitat_dynamics_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Make parameters for the null model for habitat dynamics (do nothing) +} diff --git a/man/setup_habitats_forced.Rd b/man/setup_habitats_forced.Rd deleted file mode 100644 index 7e54701f..00000000 --- a/man/setup_habitats_forced.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/habitat_dynamics.R -\name{setup_habitats_forced} -\alias{setup_habitats_forced} -\title{Set up forcing for the availability of habitats} -\usage{ -setup_habitats_forced( - pars, - habitats_Opts = list(), - habitats_scale = 0, - habitats_t = NULL -) -} -\arguments{ -\item{pars}{a \link{list}} - -\item{habitats_Opts}{a list, overwrites default values} - -\item{habitats_scale}{a non-negative numeric value to scale the mean availability of habitats} - -\item{habitats_t}{a function that specifies the temporal pattern for the availability of habitats} -} -\value{ -none -} -\description{ -Set up forcing for the availability of habitats -} diff --git a/man/setup_habitats_null.Rd b/man/setup_habitats_null.Rd deleted file mode 100644 index d32dd947..00000000 --- a/man/setup_habitats_null.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/habitat_dynamics.R -\name{setup_habitats_null} -\alias{setup_habitats_null} -\title{Set up the null model for habitat dynamics} -\usage{ -setup_habitats_null(pars) -} -\arguments{ -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -Set up the null model for habitat dynamics -} diff --git a/man/setup_habitats_static.Rd b/man/setup_habitats_static.Rd deleted file mode 100644 index 27dd0827..00000000 --- a/man/setup_habitats_static.Rd +++ /dev/null @@ -1,17 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/habitat_dynamics.R -\name{setup_habitats_static} -\alias{setup_habitats_static} -\title{Set up the static model for habitat dynamics} -\usage{ -setup_habitats_static(pars) -} -\arguments{ -\item{pars}{a \link{list}} -} -\value{ -none -} -\description{ -Set up the static model for habitat dynamics -} diff --git a/man/setup_hydrology_null.Rd b/man/setup_hydrology_null.Rd index 63641623..40b9cd2d 100644 --- a/man/setup_hydrology_null.Rd +++ b/man/setup_hydrology_null.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-null.R +% Please edit documentation in R/hydrology.R \name{setup_hydrology_null} \alias{setup_hydrology_null} \title{Make parameters for the null model for hydrology (do nothing)} @@ -10,7 +10,7 @@ setup_hydrology_null(pars) \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ Make parameters for the null model for hydrology (do nothing) diff --git a/man/setup_mass_medical_forced.Rd b/man/setup_mass_medical_forced.Rd new file mode 100644 index 00000000..2cb21181 --- /dev/null +++ b/man/setup_mass_medical_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mass_medical.R +\name{setup_mass_medical_forced} +\alias{setup_mass_medical_forced} +\title{Set up a model for mass medical} +\usage{ +setup_mass_medical_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up a model for mass medical +} diff --git a/man/setup_mass_medical_null.Rd b/man/setup_mass_medical_null.Rd new file mode 100644 index 00000000..e92add65 --- /dev/null +++ b/man/setup_mass_medical_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mass_medical.R +\name{setup_mass_medical_null} +\alias{setup_mass_medical_null} +\title{Set up the null model for mass medical (do nothing)} +\usage{ +setup_mass_medical_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for mass medical (do nothing) +} diff --git a/man/setup_other_blood_hosts_null.Rd b/man/setup_other_blood_hosts_null.Rd new file mode 100644 index 00000000..dae3d935 --- /dev/null +++ b/man/setup_other_blood_hosts_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/other_blood_hosts.R +\name{setup_other_blood_hosts_null} +\alias{setup_other_blood_hosts_null} +\title{Make parameters for the null model for other blood hosts (do nothing)} +\usage{ +setup_other_blood_hosts_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Make