diff --git a/NAMESPACE b/NAMESPACE
index ef1c3c1bc..e5c81eba1 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/change.R b/R/change.R
index 4af50aee2..40d549410 100644
--- a/R/change.R
+++ b/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$beta)
return(pars)
diff --git a/R/human-SIS.R b/R/human-SIS.R
index 78c4bbfdc..87b93cfd3 100644
--- a/R/human-SIS.R
+++ b/R/human-SIS.R
@@ -68,12 +68,12 @@ dts_steady_state_X.SIS = function(ar, H, Xpar){with(Xpar,{
})}
#' @title Setup Xpar.SIS
-#' @description Implements [make_Xpar] for the SIS model
-#' @inheritParams make_Xpar
+#' @description Implements [setup_Xpar] for the SIS model
+#' @inheritParams setup_Xpar
#' @return a [list] vector
#' @export
-make_Xpar.SIS = function(Xname, pars, i, Xopts=list()){
- pars$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)
diff --git a/R/human-hMoI.R b/R/human-hMoI.R
index 58c513f42..05fec3daf 100644
--- a/R/human-hMoI.R
+++ b/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$nStrata[i], m1=m1, m2=m2)
return(pars)
})}
diff --git a/R/human-interface.R b/R/human-interface.R
index 5740a167c..baddda81a 100644
--- a/R/human-interface.R
+++ b/R/human-interface.R
@@ -25,9 +25,9 @@ dXdt <- function(t, y, pars, i) {
#' @param Xopts a [list]
#' @return an **`xds`** object
#' @export
-make_Xpar = function(Xname, pars, i, Xopts=list()){
+setup_Xpar = function(Xname, pars, i, Xopts=list()){
class(Xname) <- Xname
- UseMethod("make_Xpar", Xname)
+ UseMethod("setup_Xpar", Xname)
}
#' @title Update X states for a discrete time system
@@ -98,8 +98,8 @@ F_b <- function(y, pars, i) {
#' @param Xopts a [list]
#' @return an **`xds`** object
#' @export
-make_Xinits = function(pars, H, i, Xopts=list()){
- UseMethod("make_Xinits", pars$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$Xpar[[i]])
}
#' @title Return the variables as a list
diff --git a/R/human-trivial.R b/R/human-trivial.R
index 9f52cc856..f92d49ccc 100644
--- a/R/human-trivial.R
+++ b/R/human-trivial.R
@@ -29,7 +29,7 @@ F_H.trivial <- function(t, y, pars, i) {
#' @param F_trend a function returning a trend
#' @return a [list]
#' @export
-create_Xpar_trivial <- function(nPatches, Xopts, kappa=.1, HPop=1,
+make_Xpar_trivial <- function(nPatches, Xopts, kappa=.1, HPop=1,
F_season=F_flat, F_trend=F_flat){
with(Xopts,{
Xpar <- list()
@@ -119,33 +119,33 @@ F_b.trivial <- function(y, pars, i) {
#' @title xde_setup Xpar.trivial
-#' @description Implements [make_Xpar] for the trivial model
-#' @inheritParams make_Xpar
+#' @description Implements [setup_Xpar] for the trivial model
+#' @inheritParams setup_Xpar
#' @return a [list] vectord
#' @export
-make_Xpar.trivial = function(Xname, pars, i, Xopts=list()){
- pars$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]]$H = H
return(pars)
}
#' @title Add indices for human population to parameter list
-#' @description Implements [make_X_indices] for the trivial model.
-#' @inheritParams make_X_indices
+#' @description Implements [setup_X_indices] for the trivial model.
