Dev

.gitignore

@@ -111,3 +111,6 @@ inst/doc
 CRAN-SUBMISSION
 cran-comments.md
 docs
+.Rproj.user
+.Rdata
+.quarto

NAMESPACE

@@ -222,6 +222,10 @@ S3method(update_inits_X,SIP)
 S3method(update_inits_X,SIS)
 S3method(update_inits_X,hMoI)
 S3method(update_inits_X,trace)
+S3method(xde_lines_X,SIP)
+S3method(xde_lines_X,SIS)
+S3method(xde_plot_X,SIP)
+S3method(xde_plot_X,SIS)
 S3method(xde_solve,aqua)
 S3method(xde_solve,aqua_dde)
 S3method(xde_solve,cohort)
@@ -458,6 +462,20 @@ export(xDE_diffeqn_aquatic)
 export(xDE_diffeqn_cohort)
 export(xDE_diffeqn_human)
 export(xDE_diffeqn_mosy)
+export(xde_lines_EIR)
+export(xde_lines_M)
+export(xde_lines_PR)
+export(xde_lines_X)
+export(xde_lines_YZ)
+export(xde_lines_YZ_fracs)
+export(xde_lines_aEIR)
+export(xde_plot_EIR)
+export(xde_plot_M)
+export(xde_plot_PR)
+export(xde_plot_X)
+export(xde_plot_YZ)
+export(xde_plot_YZ_fracs)
+export(xde_plot_aEIR)
 export(xde_setup)
 export(xde_setup_aquatic)
 export(xde_setup_cohort)

R/adult-RM.R

@@ -386,8 +386,12 @@ get_inits_MYZ.RM_ode <- function(pars) {with(pars$MYZinits,{
 #' @title Return initial values as a vector
 #' @description Implements [get_inits_MYZ] for the RM model.
 #' @inheritParams get_inits_MYZ
-#' @return none
+#' @return [numeric]
 #' @export
 get_inits_MYZ.RM_dde <- function(pars) {with(pars$MYZinits,{
   c(M0, P0, Y0, Z0, as.vector(Upsilon0), rep(0, 3*pars$nPatches))
 })}
+
+
+
+

R/adult-interface.R

@@ -122,6 +122,7 @@ parse_deout_MYZ <- function(deout, pars) {
   UseMethod("parse_deout_MYZ", pars$MYZpar)
 }
 
+
 #' @title Return initial values as a vector
 #' @description This method dispatches on the type of `pars$MYZpar`.
 #' @param pars a [list]
@@ -151,4 +152,3 @@ update_inits_MYZ <- function(pars, y0) {
 make_Omega <- function(g, sigma, K, nPatches) {
   diag(g, nPatches) + ((diag(nPatches) - K) %*% diag(sigma, nPatches))
 }
-

R/human-SIP.R

@@ -228,3 +228,42 @@ update_inits_X.SIP <- function(pars, y0) {
 get_inits_X.SIP <- function(pars){with(pars$Xinits,{
   c(X0, P0)
 })}
+
+
+#' Plot the density of infected individuals for the SIP model
+#'
+#' @inheritParams xde_plot_X
+#' @export
+xde_plot_X.SIP = function(pars, clrs=c("black", "darkgreen"), llty=1, stable=FALSE, add_axes=TRUE){
+  vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
+
+  if(add_axes==TRUE)
+    with(vars$XH,
+         plot(time, 0*time, type = "n", ylim = c(0, max(H)),
+              ylab = "# Infected", xlab = "Time"))
+
+  xde_lines_X(vars$XH, pars, clrs, llty)
+}
+
+
+#' Add lines for the density of infected individuals for the SIP model
+#'
+#' @inheritParams xde_lines_X
+#'
+#' @export
+xde_lines_X.SIP = function(XH, pars, clrs=c("black", "darkgreen"), llty=1){
+  with(XH,{
+    if(pars$nStrata==1) {
+      lines(time, X, col=clrs[1], lty = llty[1])
+      lines(time, P, col=clrs[2], lty = llty[1])
+    }
+    if(pars$nStrata>1){
+      if (length(clrs)==1) clrs=matrix(clrs, 2, pars$nStrata)
+      if (length(llty)==1) llty=rep(llty, pars$nStrata)
+      for(i in 1:pars$nStrata){
+        lines(time, X[,i], col=clrs[1,i], lty = llty[i])
+        lines(time, P[,i], col=clrs[2,i], lty = llty[i])
+      }
+    }
+  })}
+

