name change

make_X* changed to setup_X*
create_X* changed to make_X*

NAMESPACE

@@ -223,15 +223,6 @@ S3method(make_Omega,xde)
 S3method(make_TimeSpent,as_matrix)
 S3method(make_TimeSpent,athome)
 S3method(make_TimeSpent,xy)
-S3method(make_X_indices,SIS)
-S3method(make_X_indices,hMoI)
-S3method(make_X_indices,trivial)
-S3method(make_Xinits,SIS)
-S3method(make_Xinits,hMoI)
-S3method(make_Xinits,trivial)
-S3method(make_Xpar,SIS)
-S3method(make_Xpar,hMoI)
-S3method(make_Xpar,trivial)
 S3method(make_calK,as_matrix)
 S3method(make_calK,herethere)
 S3method(make_calK,xy)
@@ -299,6 +290,15 @@ S3method(setup_MYZpar,SI)
 S3method(setup_MYZpar,basicM)
 S3method(setup_MYZpar,macdonald)
 S3method(setup_MYZpar,trivial)
+S3method(setup_X_indices,SIS)
+S3method(setup_X_indices,hMoI)
+S3method(setup_X_indices,trivial)
+S3method(setup_Xinits,SIS)
+S3method(setup_Xinits,hMoI)
+S3method(setup_Xinits,trivial)
+S3method(setup_Xpar,SIS)
+S3method(setup_Xpar,hMoI)
+S3method(setup_Xpar,trivial)
 S3method(setup_development,func)
 S3method(setup_exposure_nb,dts)
 S3method(setup_exposure_nb,xde)
@@ -448,11 +448,6 @@ export(compute_kappa)
 export(compute_local_frac)
 export(create_TimeSpent_athome)
 export(create_TimeSpent_xy)
-export(create_Xinits_SIS)
-export(create_Xinits_hMoI)
-export(create_Xpar_SIS)
-export(create_Xpar_hMoI)
-export(create_Xpar_trivial)
 export(create_calK_herethere)
 export(create_calK_xy)
 export(create_habitat_matrix)
@@ -525,9 +520,11 @@ export(make_RBR)
 export(make_TaR)
 export(make_TimeSpent)
 export(make_WB)
-export(make_X_indices)
-export(make_Xinits)
-export(make_Xpar)
+export(make_Xinits_SIS)
+export(make_Xinits_hMoI)
+export(make_Xpar_SIS)
+export(make_Xpar_hMoI)
+export(make_Xpar_trivial)
 export(make_beta)
 export(make_calK)
 export(make_calU)
@@ -577,6 +574,9 @@ export(setup_Lpar)
 export(setup_MYZinits)
 export(setup_MYZpar)
 export(setup_TRANSMISSION)
+export(setup_X_indices)
+export(setup_Xinits)
+export(setup_Xpar)
 export(setup_care_seeking_no_behavior)
 export(setup_development)
 export(setup_development_func)

R/change.R

@@ -8,7 +8,7 @@
 set_H = function(H, pars, i=1){
   stopifnot(length(H) == pars$nStrata[i])
   vars <- as.list(get_Xinits(pars,i))
-  pars <- make_Xinits(pars, H, i, vars)
+  pars <- setup_Xinits(pars, H, i, vars)
   class(pars$BFpar) <- trigger_setup(pars$BFpar)
   class(pars$beta) <- trigger_setup(pars$beta)
   return(pars)

R/human-SIS.R

@@ -68,12 +68,12 @@ dts_steady_state_X.SIS = function(ar, H, Xpar){with(Xpar,{
 })}
 
 #' @title Setup Xpar.SIS
-#' @description Implements [make_Xpar] for the SIS model
-#' @inheritParams make_Xpar
+#' @description Implements [setup_Xpar] for the SIS model
+#' @inheritParams setup_Xpar
 #' @return a [list] vector
 #' @export
-make_Xpar.SIS = function(Xname, pars, i, Xopts=list()){
-  pars$Xpar[[i]] = create_Xpar_SIS(pars$nStrata[1], Xopts)
+setup_Xpar.SIS = function(Xname, pars, i, Xopts=list()){
+  pars$Xpar[[i]] = make_Xpar_SIS(pars$nStrata[1], Xopts)
   return(pars)
 }
 