+#' @inheritParams setup_X_indices
#' @return none
#' @importFrom utils tail
#' @export
-make_X_indices.trivial <- function(pars, i) {
+setup_X_indices.trivial <- function(pars, i) {
return(pars)
}
diff --git a/R/human.R b/R/human.R
deleted file mode 100644
index e69de29bb..000000000
diff --git a/R/utils.R b/R/utils.R
index 5a46d6ab7..65d1bfa2d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -19,7 +19,7 @@ make_indices <- function(pars) {
i = length(pars$Xinits)
if(i>0)
for(ix in 1:i)
- pars = make_X_indices(pars, ix)
+ pars = setup_X_indices(pars, ix)
return(pars)
}
diff --git a/R/xds_setup.R b/R/xds_setup.R
index 78c9e9d04..0958377a1 100644
--- a/R/xds_setup.R
+++ b/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)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index b9ef1d3a3..2c12055ea 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -570,13 +570,13 @@ reference:
contents:
- dXdt
- Update_Xt
- - make_Xinits
- - make_X_indices
+ - setup_Xinits
+ - setup_X_indices
- list_Xvars
- get_Xpars
- set_Xpars
- put_Xvars
- - make_Xpar
+ - setup_Xpar
- F_X
- F_H
- F_b
@@ -607,10 +607,10 @@ reference:
- F_b.trivial
- dXdt.trivial
- Update_Xt.trivial
- - make_Xpar.trivial
- - create_Xpar_trivial
- - make_Xinits.trivial
- - make_X_indices.trivial
+ - setup_Xpar.trivial
+ - make_Xpar_trivial
+ - setup_Xinits.trivial
+ - setup_X_indices.trivial
- parse_Xorbits.trivial
- get_Xinits.trivial
- set_Xinits.trivial
@@ -622,12 +622,12 @@ reference:
Specialized methods for a hybrid model of MoI (Multiplicity of Infection) for human infection dynamics.
contents:
- dXdt.hMoI
- - make_Xpar.hMoI
- - create_Xpar_hMoI
+ - setup_Xpar.hMoI
+ - make_Xpar_hMoI
- xde_steady_state_X.hMoI
- - make_Xinits.hMoI
- - create_Xinits_hMoI
- - make_X_indices.hMoI
+ - setup_Xinits.hMoI
+ - make_Xinits_hMoI
+ - setup_X_indices.hMoI
- F_X.hMoI
- F_H.hMoI
- F_b.hMoI
@@ -648,11 +648,11 @@ reference:
contents:
- dXdt.SIS
- Update_Xt.SIS
- - make_Xpar.SIS
- - create_Xpar_SIS
- - make_Xinits.SIS
- - create_Xinits_SIS
- - make_X_indices.SIS
+ - setup_Xpar.SIS
+ - make_Xpar_SIS
+ - setup_Xinits.SIS
+ - make_Xinits_SIS
+ - setup_X_indices.SIS
- list_Xvars.SIS
- get_Xpars.SIS
- set_Xpars.SIS
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index dd292d7a6..b692cbcb9 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -25,7 +25,7 @@ articles:
Understanding_ramp.xds: Understanding_ramp.xds.html
VectorControl: VectorControl.html
Working: Working.html
-last_built: 2024-10-03T23:28Z
+last_built: 2024-10-04T00:02Z
urls:
reference: https://dd-harp.github.io/ramp.xds/reference
article: https://dd-harp.github.io/ramp.xds/articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 4c6e41e60..af11ac04c 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1767,11 +1767,11 @@
Human Infection Dynamics make_Xinits()
+
setup_Xinits()
A function to set up Xpar |
- make_X_indices()
+ setup_X_indices()
|
Add indices for human population to parameter list |
@@ -1791,7 +1791,7 @@ Human Infection Dynamics make_Xpar()
+ setup_Xpar()
|
Make Parameters for a \(cal X\) - Component Model |
@@ -1903,19 +1903,19 @@ trivial
|
Update States for the trivial \(\cal X\) Model |
- make_Xpar(<trivial>)
+ setup_Xpar(<trivial>)
|
xde_setup Xpar.trivial |
- create_Xpar_trivial()
+ make_Xpar_trivial()
|
Make parameters for trivial human model |
- make_Xinits(<trivial>)
+ setup_Xinits(<trivial>)