R/human-SIS.R

@@ -198,3 +198,36 @@ update_inits_X.SIS <- function(pars, y0) {
 get_inits_X.SIS <- function(pars){
   pars$Xinits$X0
 }
+
+#' Plot the density of infected individuals for the SIS model
+#'
+#' @inheritParams xde_plot_X
+#' @export
+xde_plot_X.SIS = function(pars, clrs="black", llty=1, stable=FALSE, add_axes=TRUE){
+  vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
+
+  if(add_axes==TRUE)
+    with(vars$XH,
+         plot(time, 0*time, type = "n", ylim = c(0, max(H)),
+              ylab = "# Infected", xlab = "Time"))
+
+  xde_lines_X(vars$XH, pars, clrs, llty)
+}
+
+
+#' Add lines for the density of infected individuals for the SIS model
+#'
+#' @inheritParams xde_lines_X
+#'
+#' @export
+xde_lines_X.SIS = function(XH, pars, clrs="black", llty=1){
+  with(XH,{
+    if(pars$nStrata==1) lines(time, X, col=clrs[1], lty = llty[1])
+    if(model$nStrata>1){
+      if (length(clrs)==1) clrs=rep(clrs, model$nStrata)
+      if (length(llty)==1) llty=rep(llty, model$nStrata)
+      for(i in 1:model$nStrata){
+        lines(time, X[,i], col=clrs[i], lty = llty[i])
+      }
+    }
+  })}

R/human-interface.R

@@ -102,3 +102,28 @@ HTC <- function(pars) {
   UseMethod("get_inits_X", pars$Xpar)
 }
 
+#' Basic plotting for epidemiological models
+#'
+#' @param pars a [list] that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param clrs a [character] vector of colors
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#' @param stable a [logical] set to FALSE for `orbits` and TRUE for `stable_orbits`
+#' @param add_axes a [logical] to plot axes only if TRUE
+#'
+#' @export
+xde_plot_X = function(pars, clrs="black", llty=1, stable=FALSE, add_axes=TRUE){
+  UseMethod("xde_plot_X", pars$Xpar)
+}
+
+#' Add lines for basic outputs of epidemiological models
+#'
+#' @param XH a [list] with the outputs of `exDE::parse_deout()`
+#' @param pars a [list] that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param clrs a [character] vector of colors
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#'
+#' @export
+xde_lines_X = function(XH, pars, clrs="black", llty=1){
+  UseMethod("xde_lines_X", pars$Xpar)
+}
+