parameters for the null model for other blood hosts (do nothing) +} diff --git a/man/setup_otherblood_forced.Rd b/man/setup_otherblood_forced.Rd deleted file mode 100644 index 6bbbf1be..00000000 --- a/man/setup_otherblood_forced.Rd +++ /dev/null @@ -1,28 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/other_blood_hosts.R -\name{setup_otherblood_forced} -\alias{setup_otherblood_forced} -\title{Set up forcing for the availability of other blood hosts} -\usage{ -setup_otherblood_forced( - pars, - otherblood_Opts = list(), - otherblood_scale = 0, - otherblood_t = NULL -) -} -\arguments{ -\item{pars}{a \link{list}} - -\item{otherblood_Opts}{a list, overwrites default values} - -\item{otherblood_scale}{a non-negative numeric value to scale the mean availability of other blood hosts} - -\item{otherblood_t}{a function that specifies the temporal pattern for the availability of other blood hosts} -} -\value{ -none -} -\description{ -Set up forcing for the availability of other blood hosts -} diff --git a/man/setup_ovitraps_null.Rd b/man/setup_ovitraps_null.Rd new file mode 100644 index 00000000..c5bbc14d --- /dev/null +++ b/man/setup_ovitraps_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ovitrap.R +\name{setup_ovitraps_null} +\alias{setup_ovitraps_null} +\title{Set up the null model for oviposition traps (do nothing)} +\usage{ +setup_ovitraps_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for oviposition traps (do nothing) +} diff --git a/man/setup_rainfall_null.Rd b/man/setup_rainfall_null.Rd new file mode 100644 index 00000000..49d5ebc6 --- /dev/null +++ b/man/setup_rainfall_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/weather.R +\name{setup_rainfall_null} +\alias{setup_rainfall_null} +\title{Set up the null model for RAINFALL} +\usage{ +setup_rainfall_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for RAINFALL +} diff --git a/man/setup_relative_humidity_null.Rd b/man/setup_relative_humidity_null.Rd new file mode 100644 index 00000000..4ecedc08 --- /dev/null +++ b/man/setup_relative_humidity_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/weather.R +\name{setup_relative_humidity_null} +\alias{setup_relative_humidity_null} +\title{Set up the null model for HUMIDITY} +\usage{ +setup_relative_humidity_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for HUMIDITY +} diff --git a/man/setup_resources_forced.Rd b/man/setup_resources_forced.Rd new file mode 100644 index 00000000..e646f084 --- /dev/null +++ b/man/setup_resources_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/resources-forced.R +\name{setup_resources_forced} +\alias{setup_resources_forced} +\title{Set up a model for mass medical} +\usage{ +setup_resources_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up a model for mass medical +} diff --git a/man/setup_resources_static.Rd b/man/setup_resources_static.Rd deleted file mode 100644 index da2fa121..00000000 --- a/man/setup_resources_static.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-static.R -\name{setup_resources_static} -\alias{setup_resources_static} -\title{Set up parameters for a static model for resource availability} -\usage{ -setup_resources_static(pars, RAopts, other = 0, sugar = 0) -} -\arguments{ -\item{pars}{a \link{list}} - -\item{RAopts}{a set of options that would override the defaults} - -\item{other}{the availability of other blood hosts} - -\item{sugar}{the availability of sugar} -} -\value{ -none -} -\description{ -Set up parameters for a static model for resource availability -} diff --git a/man/setup_shock_null.Rd b/man/setup_shock_null.Rd new file mode 100644 index 00000000..bc2252b1 --- /dev/null +++ b/man/setup_shock_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/shock.R +\name{setup_shock_null} +\alias{setup_shock_null} +\title{Set up the null model for shocks (do nothing)} +\usage{ +setup_shock_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for shocks (do nothing) +} diff --git a/man/setup_sugar_baits_null.Rd b/man/setup_sugar_baits_null.Rd new file mode 100644 index 00000000..9822e04e --- /dev/null +++ b/man/setup_sugar_baits_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar_baits-interface.R +\name{setup_sugar_baits_null} +\alias{setup_sugar_baits_null} +\title{Set up the null model for sugar baits (do nothing)} +\usage{ +setup_sugar_baits_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for sugar baits (do nothing) +} diff --git a/man/setup_sugar_forced.Rd b/man/setup_sugar_forced.Rd deleted file mode 100644 index b6beb41b..00000000 --- a/man/setup_sugar_forced.