|
Setup Xinits.trivial |
- make_X_indices(<trivial>)
+ setup_X_indices(<trivial>)
|
Add indices for human population to parameter list |
@@ -1951,11 +1951,11 @@ hMoI
|
X Component Derivatives for the hMoI module |
- make_Xpar(<hMoI>)
+ setup_Xpar(<hMoI>)
|
Setup Xpar.hMoI |
- create_Xpar_hMoI()
+ make_Xpar_hMoI()
|
Make parameters for hybrid MoI human model |
@@ -1963,15 +1963,15 @@ hMoI
|
Steady States: hMoI |
- make_Xinits(<hMoI>)
+ setup_Xinits(<hMoI>)
|
Setup Xinits.hMoI |
- create_Xinits_hMoI()
+ make_Xinits_hMoI()
|
Make inits for hybrid MoI human model |
- make_X_indices(<hMoI>)
+ setup_X_indices(<hMoI>)
|
Add indices for human population to parameter list |
@@ -2043,23 +2043,23 @@ SIS
|
DTS updating for the SIS model for human / vertebrate host infections |
- make_Xpar(<SIS>)
+ setup_Xpar(<SIS>)
|
Setup Xpar.SIS |
- create_Xpar_SIS()
+ make_Xpar_SIS()
|
Make parameters for SIS xde human model, with defaults |
- make_Xinits(<SIS>)
+ setup_Xinits(<SIS>)
|
Setup Xinits.SIS |
- create_Xinits_SIS()
+ make_Xinits_SIS()
|
Make initial values for the SIS xde human model, with defaults |
- make_X_indices(<SIS>)
+ setup_X_indices(<SIS>)
|
Add indices for human population to parameter list |
diff --git a/man/get_Xpars.hMoI.Rd b/man/get_Xpars.hMoI.Rd
index f7576d229..94152396d 100644
--- a/man/get_Xpars.hMoI.Rd
+++ b/man/get_Xpars.hMoI.Rd
@@ -20,5 +20,5 @@ stored as \code{pars$Xpar[[i]]}. This returns the stored parameter
values as a list.
}
\seealso{
-\link{create_Xpar_hMoI}
+\link{make_Xpar_hMoI}
}
diff --git a/man/create_Xinits_SIS.Rd b/man/make_Xinits_SIS.Rd
similarity index 82%
rename from man/create_Xinits_SIS.Rd
rename to man/make_Xinits_SIS.Rd
index ff8096298..81cc4c47d 100644
--- a/man/create_Xinits_SIS.Rd
+++ b/man/make_Xinits_SIS.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-SIS.R
-\name{create_Xinits_SIS}
-\alias{create_Xinits_SIS}
+\name{make_Xinits_SIS}
+\alias{make_Xinits_SIS}
\title{Make initial values for the SIS xde human model, with defaults}
\usage{
-create_Xinits_SIS(nStrata, H, Xopts = list(), I = 1)
+make_Xinits_SIS(nStrata, H, Xopts = list(), I = 1)
}
\arguments{
\item{nStrata}{the number of strata in the model}
diff --git a/man/create_Xinits_hMoI.Rd b/man/make_Xinits_hMoI.Rd
similarity index 81%
rename from man/create_Xinits_hMoI.Rd
rename to man/make_Xinits_hMoI.Rd
index 2792e2177..660f3f47a 100644
--- a/man/create_Xinits_hMoI.Rd
+++ b/man/make_Xinits_hMoI.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-hMoI.R
-\name{create_Xinits_hMoI}
-\alias{create_Xinits_hMoI}
+\name{make_Xinits_hMoI}
+\alias{make_Xinits_hMoI}
\title{Make inits for hybrid MoI human model}
\usage{
-create_Xinits_hMoI(nStrata, Xopts = list(), m1 = 2, m2 = 1)
+make_Xinits_hMoI(nStrata, Xopts = list(), m1 = 2, m2 = 1)
}
\arguments{
\item{nStrata}{the number of population strata}
diff --git a/man/create_Xpar_SIS.Rd b/man/make_Xpar_SIS.Rd
similarity index 82%
rename from man/create_Xpar_SIS.Rd
rename to man/make_Xpar_SIS.Rd
index 462bce0e3..c6c31380e 100644
--- a/man/create_Xpar_SIS.Rd
+++ b/man/make_Xpar_SIS.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-SIS.R
-\name{create_Xpar_SIS}
-\alias{create_Xpar_SIS}
+\name{make_Xpar_SIS}
+\alias{make_Xpar_SIS}
\title{Make parameters for SIS xde human model, with defaults}
\usage{
-create_Xpar_SIS(nStrata, Xopts = list(), b = 0.55, r = 1/180, c = 0.15)