@@ -85,7 +85,7 @@ make_Xpar.SIS = function(Xname, pars, i, Xopts=list()){
 #' @param r recovery rate
 #' @return a [list]
 #' @export
-create_Xpar_SIS = function(nStrata, Xopts=list(),
+make_Xpar_SIS = function(nStrata, Xopts=list(),
                            b=0.55, r=1/180, c=0.15){
   with(Xopts,{
     Xpar = list()
@@ -188,7 +188,7 @@ set_Xpars.SIS <- function(pars, i=1, Xopts=list()) {
 #' @param I the initial values of the parameter I
 #' @return a [list]
 #' @export
-create_Xinits_SIS = function(nStrata, H, Xopts = list(), I=1){with(Xopts,{
+make_Xinits_SIS = function(nStrata, H, Xopts = list(), I=1){with(Xopts,{
   S = unname(as.vector(checkIt(H-I, nStrata)))
   I = unname(as.vector(checkIt(I, nStrata)))
   return(list(S=S, I=I))
@@ -198,12 +198,12 @@ create_Xinits_SIS = function(nStrata, H, Xopts = list(), I=1){with(Xopts,{
 
 
 #' @title Setup Xinits.SIS
-#' @description Implements [make_Xinits] for the SIS model
-#' @inheritParams make_Xinits
+#' @description Implements [setup_Xinits] for the SIS model
+#' @inheritParams setup_Xinits
 #' @return a [list] vector
 #' @export
-make_Xinits.SIS = function(pars, H, i, Xopts=list()){
-  pars$Xinits[[i]] = with(pars, create_Xinits_SIS(pars$nStrata[i], H, Xopts))
+setup_Xinits.SIS = function(pars, H, i, Xopts=list()){
+  pars$Xinits[[i]] = with(pars, make_Xinits_SIS(pars$nStrata[i], H, Xopts))
   return(pars)
 }
 
@@ -228,12 +228,12 @@ get_Xinits.SIS <- function(pars, i=1){pars$Xinits[[i]]}
 
 
 #' @title Add indices for human population to parameter list
-#' @description Implements [make_X_indices] for the SIS model.
-#' @inheritParams make_X_indices
+#' @description Implements [setup_X_indices] for the SIS model.
+#' @inheritParams setup_X_indices
 #' @return none
 #' @importFrom utils tail
 #' @export
-make_X_indices.SIS <- function(pars, i) {with(pars,{
+setup_X_indices.SIS <- function(pars, i) {with(pars,{
 
   S_ix <- seq(from = max_ix+1, length.out=nStrata[i])
   max_ix <- tail(S_ix, 1)

R/human-hMoI.R

@@ -43,7 +43,7 @@ xde_steady_state_X.hMoI = function(foi, H, Xpar){with(Xpar,{
 #' @param r2 recovery rate from patent infections
 #' @return none
 #' @export
-create_Xpar_hMoI = function(nStrata, Xopts=list(),
+make_Xpar_hMoI = function(nStrata, Xopts=list(),
                             b=0.55, r1=1/180, r2 = 1/70,
                             c1=0.015, c2=0.15){
   with(Xopts,{
@@ -65,7 +65,7 @@ create_Xpar_hMoI = function(nStrata, Xopts=list(),
 #' values as a list.
 #' @inheritParams get_Xpars
 #' @return a [list]
-#' @seealso [create_Xpar_hMoI]
+#' @seealso [make_Xpar_hMoI]
 #' @export
 get_Xpars.hMoI<- function(pars, i=1) {
   with(pars$Xpar[[i]],list(b=b, c1=c1, c2=c2, r1=r1, r2=r2))
@@ -89,12 +89,12 @@ set_Xpars.hMoI <- function(pars, i=1, Xopts=list()) {
   }))}
 
 #' @title Setup Xpar.hMoI
-#' @description Implements [make_Xpar] for the hMoI model
-#' @inheritParams make_Xpar
+#' @description Implements [setup_Xpar] for the hMoI model
+#' @inheritParams setup_Xpar
 #' @return a [list] vector
 #' @export
-make_Xpar.hMoI = function(Xname, pars, i, Xopts=list()){
-  pars$Xpar[[i]] = create_Xpar_hMoI(pars$nStrata[i], Xopts)
+setup_Xpar.hMoI = function(Xname, pars, i, Xopts=list()){
+  pars$Xpar[[i]] = make_Xpar_hMoI(pars$nStrata[i], Xopts)
   return(pars)
 }
 