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/sugar.R -\name{setup_sugar_forced} -\alias{setup_sugar_forced} -\title{Set up forcing for the availability of sugar} -\usage{ -setup_sugar_forced(pars, sugar_Opts = list(), sugar_scale = 0, sugar_t = NULL) -} -\arguments{ -\item{pars}{a \link{list}} - -\item{sugar_Opts}{a list, overwrites default values} - -\item{sugar_scale}{a non-negative numeric value to scale the mean availability of sugar} - -\item{sugar_t}{a function that specifies the temporal pattern for the availability of sugar} -} -\value{ -none -} -\description{ -Set up forcing for the availability of sugar -} diff --git a/man/setup_sugar_null.Rd b/man/setup_sugar_null.Rd new file mode 100644 index 00000000..30c2c7a4 --- /dev/null +++ b/man/setup_sugar_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/sugar.R +\name{setup_sugar_null} +\alias{setup_sugar_null} +\title{Make parameters for the null model for sugar (do nothing)} +\usage{ +setup_sugar_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Make parameters for the null model for sugar (do nothing) +} diff --git a/man/setup_temperature_null.Rd b/man/setup_temperature_null.Rd new file mode 100644 index 00000000..2e18ee15 --- /dev/null +++ b/man/setup_temperature_null.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/weather.R +\name{setup_temperature_null} +\alias{setup_temperature_null} +\title{Set up the null model for temperature} +\usage{ +setup_temperature_null(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the null model for temperature +} diff --git a/man/setup_vc_control.Rd b/man/setup_vc_control.Rd index 98fe30a0..d36dd108 100644 --- a/man/setup_vc_control.Rd +++ b/man/setup_vc_control.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/vectorcontrol-control.R +% Please edit documentation in R/vector_control-control.R \name{setup_vc_control} \alias{setup_vc_control} \title{Make parameters for the control model of vector control (do nothing)} diff --git a/man/setup_vc_null.Rd b/man/setup_vc_null.Rd index 3a95fc5c..0b8e9e2f 100644 --- a/man/setup_vc_null.Rd +++ b/man/setup_vc_null.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/vectorcontrol-null.R +% Please edit documentation in R/vector_control-null.R \name{setup_vc_null} \alias{setup_vc_null} -\title{Set up the vector control null model (do nothing)} +\title{Distribute vector control, the null model} \usage{ setup_vc_null(pars) } @@ -13,5 +13,5 @@ setup_vc_null(pars) none } \description{ -Set up the vector control null model (do nothing) +Distribute vector control, the null model } diff --git a/man/setup_visitors_basic.Rd b/man/setup_visitors_basic.Rd index d63f038d..0dfb0ce9 100644 --- a/man/setup_visitors_basic.Rd +++ b/man/setup_visitors_basic.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/visitors-basic.R +% Please edit documentation in R/visitors.R \name{setup_visitors_basic} \alias{setup_visitors_basic} \title{Make parameters and functions for the basic model for visitors} @@ -27,7 +27,7 @@ setup_visitors_basic( \item{Vt}{a function to set the temporal pattern for availability of Visitors} } \value{ -none +\link{list} } \description{ Make parameters and functions for the basic model for visitors diff --git a/man/setup_visitors_null.Rd b/man/setup_visitors_null.Rd index 8e5b7e42..10c5d2bd 100644 --- a/man/setup_visitors_null.Rd +++ b/man/setup_visitors_null.