+make_Xpar_SIS(nStrata, Xopts = list(), b = 0.55, r = 1/180, c = 0.15)
}
\arguments{
\item{nStrata}{is the number of population strata}
diff --git a/man/create_Xpar_hMoI.Rd b/man/make_Xpar_hMoI.Rd
similarity index 92%
rename from man/create_Xpar_hMoI.Rd
rename to man/make_Xpar_hMoI.Rd
index 286e2d095..354b19996 100644
--- a/man/create_Xpar_hMoI.Rd
+++ b/man/make_Xpar_hMoI.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-hMoI.R
-\name{create_Xpar_hMoI}
-\alias{create_Xpar_hMoI}
+\name{make_Xpar_hMoI}
+\alias{make_Xpar_hMoI}
\title{Make parameters for hybrid MoI human model}
\usage{
-create_Xpar_hMoI(
+make_Xpar_hMoI(
nStrata,
Xopts = list(),
b = 0.55,
diff --git a/man/create_Xpar_trivial.Rd b/man/make_Xpar_trivial.Rd
similarity index 88%
rename from man/create_Xpar_trivial.Rd
rename to man/make_Xpar_trivial.Rd
index e1689f641..b56d2d89d 100644
--- a/man/create_Xpar_trivial.Rd
+++ b/man/make_Xpar_trivial.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-trivial.R
-\name{create_Xpar_trivial}
-\alias{create_Xpar_trivial}
+\name{make_Xpar_trivial}
+\alias{make_Xpar_trivial}
\title{Make parameters for trivial human model}
\usage{
-create_Xpar_trivial(
+make_Xpar_trivial(
nPatches,
Xopts,
kappa = 0.1,
diff --git a/man/make_X_indices.Rd b/man/setup_X_indices.Rd
similarity index 83%
rename from man/make_X_indices.Rd
rename to man/setup_X_indices.Rd
index f6157172a..79981a1cb 100644
--- a/man/make_X_indices.Rd
+++ b/man/setup_X_indices.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-interface.R
-\name{make_X_indices}
-\alias{make_X_indices}
+\name{setup_X_indices}
+\alias{setup_X_indices}
\title{Add indices for human population to parameter list}
\usage{
-make_X_indices(pars, i)
+setup_X_indices(pars, i)
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
diff --git a/man/make_X_indices.SIS.Rd b/man/setup_X_indices.SIS.Rd
similarity index 65%
rename from man/make_X_indices.SIS.Rd
rename to man/setup_X_indices.SIS.Rd
index 16a746136..e8825e77e 100644
--- a/man/make_X_indices.SIS.Rd
+++ b/man/setup_X_indices.SIS.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-SIS.R
-\name{make_X_indices.SIS}
-\alias{make_X_indices.SIS}
+\name{setup_X_indices.SIS}
+\alias{setup_X_indices.SIS}
\title{Add indices for human population to parameter list}
\usage{
-\method{make_X_indices}{SIS}(pars, i)
+\method{setup_X_indices}{SIS}(pars, i)
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
@@ -15,5 +15,5 @@
none
}
\description{
-Implements \link{make_X_indices} for the SIS model.
+Implements \link{setup_X_indices} for the SIS model.
}
diff --git a/man/make_X_indices.hMoI.Rd b/man/setup_X_indices.hMoI.Rd
similarity index 64%
rename from man/make_X_indices.hMoI.Rd
rename to man/setup_X_indices.hMoI.Rd
index 25a664358..b536b78d7 100644
--- a/man/make_X_indices.hMoI.Rd
+++ b/man/setup_X_indices.hMoI.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-hMoI.R
-\name{make_X_indices.hMoI}
-\alias{make_X_indices.hMoI}
+\name{setup_X_indices.hMoI}
+\alias{setup_X_indices.hMoI}
\title{Add indices for human population to parameter list}
\usage{
-\method{make_X_indices}{hMoI}(pars, i)
+\method{setup_X_indices}{hMoI}(pars, i)
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
@@ -15,5 +15,5 @@
none
}
\description{
-Implements \link{make_X_indices} for the hybrid MoI model.
+Implements \link{setup_X_indices} for the hybrid MoI model.
