basic plotting moved to exDE

dd-harp · Dec 14, 2023 · 86fce99 · 86fce99
1 parent 1a1103f
commit 86fce99
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diff --git a/NAMESPACE b/NAMESPACE
@@ -5,45 +5,17 @@ S3method(F_fqZ,RMG)
 S3method(MBionomics,RMG)
 S3method(dMYZdt,RMG)
 S3method(get_inits_MYZ,RMG)
-S3method(lines_M,RM)
-S3method(lines_M,RMG)
-S3method(lines_X,SIS)
-S3method(lines_YZ,RM)
-S3method(lines_YZ,RMG)
-S3method(lines_YZ_fracs,RM)
-S3method(lines_YZ_fracs,RMG)
 S3method(make_indices_MYZ,RMG)
 S3method(parse_deout_MYZ,RMG)
-S3method(plot_M,RM)
-S3method(plot_M,RMG)
-S3method(plot_X,SIS)
-S3method(plot_YZ,RM)
-S3method(plot_YZ,RMG)
-S3method(plot_YZ_fracs,RM)
-S3method(plot_YZ_fracs,RMG)
 S3method(setup_MYZ,RMG)
 S3method(split_stratum_by_biting,SIS)
 S3method(update_inits_MYZ,RMG)
-export(lines_EIR)
-export(lines_M)
-export(lines_PR)
-export(lines_X)
-export(lines_YZ)
-export(lines_YZ_fracs)
-export(lines_aEIR)
 export(lines_eirVpr)
 export(lines_eirpr)
 export(make_MYZinits_RMG)
 export(make_MYZpar_RMG)
 export(make_inits_MYZ_RMG)
 export(make_parameters_MYZ_RMG)
-export(plot_EIR)
-export(plot_M)
-export(plot_PR)
-export(plot_X)
-export(plot_YZ)
-export(plot_YZ_fracs)
-export(plot_aEIR)
 export(plot_eirVpr)
 export(plot_eirpr)
 export(pr2Lambda)

diff --git a/R/MYZmod-RM.R b/R/MYZmod-RM.R
diff --git a/R/MYZmod-RMG.R b/R/MYZmod-RMG.R
@@ -278,124 +278,3 @@ get_inits_MYZ.RMG <- function(pars) {with(pars$MYZinits,{
   c(U0, Gu0, Y0, Gy0, Z0, Gz0)
 })}
 