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/visitors-null.R +% Please edit documentation in R/visitors.R \name{setup_visitors_null} \alias{setup_visitors_null} \title{Make parameters for the null model visitors (no visitors)} @@ -10,7 +10,7 @@ setup_visitors_null(pars) \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ Make parameters for the null model visitors (no visitors) diff --git a/man/setup_weather_forced.Rd b/man/setup_weather_forced.Rd new file mode 100644 index 00000000..b61111fe --- /dev/null +++ b/man/setup_weather_forced.Rd @@ -0,0 +1,17 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/weather.R +\name{setup_weather_forced} +\alias{setup_weather_forced} +\title{Set up the forced model for weather} +\usage{ +setup_weather_forced(pars) +} +\arguments{ +\item{pars}{a \link{list}} +} +\value{ +\link{list} +} +\description{ +Set up the forced model for weather +} diff --git a/man/setup_weather_null.Rd b/man/setup_weather_null.Rd index 0ffe58ef..0c4052a5 100644 --- a/man/setup_weather_null.Rd +++ b/man/setup_weather_null.Rd @@ -1,8 +1,8 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/exogenous-null.R +% Please edit documentation in R/weather.R \name{setup_weather_null} \alias{setup_weather_null} -\title{Set up the null model for weather (do nothing)} +\title{Set up the null model for weather} \usage{ setup_weather_null(pars) } @@ -10,8 +10,8 @@ setup_weather_null(pars) \item{pars}{a \link{list}} } \value{ -none +\link{list} } \description{ -Set up the null model for weather (do nothing) +Set up the null model for weather } diff --git a/man/travel_malaria.Rd b/man/travel_malaria.Rd index 3fb45fa6..6c5d1ce2 100644 --- a/man/travel_malaria.Rd +++ b/man/travel_malaria.Rd @@ -15,5 +15,5 @@ travel_malaria(t, pars) a \link{numeric} value } \description{ -This method dispatches on the type of \code{pars$TRVpar}. +This method dispatches on the type of \code{pars$TRAVEL}. } diff --git a/man/update_BloodFeeding.dynamic.Rd b/man/update_BloodFeeding.dynamic.Rd deleted file mode 100644 index b9ce9974..00000000 --- a/man/update_BloodFeeding.dynamic.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-dynamic.R -\name{update_BloodFeeding.dynamic} -\alias{update_BloodFeeding.dynamic} -\title{Update total availability of blood hosts for dynamical models} -\usage{ -\method{update_BloodFeeding}{dynamic}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_BloodFeeding} for a dynamic model -} diff --git a/man/update_BloodFeeding.static.Rd b/man/update_BloodFeeding.static.Rd deleted file mode 100644 index ffa6bfe6..00000000 --- a/man/update_BloodFeeding.static.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-static.R -\name{update_BloodFeeding.static} -\alias{update_BloodFeeding.static} -\title{Update blood feeding for static models} -\usage{ -\method{update_BloodFeeding}{static}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_BloodFeeding} for a dynamic model -} diff --git a/man/update_EggLaying.Rd b/man/update_EggLaying.Rd deleted file mode 100644 index 96c204fe..00000000 --- a/man/update_EggLaying.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-interface.R -\name{update_EggLaying} -\alias{update_EggLaying} -\title{Update the availability of habitats and egg laying} -\usage{ -update_EggLaying(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -This method dispatches on the type of \code{pars$Q}. It -computes availability of all blood hosts at time \code{t} -} diff --git a/man/update_EggLaying.dynamic.Rd b/man/update_EggLaying.dynamic.Rd deleted file mode 100644 index accd77ae..00000000 --- a/man/update_EggLaying.dynamic.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-dynamic.R -\name{update_EggLaying.dynamic} -\alias{update_EggLaying.dynamic} -\title{Update the total availability of aquatic habitats and egg laying} -\usage{ -\method{update_EggLaying}{dynamic}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_EggLaying} for a dynamic model -} diff --git a/man/update_EggLaying.static.Rd b/man/update_EggLaying.static.Rd deleted file mode 100644 index 7117c812..00000000 --- a/man/update_EggLaying.static.