}
diff --git a/man/make_X_indices.trivial.Rd b/man/setup_X_indices.trivial.Rd
similarity index 63%
rename from man/make_X_indices.trivial.Rd
rename to man/setup_X_indices.trivial.Rd
index c59bff672..4d00b3dfd 100644
--- a/man/make_X_indices.trivial.Rd
+++ b/man/setup_X_indices.trivial.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-trivial.R
-\name{make_X_indices.trivial}
-\alias{make_X_indices.trivial}
+\name{setup_X_indices.trivial}
+\alias{setup_X_indices.trivial}
\title{Add indices for human population to parameter list}
\usage{
-\method{make_X_indices}{trivial}(pars, i)
+\method{setup_X_indices}{trivial}(pars, i)
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
@@ -15,5 +15,5 @@
none
}
\description{
-Implements \link{make_X_indices} for the trivial model.
+Implements \link{setup_X_indices} for the trivial model.
}
diff --git a/man/make_Xinits.Rd b/man/setup_Xinits.Rd
similarity index 83%
rename from man/make_Xinits.Rd
rename to man/setup_Xinits.Rd
index 68b084dca..4d45521b0 100644
--- a/man/make_Xinits.Rd
+++ b/man/setup_Xinits.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-interface.R
-\name{make_Xinits}
-\alias{make_Xinits}
+\name{setup_Xinits}
+\alias{setup_Xinits}
\title{A function to set up Xpar}
\usage{
-make_Xinits(pars, H, i, Xopts = list())
+setup_Xinits(pars, H, i, Xopts = list())
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
diff --git a/man/make_Xinits.SIS.Rd b/man/setup_Xinits.SIS.Rd
similarity index 68%
rename from man/make_Xinits.SIS.Rd
rename to man/setup_Xinits.SIS.Rd
index c60e179e8..e4f25187a 100644
--- a/man/make_Xinits.SIS.Rd
+++ b/man/setup_Xinits.SIS.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-SIS.R
-\name{make_Xinits.SIS}
-\alias{make_Xinits.SIS}
+\name{setup_Xinits.SIS}
+\alias{setup_Xinits.SIS}
\title{Setup Xinits.SIS}
\usage{
-\method{make_Xinits}{SIS}(pars, H, i, Xopts = list())
+\method{setup_Xinits}{SIS}(pars, H, i, Xopts = list())
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
@@ -19,5 +19,5 @@
a \link{list} vector
}
\description{
-Implements \link{make_Xinits} for the SIS model
+Implements \link{setup_Xinits} for the SIS model
}
diff --git a/man/make_Xinits.hMoI.Rd b/man/setup_Xinits.hMoI.Rd
similarity index 68%
rename from man/make_Xinits.hMoI.Rd
rename to man/setup_Xinits.hMoI.Rd
index 8ac86af13..ba75daad5 100644
--- a/man/make_Xinits.hMoI.Rd
+++ b/man/setup_Xinits.hMoI.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-hMoI.R
-\name{make_Xinits.hMoI}
-\alias{make_Xinits.hMoI}
+\name{setup_Xinits.hMoI}
+\alias{setup_Xinits.hMoI}
\title{Setup Xinits.hMoI}
\usage{
-\method{make_Xinits}{hMoI}(pars, H, i, Xopts = list())
+\method{setup_Xinits}{hMoI}(pars, H, i, Xopts = list())
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
@@ -19,5 +19,5 @@
a \link{list} vector
}
\description{
-Implements \link{make_Xinits} for the hMoI model
+Implements \link{setup_Xinits} for the hMoI model
}
diff --git a/man/make_Xinits.trivial.Rd b/man/setup_Xinits.trivial.Rd
similarity index 66%
rename from man/make_Xinits.trivial.Rd
rename to man/setup_Xinits.trivial.Rd
index 9dd6063f1..8cea534a1 100644
--- a/man/make_Xinits.trivial.Rd
+++ b/man/setup_Xinits.trivial.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-trivial.R
-\name{make_Xinits.trivial}
-\alias{make_Xinits.trivial}