-#' Basic plotting: plot mosquito population density for the "RMG" model
-#'
-#' @inheritParams plot_M
-#'
-#' @export
-plot_M.RMG = function(model, clrs = "darkblue", stable=FALSE, add=FALSE){
-  vars = if(stable==TRUE){
-    model$outputs$stable_orbits
-  }else{
-    model$outputs$orbits
-  }
-
-  if(add == FALSE) with(vars$MYZ,
-                        plot(time, 0*time, type = "n", ylim = range(0,max(M)),
-                             ylab = "Mosquito Density", xlab = "Time"))
-
-  lines_M(vars$MYZ, model, clrs)
-}
-
-#' Add the orbits for the SIS model to a plot for models of human infection and immunity
-#'
-#' @inheritParams lines_M
-#'
-#' @export
-lines_M.RMG = function(MYZ, model, clrs="darkblue"){
-  with(MYZ,{
-    if(model$nPatches==1) lines(time, M, col=clrs)
-    if(model$nPatches>1){
-      if (length(clrs)==1) clrs=rep(clrs, model$nPatches)
-      for(i in 1:model$nPatches){
-        lines(time, M[,i], col=clrs[i])
-      }
-    }
-  })}
-
-#' Basic plotting: plot mosquito population density for the "RMG" model
-#'
-#' @inheritParams plot_YZ
-#'
-#' @export
-plot_YZ.RMG = function(model, Yclrs = "purple", Zclrs="darkred", stable=FALSE, add=FALSE){
-  vars = if(stable==TRUE){
-    model$outputs$stable_orbits
-  }else{
-    model$outputs$orbits
-  }
-
-  if(add == FALSE) with(vars$MYZ,
-                        plot(time, 0*time, type = "n", ylim = range(0,max(Y)),
-                             ylab = "Mosquito Density", xlab = "Time"))
-
-  lines_YZ(vars$MYZ, model, Yclrs, Zclrs)
-}
-
-#' Add the orbits for the SIS model to a plot for models of human infection and immunity
-#'
-#' @inheritParams lines_YZ
-#'
-#' @export
-lines_YZ.RMG = function(MYZ, model, Yclrs="purple", Zclrs = "darkred"){
-  with(MYZ,{
-    if(model$nPatches==1){
-      lines(time, Y, col=Yclrs)
-      lines(time, Z, col=Zclrs)
-    }
-    if(model$nPatches>1){
-      if (length(Yclrs)==1)
-        Yclrs=rep(Yclrs, model$nPatches)
-      if (length(Zclrs)==1)
-        Zclrs=rep(Zclrs, model$nPatches)
-
-      for(i in 1:model$nPatches){
-        lines(time, Y[,i], col=Yclrs[i])
-        lines(time, Z[,i], col=Zclrs[i])
-      }
-    }
-  })}
-
-
-#' Basic plotting: plot the fraction infected and infective for the "RMG" model
-#'
-#' @inheritParams plot_YZ_fracs
-#'
-#' @export
-plot_YZ_fracs.RMG = function(model, Yclrs = "purple", Zclrs = "darkred", stable=FALSE, add=FALSE){
-  vars = if(stable==TRUE){
-    model$outputs$stable_orbits
-  }else{
-    model$outputs$orbits
-  }
-
-  if(add == FALSE) with(vars$MYZ,
-                        plot(time, 0*time, type = "n", ylim = range(0,1),
-                             ylab = "Fraction Infected", xlab = "Time"))
-
-  lines_YZ_fracs(vars$MYZ, model, Yclrs, Zclrs)
-}
-
-#' Add lines for the fraction infected and infective for the "RMG" model
-#'
-#' @inheritParams lines_YZ_fracs
-#'
-#' @export
-lines_YZ_fracs.RMG = function(MYZ, model, Yclrs="purple", Zclrs="darkred"){
-  with(MYZ,{
-    if(model$nPatches==1) {
-      lines(time, y, col=Yclrs)
-      lines(time, z, col=Zclrs)
-    }
-    if(model$nPatches>1){
-      if (length(Yclrs)==1)
-        Yclrs=rep(Yclrs, model$nPatches)
-      if (length(Zclrs)==1)
-        Zclrs=rep(Zclrs, model$nPatches)
-
-      for(i in 1:model$nPatches){
-        lines(time, y[,i], col=Yclrs[i])
-        lines(time, z[,i], col=Zclrs[i])
-      }
-    }
-})}
diff --git a/R/Xmod-SIS.R b/R/Xmod-SIS.R
@@ -1,37 +1,3 @@
-#' Basic plotting: plot the density of infected humans for an SIS model
-#'
-#' @inheritParams plot_X
-#' @export
-plot_X.SIS = function(model, clrs="black", stable=FALSE, add=FALSE){
-  vars = if(stable==TRUE){
-    model$outputs$stable_orbits
-  }else{
-    model$outputs$orbits
-  }
-
-  if(add==FALSE) with(vars$XH,
-      plot(time, 0*time, type = "n", ylim = c(0, max(H)),
-           ylab = "# Infected", xlab = "Time"))
-
-  lines_X(vars$XH, model, clrs)
-}
-
-#' Add the orbits for the SIS model to a plot for models of human infection and immunity
-#'
-#' @inheritParams lines_X
-#'
-#' @export
-lines_X.SIS = function(XH, model, clrs="black"){
-  with(XH,{
-    if(model$nStrata==1) lines(time, X, col=clrs)
-    if(model$nStrata>1){
-      if (length(clrs)==1) clrs=rep(clrs, model$nStrata)
-      for(i in 1:model$nStrata){
-        lines(time, X[,i], col=clrs[i])
-      }
-    }
-})}
-
 #' Split a stratum into two strata, assigning a fraction `p` a new biting weight that is multiplied by a factor `fac` compared with the old one. The biting weight for the remaining `1-p` gets a new factor `1/fac`
 #'
 #' @inheritParams split_stratum_by_biting