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-static.R -\name{update_EggLaying.static} -\alias{update_EggLaying.static} -\title{Update blood feeding for static models} -\usage{ -\method{update_EggLaying}{static}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state variables} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_EggLaying} for a dynamic model -} diff --git a/man/update_O.Rd b/man/update_O.Rd deleted file mode 100644 index bdecb91e..00000000 --- a/man/update_O.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-interface.R -\name{update_O} -\alias{update_O} -\title{Update the availability of other blood hosts} -\usage{ -update_O(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -This method dispatches on the type of \code{pars$O}. It -computes availability of blood hosts at time \code{t}. Other blood hosts -include any vertebrate host that does not serve as a host for the pathogen. -} diff --git a/man/update_O.dynamic.Rd b/man/update_O.dynamic.Rd deleted file mode 100644 index 34b67060..00000000 --- a/man/update_O.dynamic.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-dynamic.R -\name{update_O.dynamic} -\alias{update_O.dynamic} -\title{Update other host availability dynamically} -\usage{ -\method{update_O}{dynamic}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_O} for a static model -} diff --git a/man/update_O.static.Rd b/man/update_O.static.Rd deleted file mode 100644 index 3c8bda32..00000000 --- a/man/update_O.static.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-static.R -\name{update_O.static} -\alias{update_O.static} -\title{Update other host availability for static models} -\usage{ -\method{update_O}{static}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_O} when pars$O doesn't change -} diff --git a/man/update_S.Rd b/man/update_S.Rd deleted file mode 100644 index 1086642e..00000000 --- a/man/update_S.Rd +++ /dev/null @@ -1,20 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-interface.R -\name{update_S} -\alias{update_S} -\title{Update the total availability of sugar} -\usage{ -update_S(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -This method dispatches on the type of \code{pars$S}. It should -update, and if necessary compute, the availability of sugar at time \code{t} -} diff --git a/man/update_S.dynamic.Rd b/man/update_S.dynamic.Rd deleted file mode 100644 index d21b79a0..00000000 --- a/man/update_S.dynamic.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-dynamic.R -\name{update_S.dynamic} -\alias{update_S.dynamic} -\title{Dynamically update the total availability of sugar} -\usage{ -\method{update_S}{dynamic}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_S} for a dynamic model -} diff --git a/man/update_S.static.Rd b/man/update_S.static.Rd deleted file mode 100644 index 56bb218b..00000000 --- a/man/update_S.static.Rd +++ /dev/null @@ -1,19 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-static.R -\name{update_S.static} -\alias{update_S.static} -\title{Update sugar availability for static models} -\usage{ -\method{update_S}{static}(t, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{pars}{an \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_S} when pars$S doesn't change -} diff --git a/man/update_W.Rd b/man/update_W.Rd deleted file mode 100644 index 5fd0de48..00000000 --- a/man/update_W.Rd +++ /dev/null @@ -1,22 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-interface.R -\name{update_W} -\alias{update_W} -\title{Update host availability} -\usage{ -update_W(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -This method dispatches on the type of \code{pars$W}. It should -update the availability of the pathogen's hosts for blood feeding at time \code{t} -} diff --git a/man/update_W.dynamic.Rd b/man/update_W.dynamic.Rd deleted file mode 100644 index b345702b..00000000 --- a/man/update_W.dynamic.