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

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 ```