@@ -142,13 +142,13 @@ F_b.hMoI <- function(y, pars,i) {
 
 
 #' @title Setup Xinits.hMoI
-#' @description Implements [make_Xinits] for the hMoI model
-#' @inheritParams make_Xinits
+#' @description Implements [setup_Xinits] for the hMoI model
+#' @inheritParams setup_Xinits
 #' @return a [list] vector
 #' @export
-make_Xinits.hMoI = function(pars, H, i, Xopts=list()){
+setup_Xinits.hMoI = function(pars, H, i, Xopts=list()){
   pars$Xpar[[i]]$H = H
-  pars$Xinits[[i]] = create_Xinits_hMoI(pars$nStrata[i], Xopts)
+  pars$Xinits[[i]] = make_Xinits_hMoI(pars$nStrata[i], Xopts)
   return(pars)
 }
 
@@ -172,7 +172,7 @@ set_Xinits.hMoI <- function(pars, i=1, Xopts=list()) {
 #' @param m2 mean MoI among patent human infections
 #' @return none
 #' @export
-create_Xinits_hMoI = function(nStrata, Xopts = list(), m1=2, m2=1){with(Xopts,{
+make_Xinits_hMoI = function(nStrata, Xopts = list(), m1=2, m2=1){with(Xopts,{
   m1 = checkIt(m1, nStrata)
   m2 = checkIt(m2, nStrata)
   return(list(m1=m1, m2=m2))
@@ -191,12 +191,12 @@ HTC.hMoI <- function(pars, i) {
 }
 
 #' @title Add indices for human population to parameter list
-#' @description Implements [make_X_indices] for the hybrid MoI model.
-#' @inheritParams make_X_indices
+#' @description Implements [setup_X_indices] for the hybrid MoI model.
+#' @inheritParams setup_X_indices
 #' @return none
 #' @importFrom utils tail
 #' @export
-make_X_indices.hMoI <- function(pars, i) {with(pars,{
+setup_X_indices.hMoI <- function(pars, i) {with(pars,{
   m1_ix <- seq(from = max_ix+1, length.out=nStrata[i])
   max_ix <- tail(m1_ix, 1)
 
@@ -218,7 +218,7 @@ update_Xinits.hMoI <- function(pars, y0, i) {
   with(pars$ix$X[[i]],{
     m1 = y0[m1_ix]
     m2 = y0[m2_ix]
-    pars$Xinits[[i]] = create_Xinits_hMoI(pars$nStrata[i], m1=m1, m2=m2)
+    pars$Xinits[[i]] = make_Xinits_hMoI(pars$nStrata[i], m1=m1, m2=m2)
     return(pars)
   })}
 

R/human-interface.R

@@ -25,9 +25,9 @@ dXdt <- function(t, y, pars, i) {
 #' @param Xopts a [list]
 #' @return an **`xds`** object
 #' @export
-make_Xpar = function(Xname, pars, i, Xopts=list()){
+setup_Xpar = function(Xname, pars, i, Xopts=list()){
   class(Xname) <- Xname
-  UseMethod("make_Xpar", Xname)
+  UseMethod("setup_Xpar", Xname)
 }
 
 #' @title Update X states for a discrete time system
@@ -98,8 +98,8 @@ F_b <- function(y, pars, i) {
 #' @param Xopts a [list]
 #' @return an **`xds`** object
 #' @export
-make_Xinits = function(pars, H, i, Xopts=list()){
-  UseMethod("make_Xinits", pars$Xpar[[i]])
+setup_Xinits = function(pars, H, i, Xopts=list()){
+  UseMethod("setup_Xinits", pars$Xpar[[i]])
 }
 
 #' @title Add indices for human population to parameter list
@@ -108,8 +108,8 @@ make_Xinits = function(pars, H, i, Xopts=list()){
 #' @param i the host species index
 #' @return an **`xds`** object
 #' @export
-make_X_indices <- function(pars, i) {
-  UseMethod("make_X_indices", pars$Xpar[[i]])
+setup_X_indices <- function(pars, i) {
+  UseMethod("setup_X_indices", pars$Xpar[[i]])
 }
 
 #' @title Return the variables as a list

R/human-trivial.R

@@ -29,7 +29,7 @@ F_H.trivial <- function(t, y, pars, i) {
 #' @param F_trend a function returning a trend
 #' @return a [list]
 #' @export
-create_Xpar_trivial <- function(nPatches, Xopts, kappa=.1, HPop=1,
+make_Xpar_trivial <- function(nPatches, Xopts, kappa=.1, HPop=1,
                                 F_season=F_flat, F_trend=F_flat){
   with(Xopts,{
     Xpar <- list()
@@ -119,33 +119,33 @@ F_b.trivial <- function(y, pars, i) {
 