R/plot-MYZ.R

@@ -0,0 +1,135 @@
+
+#' Plot adult mosquito population density
+#'
+#' @param pars a [list] that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param clrs a [character] vector of colors
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#' @param stable a [logical] set to FALSE for `orbits` and TRUE for `stable_orbits`
+#' @param add_axes a [logical] to plot axes only if TRUE
+#'
+#' @export
+xde_plot_M = function(pars, clrs="darkblue", llty=1, stable=FALSE, add_axes=TRUE){
+  vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
+
+  if(add_axes == TRUE) with(vars$MYZ,
+                            plot(time, 0*time, type = "n", ylim = range(0,max(M)),
+                                 ylab = "Mosquito Density", xlab = "Time"))
+
+  xde_lines_M(vars$MYZ, pars, clrs, llty)
+}
+
+#' Add lines for adult mosquito population density
+#'
+#' @param MYZ a [list] the output of `exDE::parse_deout()`
+#' @param pars a [list] that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param clrs a [character] vector of colors
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#'
+#' @export
+xde_lines_M = function(MYZ, pars, clrs="darkblue", llty=1){
+  with(MYZ,{
+   if(pars$nPatches==1) lines(time, M, col=clrs[1], lty = llty[1])
+   if(pars$nPatches>1){
+      if (length(clrs)==1) clrs=rep(clrs, pars$nPatches)
+      if (length(llty)==1) llty=rep(llty, pars$nPatches)
+      for(i in 1:pars$nPatches){
+        lines(time, M[,i], col=clrs[i], lty = llty[i])
+      }
+    }
+})}
+
+#' Plot the density of infected and infective mosquitoes
+#'
+#' @param pars a [list] that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param Yclrs a [character] vector of colors for infected mosquitoes
+#' @param Zclrs a [character] vector of colors for infective mosquitoes
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#' @param stable a [logical] set to FALSE for `orbits` and TRUE for `stable_orbits`
+#' @param add_axes a [logical] to plot axes only if TRUE
+#'
+#' @export
+xde_plot_YZ = function(pars, Yclrs = "purple", Zclrs="darkred", llty=1, stable=FALSE, add_axes=TRUE){
+  vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
+
+  if(add_axes == TRUE)
+    with(vars$MYZ,
+         plot(time, 0*time, type = "n", ylim = range(0,max(Y)),
+              ylab = "Mosquito Density", xlab = "Time"))
+
+  xde_lines_YZ(vars$MYZ, pars, Yclrs, Zclrs, llty)
+}
+
+#' Add lines for the density of infected and infective mosquitoes
+#'
+#' @param MYZ a [list] the output of `exDE::parse_deout()`
+#' @param pars a [list] that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param Yclrs a [character] vector of colors
+#' @param Zclrs a [character] vector of colors
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#'
+#' @export
+xde_lines_YZ = function(MYZ, pars, Yclrs="purple", Zclrs = "darkred", llty=1){
+  with(MYZ,{
+    if(pars$nPatches==1){
+      lines(time, Y, col=Yclrs[1], lty = llty[1])
+      lines(time, Z, col=Zclrs[1], lty = llty[1])
+    }
+    if(pars$nPatches>1){
+      if (length(Yclrs)==1) Yclrs=rep(Yclrs, pars$nPatches)
+      if (length(Zclrs)==1) Zclrs=rep(Zclrs, pars$nPatches)
+      if (length(llty)==1) llty=rep(llty, pars$nPatches)
+
+      for(i in 1:pars$nPatches){
+        lines(time, Y[,i], col=Yclrs[i], lty = llty[i])
+        lines(time, Z[,i], col=Zclrs[i], lty = llty[i])
+      }
+    }
+})}
+
+#' Plot the fraction of infected and infective mosquitoes
+#'
+#' @param pars a [list] that defines an `exDE` model (*e.g.*,  generated by `xde_setup()`)
+#' @param Yclrs a [character] vector of colors for infected mosquitoes
+#' @param Zclrs a [character] vector of colors for infective mosquitoes
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#' @param stable a [logical] set to FALSE for `orbits` and TRUE for `stable_orbits`
+#' @param add_axes a [logical] to plot axes only if TRUE
+#'
+#' @export
+xde_plot_YZ_fracs = function(pars, Yclrs = "purple", Zclrs = "darkred", llty=1, stable=FALSE, add_axes=TRUE){
+  vars=with(pars$outputs,if(stable==TRUE){stable_orbits}else{orbits})
+
+  if(add_axes == TRUE)
+    with(vars$MYZ,
+         plot(time, 0*time, type = "n", ylim = range(0,1),
+              ylab = "Fraction Infected", xlab = "Time"))
+
+  xde_lines_YZ_fracs(vars$MYZ, pars, Yclrs, Zclrs, llty)
+}
+
+#' Add lines for the fraction of infected and infective mosquitoes
+#'
+#' @param MYZ a [list] the output of `exDE::parse_deout()`
+#' @param pars a [list] specifying the model
+#' @param Yclrs a [list] of colors
+#' @param Zclrs a [list] of colors
+#' @param llty an [integer] (or integers) to set the `lty` for plotting
+#'
+#' @export
+xde_lines_YZ_fracs = function(MYZ, pars, Yclrs="purple", Zclrs="darkred", llty=1){
+  with(MYZ,{
+    if(pars$nPatches==1) {
+      lines(time, y, col=Yclrs, lty = llty[1])
+      lines(time, z, col=Zclrs, lty = llty[1])
+    }
+    if(pars$nPatches>1){
+      if (length(Yclrs)==1) Yclrs=rep(Yclrs, pars$nPatches)
+      if (length(Zclrs)==1) Zclrs=rep(Zclrs, pars$nPatches)
+      if (length(llty)==1) llty=rep(llty, pars$nPatches)
+
+      for(i in 1:pars$nPatches){
+        lines(time, y[,i], col=Yclrs[i], lty = llty[i])
+        lines(time, z[,i], col=Zclrs[i], lty = llty[i])
+      }
+    }
+})}