Major update

+ Exposure :: a basic change to the way exposure is calculated. The function Exposure transforms the local EIR to the FoI under 1) a model of environmental heterogeneity; and 2) a model of travel malaria

+ MosquitoBehavior is now called MBionomics; it is called to compute bionomic parameters or reset to baseline (prior to secondary modification, perhaps, by some vector control modules).

+ LBionomics has also been introduced and called to compute baseline parameters for aquatic dynamics;

+ Exogenous forcing and vector control were reconfigured to handle contingencies. This is a working version. Documentation needs to get cleaned up and many function families are stubs. In the coming days, I will be writing examples of all this.

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)
@@ -290,46 +352,60 @@ 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)
 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)
 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)