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-dynamic.R -\name{update_W.dynamic} -\alias{update_W.dynamic} -\title{Update host availability dynamically} -\usage{ -\method{update_W}{dynamic}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_W} for a static model -} diff --git a/man/update_W.static.Rd b/man/update_W.static.Rd deleted file mode 100644 index b48c7f72..00000000 --- a/man/update_W.static.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/resources-static.R -\name{update_W.static} -\alias{update_W.static} -\title{Update host availability for static models} -\usage{ -\method{update_W}{static}(t, y, pars) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{a \link{list}} -} -\value{ -a \link{list} -} -\description{ -Implements \link{update_W} when pars$W doesn't change -} diff --git a/man/xde_setup_cohort.Rd b/man/xde_setup_cohort.Rd new file mode 100644 index 00000000..f8d6d880 --- /dev/null +++ b/man/xde_setup_cohort.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/setup.R +\name{xde_setup_cohort} +\alias{xde_setup_cohort} +\title{Set up a model for xde_diffeqn_cohort} +\usage{ +xde_setup_cohort( + modelName, + F_eir, + Xname = "SIS", + HPop = 1000, + Xopts = list(), + Hopts = list() +) +} +\arguments{ +\item{modelName}{is a name for the model (arbitrary)} + +\item{F_eir}{is a function F_eir(t, pars) that returns the daily FoI} + +\item{Xname}{is a character string defining a X model} + +\item{HPop}{is the number of humans in each patch} + +\item{Xopts}{a list to configure the X model} + +\item{Hopts}{a list to configure the H model} +} +\value{ +a \link{list} +} +\description{ +Set up a model for xde_diffeqn_cohort +} diff --git a/man/xde_solve.cohort.Rd b/man/xde_solve.cohort.Rd new file mode 100644 index 00000000..36751e06 --- /dev/null +++ b/man/xde_solve.cohort.Rd @@ -0,0 +1,21 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/solving.R +\name{xde_solve.cohort} +\alias{xde_solve.cohort} +\title{Solve a system of equations with xDE_diffeqn_cohort} +\usage{ +\method{xde_solve}{cohort}(pars, Tmax = 365, dt = 1) +} +\arguments{ +\item{pars}{a \link{list} that defines a model} + +\item{Tmax}{the last time point, run from 0...Tmax} + +\item{dt}{the time interval for outputs} +} +\value{ +a \link{matrix} +} +\description{ +Implements \link{xde_solve} for mosquito dynamics (no transmission) +} diff --git a/tests/testthat/test-human-hMoI.R b/tests/testthat/test-human-hMoI.R index ca341507..7cfed8d8 100644 --- a/tests/testthat/test-human-hMoI.R +++ b/tests/testthat/test-human-hMoI.R @@ -15,10 +15,8 @@ test_that("human hybrid MoI model remains at equilibrium", { TaR <- matrix(data = 1,nrow = 1, ncol = nStrata) m20 <- 1.5 - h <- r2*m20 - m10 <- h/r1 - - EIR <- h/b + foi <- r2*m20 + m10 <- foi/r1 params <- make_parameters_xde() params$nStrata = nStrata @@ -33,9 +31,9 @@ test_that("human hybrid MoI model remains at equilibrium", { # set initial conditions y0 <- get_inits(params) - out <- deSolve::ode(y = y0, times = c(0, 365), func = function(t, y, pars, EIR) { - list(dXdt(t, y, pars, EIR)) - }, parms = params, method = 'lsoda', EIR = as.vector(EIR)) + out <- deSolve::ode(y = y0, times = c(0, 365), func = function(t, y, pars, foi) { + list(dXdt(t, y, pars, foi)) + }, parms = params, method = 'lsoda', foi= as.vector(foi)) expect_equal(as.vector(out[2L, params$Xpar$m1_ix+1]), rep(m10, nStrata), tolerance = numeric_tol) expect_equal(as.vector(out[2L, params$Xpar$m2_ix+1]), rep(m20, nStrata), tolerance = numeric_tol) diff --git a/tests/testthat/test-human-sip.R b/tests/testthat/test-human-sip.R index 87c0a8ad..b9311818 100644 --- a/tests/testthat/test-human-sip.R +++ b/tests/testthat/test-human-sip.R @@ -18,6 +18,7 @@ test_that("human SIP model remains at equilibrium", { P <- diag(1/eta) %*% diag(rho/(1-rho)) %*% (r*X) EIR <- diag(1/b, nStrata) %*% diag(1/(1-rho)) %*% ((r*X)/(H-X-P)) + foi <- b*EIR params <- make_parameters_xde() params$nStrata <- nStrata @@ -35,9 +36,9 @@ test_that("human SIP model remains at equilibrium", { y0 <- get_inits(params) - out <- deSolve::ode(y = y0, times = c(0, 365), func = function(t, y, pars, EIR) { - list(dXdt(t, y, pars, EIR)) - }, parms = params, method = 'lsoda', EIR = as.vector(EIR)) + out <- deSolve::ode(y = y0, times = c(0, 365), func = function(t, y, pars, foi) { + list(dXdt(t, y, pars, foi)) + }, parms = params, method = 'lsoda', foi = as.vector(foi)) expect_equal(as.vector(out[2L, params$Xpar$X_ix+1]), X, tolerance = numeric_tol) expect_equal(as.vector(out[2L, params$Xpar$P_ix+1]), as.vector(P), tolerance = numeric_tol) diff --git a/tests/testthat/test-human-sis.R b/tests/testthat/test-human-sis.R index 0f1db8d9..829b398a 100644 --- a/tests/testthat/test-human-sis.R +++ b/tests/testthat/test-human-sis.R @@ -14,6 +14,7 @@ test_that("human SIS model remains at equilibrium", { TaR <- matrix(data = 1,nrow = 1, ncol = nStrata) EIR <- diag(1/b, nStrata) %*% ((r*X)/(H-X)) + foi <- b*EIR params <- make_parameters_xde() params$nStrata <- nStrata @@ -33,9 +34,9 @@ test_that("human SIS model remains at equilibrium", { y0 <- rep(0, 3) y0[params$Xpar$X_ix] <- X - out <- deSolve::ode(y = y0, times = c(0, 365), func = function(t, y, pars, EIR) { - list(dXdt(t, y, pars, EIR)) - }, parms = params, method = 'lsoda', EIR = as.vector(EIR)) + out <- deSolve::ode(y = y0, times = c(0, 365), func = function(t, y, pars, foi) { + list(dXdt(t, y, pars, foi)) + }, parms = params, method = 'lsoda', foi= as.vector(foi)) expect_equal(as.vector(out[2L, params$Xpar$X_ix+1]), X, tolerance = numeric_tol) }) diff --git a/vignettes/adult_RM.Rmd b/vignettes/adult_RM.Rmd index 434073f2..e345e69c 100644 --- a/vignettes/adult_RM.Rmd +++ b/vignettes/adult_RM.Rmd @@ -117,6 +117,7 @@ We can use the same equation for $P$ as above. ```{r, message=FALSE, warning=FALSE} library(exDE) +#devtools::load_all() library(expm) library(deSolve) library(data.table) @@ -156,7 +157,7 @@ Now we set up the parameter environment with the correct class using `exDE::make ```{r} params <- list(nPatches = nPatches) -params = make_MYZpar_RM(params, +params = make_parameters_MYZ_RM(params, g = g, sigma = sigma, calK = calK, f = f, q = q, nu = nu, eggsPerBatch = eggsPerBatch, @@ -165,7 +166,7 @@ params = make_MYZpar_RM(params, Now we set the values of $\kappa$ and $\Lambda$ and solve for the equilibrium values. -```{r} +```{r kappa & lambda} kappa <- c(0.1, 0.075, 0.025) Lambda <- c(5, 10, 8) @@ -193,7 +194,7 @@ params = make_indices(params) Then we can set up the initial conditions vector and use `deSolve::ode` to solve the model. Normally these values would be computed within `exDE::xDE_diffeqn`. Here, we set up a local version: -```{r, out.width = "100%"} +```{r solve, out.width = "100%"} y0 = get_inits_MYZ(params) @@ -264,7 +265,7 @@ To set up the model, we call `xde_setup` with Otherwise, setup takes care of all the internals: -```{r} +```{r using setup} MYZeg <- xde_setup("RMexample", MYZname = "RM", Xname = "trace", Lname = "trace", nPatches=3, calK=calK, membership = c(1:3), @@ -273,7 +274,7 @@ MYZeg <- xde_setup("RMexample", Now, we can solve the equations using `xde_solve` and compare the output to what we got above. If they are identical, the two objects should be identical, so can simply add the absolute value of their differences: -```{r} +```{r xde_solve} out2 <- xde_solve(MYZeg, Tmax=50, dt=1)$deout sum(abs(out1-out2))==0 ``` diff --git a/vignettes/aqua_basic.Rmd b/vignettes/aqua_basic.Rmd index 11d97d31..7a99dce6 100644 --- a/vignettes/aqua_basic.Rmd +++ b/vignettes/aqua_basic.Rmd @@ -50,6 +50,7 @@ $$ ```{r, message=FALSE, warning=FALSE} library(exDE) +#devtools::load_all(".") library(deSolve) library(data.table) library(ggplot2) diff --git a/vignettes/human_hmoi.Rmd b/vignettes/human_hmoi.Rmd index 56a68e69..72181b36 100644 --- a/vignettes/human_hmoi.Rmd +++ b/vignettes/human_hmoi.Rmd @@ -58,6 +58,7 @@ We can use this to calculate the net infectious probability, and then $\kappa = ```{r, message=FALSE, warning=FALSE} library(exDE) +#devtools::load_all() library(deSolve) library(data.table) library(ggplot2) @@ -142,16 +143,18 @@ Xo$m10 = with(Xo, h/r1) Hpop = c(100, 500, 250) ``` -To use `xde_setup_human` we must set the values of $Z$ that give us the correct EIR values, and we set these as $Zm$. The function call is to `Ztrace` - ```{r} -MYZo = list(f=0.3, q=0.95) -MYZo$Zm = with(c(MYZo,Xo), h/b/f/q*Hpop) +h/b ``` +```{r} +F_eir1 = function(t, pars){ + 0.05454545 +} +``` ```{r} -xde_setup_human("test_hMoI", "hMoI", HPop=Hpop, Xopts = Xo, MYZopts = MYZo) -> test_hMoI +xde_setup_cohort("test_hMoI", F_eir1, "hMoI", HPop=Hpop, Xopts = Xo) -> test_hMoI ``` ```{r} diff --git a/vignettes/human_sip.Rmd b/vignettes/human_sip.Rmd index 27d88523..078cd0fe 100644 --- a/vignettes/human_sip.Rmd +++ b/vignettes/human_sip.Rmd @@ -124,17 +124,19 @@ Xo = list(b=0.55, c=0.15, r=1/200, eta = c(1/30, 1/40, 1/35), rho = c(0.05, .1, Hpop = c(100, 500, 250) ``` -To use `xde_setup_human` we must set the values of $Z$ that give us the correct EIR values, and we set these as $Zm$. The function call is to `Ztrace` +To use `xde_setup_cohort` we must set up a function `F_eir` returns the value of EIR we computed above: ```{r} -EIR <- with(Xo, diag(1/b, nStrata) %*% diag(1/(1-rho)) %*% ((r*X0)/(Hpop-X0-P0))) -MYZo = list(f=0.3, q=0.95) -MYZo$Zm = with(c(MYZo,Xo), EIR/f/q*Hpop) +EIR +``` +```{r} +F_eir1 = function(t, pars){ + 0.05454545 +} ``` - ```{r} -xde_setup_human("test_SIP", "SIP", HPop=Hpop, Xopts = Xo, MYZopts = MYZo) -> test_SIP +xde_setup_cohort("test_SIP", F_eir1, "SIP", HPop=Hpop, Xopts = Xo) -> test_SIP ``` ```{r} diff --git a/vignettes/human_sis.Rmd b/vignettes/human_sis.Rmd index 52e9fcb5..9c8401f4 100644 --- a/vignettes/human_sis.Rmd +++ b/vignettes/human_sis.Rmd @@ -50,6 +50,7 @@ Note that in the final line, $EIR$ is a column vector of dimension $n$ due to th ```{r, message=FALSE, warning=FALSE} library(exDE) +#devtools::load_all(".") library(deSolve) library(data.table) library(ggplot2) @@ -124,17 +125,21 @@ Xo = list(b=0.55, c=0.15, r=1/200, X0 = X) Hpop = c(100, 500, 250) ``` -To use `xde_setup_human` we must set the values of $Z$ that give us the correct EIR values, and we set these as $Zm$. The function call is to `Ztrace` + +To use `xde_setup_cohort` we must set up a function `F_eir` returns the value of EIR we computed above: ```{r} -EIR <- with(Xo, diag(1/b, nStrata) %*% ((r*X0)/(Hpop-X0))) -MYZo = list(f=0.3, q=0.95) -MYZo$Zm = with(c(MYZo,Xo), EIR/f/q*Hpop) +EIR ``` +```{r} +F_eir1 = function(t, pars){ + 0.05454545 +} +``` ```{r} -xde_setup_human("test_SIS", "SIS", HPop=Hpop, Xopts = Xo, MYZopts = MYZo) -> test_SIS +xde_setup_cohort("test_SIS", F_eir1, "SIS", HPop=Hpop, Xopts = Xo) -> test_SIS ``` ```{r} diff --git a/vignettes/vc_lemenach.Rmd b/vignettes/vc_lemenach.Rmd index cdf3153a..15982d88 100644 --- a/vignettes/vc_lemenach.Rmd +++ b/vignettes/vc_lemenach.Rmd @@ -19,6 +19,7 @@ In this vignette we demonstrate how to set up a model incorporating the Le Menac ```{r, message=FALSE, warning=FALSE} library(exDE) +#devtools::load_all(".") library(MASS) library(expm) library(deSolve) @@ -148,7 +149,10 @@ xde_setup("itn", "RM", "SIS", "basic", 3, Hpop, 1:3, MYZo, calK, list(), Xo, list(), 1:3, rep(1,3), TaR, list(), 1:3, Lo) -> itn_mod +``` +```{r} +itn_mod <- setup_control(itn_mod) ``` If we ran the model at this point, we would get the baseline. Instead, we set up a time-varying function to compute the coverage of ITNs at any time point. We use a sine curve with a period of 365 days which goes from 0 to 1 over that period, with the phase shifted so that at 0 it returns 0. The function also returns 0 for any $t<0$. This must be a function that takes a single argument `t` (time) and returns a scalar value. @@ -161,7 +165,6 @@ ITN_cov <- function(t) {ifelse(t < 0, 0, (sin(2*pi*(t-365/4) / 365) + 1) / 2)} We use the null model of human demographic dynamics, which assumes $H$ is constant for all time. ```{r} -itn_mod = setup_vc_control(itn_mod) itn_mod = setup_itn_lemenach(itn_mod, phi = ITN_cov) ```