 
 #' @title xde_setup Xpar.trivial
-#' @description Implements [make_Xpar] for the trivial model
-#' @inheritParams make_Xpar
+#' @description Implements [setup_Xpar] for the trivial model
+#' @inheritParams setup_Xpar
 #' @return a [list] vectord
 #' @export
-make_Xpar.trivial = function(Xname, pars, i, Xopts=list()){
-  pars$Xpar[[i]] = create_Xpar_trivial(pars$nPatches, Xopts)
+setup_Xpar.trivial = function(Xname, pars, i, Xopts=list()){
+  pars$Xpar[[i]] = make_Xpar_trivial(pars$nPatches, Xopts)
   return(pars)
 }
 
 
 #' @title Setup Xinits.trivial
-#' @description Implements [make_Xinits] for the trivial model
-#' @inheritParams make_Xinits
+#' @description Implements [setup_Xinits] for the trivial model
+#' @inheritParams setup_Xinits
 #' @return a [list] vector
 #' @export
-make_Xinits.trivial = function(pars, H, i, Xopts=list()){
+setup_Xinits.trivial = function(pars, H, i, Xopts=list()){
   pars$Xpar[[i]]$H = H
   return(pars)
 }
 
 #' @title Add indices for human population to parameter list
-#' @description Implements [make_X_indices] for the trivial model.
-#' @inheritParams make_X_indices
+#' @description Implements [setup_X_indices] for the trivial model.
+#' @inheritParams setup_X_indices
 #' @return none
 #' @importFrom utils tail
 #' @export
-make_X_indices.trivial <- function(pars, i) {
+setup_X_indices.trivial <- function(pars, i) {
   return(pars)
 }
 

R/utils.R

@@ -19,7 +19,7 @@ make_indices <- function(pars) {
   i = length(pars$Xinits)
   if(i>0)
     for(ix in 1:i)
-      pars = make_X_indices(pars, ix)
+      pars = setup_X_indices(pars, ix)
 
   return(pars)
 }

R/xds_setup.R

@@ -113,8 +113,8 @@ xds_setup = function(xds = 'ode',
 
   # Human Dynamics
   pars$Xname <- Xname
-  pars       <- make_Xpar(Xname, pars,  1, Xopts)
-  pars       <- make_Xinits(pars, HPop, 1, Xopts)
+  pars       <- setup_Xpar(Xname, pars,  1, Xopts)
+  pars       <- setup_Xinits(pars, HPop, 1, Xopts)
   pars       <- setup_Hpar_static(pars, 1)
 
   pars = make_indices(pars)
@@ -210,7 +210,7 @@ xds_setup_mosy = function(xds = 'ode',
   pars       <- setup_Linits(pars, 1, Lopts)
 
   Xo <- list(kappa=kappa, HPop=HPop)
-  pars <- make_Xpar("trivial", pars, 1, Xo)
+  pars <- setup_Xpar("trivial", pars, 1, Xo)
 
   pars = make_indices(pars)
 
@@ -277,7 +277,7 @@ xds_setup_aquatic = function(xds = 'ode',
 
   # Human Dynamics
   pars$Xname <- "trivial"
-  pars <- make_Xpar("trivial", pars, 1, list())
+  pars <- setup_Xpar("trivial", pars, 1, list())
 
   pars = make_indices(pars)
   pars$model_name <- model_name
@@ -353,8 +353,8 @@ xds_setup_human = function(Xname = "SIS",
 
   # Human Dynamics
   pars$Xname <- Xname
-  pars       <- make_Xpar(Xname, pars,  1, Xopts)
-  pars       <- make_Xinits(pars, HPop, 1, Xopts)
+  pars       <- setup_Xpar(Xname, pars,  1, Xopts)
+  pars       <- setup_Xinits(pars, HPop, 1, Xopts)
   pars       <- setup_Hpar_static(pars, 1)
 
   pars = make_indices(pars)
@@ -448,8 +448,8 @@ xds_setup_cohort = function(eir=1,
 
   # Human Dynamics
   pars$Xname <- Xname
-  pars       <- make_Xpar(Xname, pars,  1, Xopts)
-  pars       <- make_Xinits(pars, HPop, 1, Xopts)
+  pars       <- setup_Xpar(Xname, pars,  1, Xopts)
+  pars       <- setup_Xinits(pars, HPop, 1, Xopts)
   pars       <- setup_Hpar_static(pars, 1)
 
   pars = make_indices(pars)