+\name{setup_Xinits.trivial}
+\alias{setup_Xinits.trivial}
\title{Setup Xinits.trivial}
\usage{
-\method{make_Xinits}{trivial}(pars, H, i, Xopts = list())
+\method{setup_Xinits}{trivial}(pars, H, i, Xopts = list())
}
\arguments{
\item{pars}{an \strong{\code{xds}} object}
@@ -19,5 +19,5 @@
a \link{list} vector
}
\description{
-Implements \link{make_Xinits} for the trivial model
+Implements \link{setup_Xinits} for the trivial model
}
diff --git a/man/make_Xpar.Rd b/man/setup_Xpar.Rd
similarity index 85%
rename from man/make_Xpar.Rd
rename to man/setup_Xpar.Rd
index 592572d5f..0e9d00d4b 100644
--- a/man/make_Xpar.Rd
+++ b/man/setup_Xpar.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-interface.R
-\name{make_Xpar}
-\alias{make_Xpar}
+\name{setup_Xpar}
+\alias{setup_Xpar}
\title{Make Parameters for a \eqn{cal X} - Component Model}
\usage{
-make_Xpar(Xname, pars, i, Xopts = list())
+setup_Xpar(Xname, pars, i, Xopts = list())
}
\arguments{
\item{Xname}{a \link{character} string}
diff --git a/man/make_Xpar.SIS.Rd b/man/setup_Xpar.SIS.Rd
similarity index 68%
rename from man/make_Xpar.SIS.Rd
rename to man/setup_Xpar.SIS.Rd
index 6a3054419..e34a5243b 100644
--- a/man/make_Xpar.SIS.Rd
+++ b/man/setup_Xpar.SIS.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-SIS.R
-\name{make_Xpar.SIS}
-\alias{make_Xpar.SIS}
+\name{setup_Xpar.SIS}
+\alias{setup_Xpar.SIS}
\title{Setup Xpar.SIS}
\usage{
-\method{make_Xpar}{SIS}(Xname, pars, i, Xopts = list())
+\method{setup_Xpar}{SIS}(Xname, pars, i, Xopts = list())
}
\arguments{
\item{Xname}{a \link{character} string}
@@ -19,5 +19,5 @@
a \link{list} vector
}
\description{
-Implements \link{make_Xpar} for the SIS model
+Implements \link{setup_Xpar} for the SIS model
}
diff --git a/man/make_Xpar.hMoI.Rd b/man/setup_Xpar.hMoI.Rd
similarity index 68%
rename from man/make_Xpar.hMoI.Rd
rename to man/setup_Xpar.hMoI.Rd
index 137e140e0..514d10403 100644
--- a/man/make_Xpar.hMoI.Rd
+++ b/man/setup_Xpar.hMoI.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-hMoI.R
-\name{make_Xpar.hMoI}
-\alias{make_Xpar.hMoI}
+\name{setup_Xpar.hMoI}
+\alias{setup_Xpar.hMoI}
\title{Setup Xpar.hMoI}
\usage{
-\method{make_Xpar}{hMoI}(Xname, pars, i, Xopts = list())
+\method{setup_Xpar}{hMoI}(Xname, pars, i, Xopts = list())
}
\arguments{
\item{Xname}{a \link{character} string}
@@ -19,5 +19,5 @@
a \link{list} vector
}
\description{
-Implements \link{make_Xpar} for the hMoI model
+Implements \link{setup_Xpar} for the hMoI model
}
diff --git a/man/make_Xpar.trivial.Rd b/man/setup_Xpar.trivial.Rd
similarity index 67%
rename from man/make_Xpar.trivial.Rd
rename to man/setup_Xpar.trivial.Rd
index 50c05a17e..3cf6ce55f 100644
--- a/man/make_Xpar.trivial.Rd
+++ b/man/setup_Xpar.trivial.Rd
@@ -1,10 +1,10 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/human-trivial.R
-\name{make_Xpar.trivial}
-\alias{make_Xpar.trivial}
+\name{setup_Xpar.trivial}
+\alias{setup_Xpar.trivial}
\title{xde_setup Xpar.trivial}
\usage{
-\method{make_Xpar}{trivial}(Xname, pars, i, Xopts = list())
+\method{setup_Xpar}{trivial}(Xname, pars, i, Xopts = list())
}
\arguments{
\item{Xname}{a \link{character} string}
@@ -19,5 +19,5 @@
a \link{list} vectord
}
\description{
-Implements \link{make_Xpar} for the trivial model
+Implements \link{setup_Xpar} for the trivial model
}
diff --git a/vignettes/adult_RM.Rmd b/vignettes/adult_RM.Rmd
index 443361248..3c3ec633f 100644
--- a/vignettes/adult_RM.Rmd
+++ b/vignettes/adult_RM.Rmd
@@ -249,8 +249,8 @@ We use `ramp.xds::make_inits_MYZ_RM_xde` to store the initial values. These equa
params <- make_xds_template("dde", "mosy", nPatches, 1:3, 1:3)
params <- setup_MYZpar("macdonald", params, 1, MYZo)
params <- setup_MYZinits(params, 1, MYZo)
-params <- make_Xpar("trivial", params, 1, Xo)
-params <- make_Xinits(params, HPop, 1)
+params <- setup_Xpar("trivial", params, 1, Xo)
+params <- setup_Xinits(params, HPop, 1)
params <- setup_Lpar("trivial", params, 1, Lo)
params <- setup_Linits(params, 1, Lo)
params <- setup_Hpar_static(params, 1)
diff --git a/vignettes/aqua_trace.Rmd b/vignettes/aqua_trace.Rmd
index 9201cc1a5..50ba13c2e 100644
--- a/vignettes/aqua_trace.Rmd
+++ b/vignettes/aqua_trace.Rmd
@@ -134,7 +134,7 @@ params = setup_MYZinits(params, 1, list(M=M_eq, P=P_eq))
```{r}
-params = make_Xpar("trivial", params, 1, list(HPop=HPop))
+params = setup_Xpar("trivial", params, 1, list(HPop=HPop))
```
diff --git a/vignettes/ex_534.Rmd b/vignettes/ex_534.Rmd
index ef9c48d22..582c83407 100644
--- a/vignettes/ex_534.Rmd
+++ b/vignettes/ex_534.Rmd
@@ -306,7 +306,7 @@ names(MYZpar)
We use a static demographic model, which assumes a constant population size (constant $H$).
-The 5-3-4 model uses the basic SIS (Susceptible-Infected-Susceptible) model for the human component (see more [here](human_sis.html)). It can be configured using `ramp.xds::xde_make_Xpar_SIS.`
+The 5-3-4 model uses the basic SIS (Susceptible-Infected-Susceptible) model for the human component (see more [here](human_sis.html)). It can be configured using `ramp.xds::xde_setup_Xpar_SIS.`
```{r X parameters}
@@ -318,7 +318,7 @@ c <- c(0.1, .02, .1, .02)
The model is configured and assigned the name `Xpar`:
```{r Xpar}
-Xpar <- create_Xpar_SIS(nStrata, list(), b, r, c)
+Xpar <- make_Xpar_SIS(nStrata, list(), b, r, c)
```
## Initial Conditions
@@ -426,7 +426,7 @@ params$Xpar[[1]] = Xpar
```{r}
params <- setup_Linits(params, 1, Linits)
params <- setup_MYZinits(params, 1, MYZinits)
-params <- make_Xinits(params, HPop, 1, Xinits)
+params <- setup_Xinits(params, HPop, 1, Xinits)
```
```{r}
diff --git a/vignettes/human_hmoi.Rmd b/vignettes/human_hmoi.Rmd
index 6150365a0..27774c98f 100644
--- a/vignettes/human_hmoi.Rmd
+++ b/vignettes/human_hmoi.Rmd
@@ -106,8 +106,8 @@ eir <- h/b
```
```{r}
-params = make_Xpar("hMoI", params, 1, Xo)
-params = make_Xinits(params, H, 1, Xo)
+params = setup_Xpar("hMoI", params, 1, Xo)
+params = setup_Xinits(params, H, 1, Xo)
```
diff --git a/vignettes/human_sis.Rmd b/vignettes/human_sis.Rmd
index 34e9d4132..51156459e 100644
--- a/vignettes/human_sis.Rmd
+++ b/vignettes/human_sis.Rmd
@@ -108,8 +108,8 @@ Xo$I=ss$I
```{r}
-params <- make_Xpar("SIS", params, 1, Xo)
-params <- make_Xinits(params, H, 1, Xo)
+params <- setup_Xpar("SIS", params, 1, Xo)
+params <- setup_Xinits(params, H, 1, Xo)
params <- setup_Hpar_static(params, 1)
params <- setup_MYZpar("trivial", params, 1)
params <- setup_Lpar("trivial", params, 1)
@@ -139,7 +139,7 @@ params = make_indices(params)
```{r}
Xo$S=H
Xo$I=H*0
-params = make_Xinits(params, H, 1, Xopts = Xo)
+params = setup_Xinits(params, H, 1, Xopts = Xo)
y0 <- get_inits(params)
y0$X
```
|