From 0b90e655bf3756fe3b23ee75f398791bfd9e7624 Mon Sep 17 00:00:00 2001 From: David Smith Date: Thu, 3 Oct 2024 17:25:15 -0700 Subject: [PATCH 1/2] renamed functions make_indices_MYZ renamed to setup_MYZix setup_indices_L renamed to setup_Lix setup_X_indices renamed to setup_Xix --- NAMESPACE | 28 +++++++++---------- R/adult-GeRM.R | 6 ++-- R/adult-RM-dts.R | 6 ++-- R/adult-basicM.R | 6 ++-- R/adult-interface.R | 4 +-- R/adult-macdonald.R | 6 ++-- R/adult-si.R | 6 ++-- R/adult-trivial.R | 6 ++-- R/aquatic-basicL.R | 4 +-- R/aquatic-interface.R | 4 +-- R/aquatic-trivial.R | 6 ++-- R/human-SIS.R | 6 ++-- R/human-hMoI.R | 6 ++-- R/human-interface.R | 4 +-- R/human-trivial.R | 6 ++-- R/utils.R | 6 ++-- _pkgdown.yml | 28 +++++++++---------- docs/pkgdown.yml | 2 +- docs/reference/index.html | 28 +++++++++---------- man/{setup_indices_L.Rd => setup_Lix.Rd} | 6 ++-- ...ndices_L.basicL.Rd => setup_Lix.basicL.Rd} | 6 ++-- ...ices_L.trivial.Rd => setup_Lix.trivial.Rd} | 8 +++--- ...ndices_MYZ.GeRM.Rd => setup_MYZix.GeRM.Rd} | 8 +++--- ...es_MYZ.RM_dts.Rd => setup_MYZix.RM_dts.Rd} | 8 +++--- man/{make_indices_MYZ.Rd => setup_MYZix.Rd} | 6 ++-- ...ke_indices_MYZ.si.Rd => setup_MYZix.SI.Rd} | 8 +++--- ...es_MYZ.basicM.Rd => setup_MYZix.basicM.Rd} | 8 +++--- ....macdonald.Rd => setup_MYZix.macdonald.Rd} | 8 +++--- ..._MYZ.trivial.Rd => setup_MYZix.trivial.Rd} | 8 +++--- man/{setup_X_indices.Rd => setup_Xix.Rd} | 6 ++-- ...etup_X_indices.SIS.Rd => setup_Xix.SIS.Rd} | 8 +++--- ...up_X_indices.hMoI.Rd => setup_Xix.hMoI.Rd} | 8 +++--- ...ndices.trivial.Rd => setup_Xix.trivial.Rd} | 8 +++--- 33 files changed, 136 insertions(+), 136 deletions(-) rename man/{setup_indices_L.Rd => setup_Lix.Rd} (84%) rename man/{setup_indices_L.basicL.Rd => setup_Lix.basicL.Rd} (80%) rename man/{setup_indices_L.trivial.Rd => setup_Lix.trivial.Rd} (64%) rename man/{make_indices_MYZ.GeRM.Rd => setup_MYZix.GeRM.Rd} (63%) rename man/{make_indices_MYZ.RM_dts.Rd => setup_MYZix.RM_dts.Rd} (62%) rename man/{make_indices_MYZ.Rd => setup_MYZix.Rd} (81%) rename man/{make_indices_MYZ.si.Rd => setup_MYZix.SI.Rd} (63%) rename man/{make_indices_MYZ.basicM.Rd => setup_MYZix.basicM.Rd} (61%) rename man/{make_indices_MYZ.macdonald.Rd => setup_MYZix.macdonald.Rd} (61%) rename man/{make_indices_MYZ.trivial.Rd => setup_MYZix.trivial.Rd} (59%) rename man/{setup_X_indices.Rd => setup_Xix.Rd} (83%) rename man/{setup_X_indices.SIS.Rd => setup_Xix.SIS.Rd} (65%) rename man/{setup_X_indices.hMoI.Rd => setup_Xix.hMoI.Rd} (64%) rename man/{setup_X_indices.trivial.Rd => setup_Xix.trivial.Rd} (63%) diff --git a/NAMESPACE b/NAMESPACE index e5c81eba1..908a65309 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -231,12 +231,6 @@ S3method(make_function,sharkfin) S3method(make_function,sigmoid) S3method(make_function,sin) S3method(make_function,sum) -S3method(make_indices_MYZ,GeRM) -S3method(make_indices_MYZ,RM_dts) -S3method(make_indices_MYZ,SI) -S3method(make_indices_MYZ,basicM) -S3method(make_indices_MYZ,macdonald) -S3method(make_indices_MYZ,trivial) S3method(make_runtime,dts) S3method(make_runtime,xde) S3method(parse_Lorbits,basicL) @@ -277,6 +271,8 @@ S3method(set_eir,cohort) S3method(setup_EIP,fixedlag_dts) S3method(setup_Linits,basicL) S3method(setup_Linits,trivial) +S3method(setup_Lix,basicL) +S3method(setup_Lix,trivial) S3method(setup_Lpar,basicL) S3method(setup_Lpar,trivial) S3method(setup_MYZinits,GeRM) @@ -285,17 +281,23 @@ S3method(setup_MYZinits,SI) S3method(setup_MYZinits,basicM) S3method(setup_MYZinits,macdonald) S3method(setup_MYZinits,trivial) +S3method(setup_MYZix,GeRM) +S3method(setup_MYZix,RM_dts) +S3method(setup_MYZix,SI) +S3method(setup_MYZix,basicM) +S3method(setup_MYZix,macdonald) +S3method(setup_MYZix,trivial) S3method(setup_MYZpar,GeRM) 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_Xix,SIS) +S3method(setup_Xix,hMoI) +S3method(setup_Xix,trivial) S3method(setup_Xpar,SIS) S3method(setup_Xpar,hMoI) S3method(setup_Xpar,trivial) @@ -306,8 +308,6 @@ S3method(setup_exposure_pois,dts) S3method(setup_exposure_pois,xde) S3method(setup_humidity,func) S3method(setup_hydrology,func) -S3method(setup_indices_L,basicL) -S3method(setup_indices_L,trivial) S3method(setup_rainfall,func) S3method(setup_shock,func) S3method(setup_temperature,func) @@ -531,7 +531,6 @@ export(make_calU) export(make_eggs_laid) export(make_function) export(make_indices) -export(make_indices_MYZ) export(make_kappa) export(make_local_frac) export(make_parameters_demography_null) @@ -570,12 +569,14 @@ export(setup_EGG_LAYING) export(setup_EIP) export(setup_Hpar_static) export(setup_Linits) +export(setup_Lix) export(setup_Lpar) export(setup_MYZinits) +export(setup_MYZix) export(setup_MYZpar) export(setup_TRANSMISSION) -export(setup_X_indices) export(setup_Xinits) +export(setup_Xix) export(setup_Xpar) export(setup_care_seeking_no_behavior) export(setup_development) @@ -589,7 +590,6 @@ export(setup_humidity) export(setup_humidity_func) export(setup_hydrology) export(setup_hydrology_func) -export(setup_indices_L) export(setup_no_active_case_detection) export(setup_no_area_spray) export(setup_no_bednets) diff --git a/R/adult-GeRM.R b/R/adult-GeRM.R index c0e100d49..ce5ffb547 100644 --- a/R/adult-GeRM.R +++ b/R/adult-GeRM.R @@ -448,12 +448,12 @@ xde_steady_state_MYZ.GeRM = function(Lambda, kappa, MYZpar){with(MYZpar,{ #' @title Add indices for adult mosquitoes to parameter list -#' @description Implements [make_indices_MYZ] for the GeRM model. -#' @inheritParams make_indices_MYZ +#' @description Implements [setup_MYZix] for the GeRM model. +#' @inheritParams setup_MYZix #' @return a [list] #' @importFrom utils tail #' @export -make_indices_MYZ.GeRM <- function(pars, s) {with(pars,{ +setup_MYZix.GeRM <- function(pars, s) {with(pars,{ M_ix <- seq(from = max_ix+1, length.out=nPatches) max_ix <- tail(M_ix, 1) diff --git a/R/adult-RM-dts.R b/R/adult-RM-dts.R index 2224ad414..64e16298a 100644 --- a/R/adult-RM-dts.R +++ b/R/adult-RM-dts.R @@ -99,12 +99,12 @@ make_MYZinits_RM_dts = function(nPatches, max_eip, MYZopts = list(), #' @title Add indices for adult mosquitoes to parameter list -#' @description Implements [make_indices_MYZ] for the RM_dts model. -#' @inheritParams make_indices_MYZ +#' @description Implements [setup_MYZix] for the RM_dts model. +#' @inheritParams setup_MYZix #' @return a [list] #' @importFrom utils tail #' @export -make_indices_MYZ.RM_dts <- function(pars, s) {with(pars,{ +setup_MYZix.RM_dts <- function(pars, s) {with(pars,{ M_ix <- seq(from = max_ix+1, length.out=nPatches) max_ix <- tail(M_ix, 1) diff --git a/R/adult-basicM.R b/R/adult-basicM.R index ba532dbc3..196baff28 100644 --- a/R/adult-basicM.R +++ b/R/adult-basicM.R @@ -267,12 +267,12 @@ set_MYZpars.GeRM <- function(pars, s=1, MYZopts=list()) { }))} #' @title Add indices for adult mosquitoes to parameter list -#' @description Implements [make_indices_MYZ] for the basic M model. -#' @inheritParams make_indices_MYZ +#' @description Implements [setup_MYZix] for the basic M model. +#' @inheritParams setup_MYZix #' @return none #' @importFrom utils tail #' @export -make_indices_MYZ.basicM <- function(pars, s) {with(pars,{ +setup_MYZix.basicM <- function(pars, s) {with(pars,{ M_ix <- seq(from = max_ix+1, length.out = nPatches) max_ix <- tail(M_ix, 1) diff --git a/R/adult-interface.R b/R/adult-interface.R index 6e4ff8bb1..9d1f93a08 100644 --- a/R/adult-interface.R +++ b/R/adult-interface.R @@ -197,8 +197,8 @@ set_MYZinits <- function(pars, s=1, MYZopts=list()) { #' @param s the species index #' @return [list] #' @export -make_indices_MYZ <- function(pars, s) { - UseMethod("make_indices_MYZ", pars$MYZpar[[s]]) +setup_MYZix <- function(pars, s) { + UseMethod("setup_MYZix", pars$MYZpar[[s]]) } #' @title Parse the outputs and return the variables by name in a list diff --git a/R/adult-macdonald.R b/R/adult-macdonald.R index 8d1af4131..5ad716c7b 100644 --- a/R/adult-macdonald.R +++ b/R/adult-macdonald.R @@ -282,12 +282,12 @@ xde_steady_state_MYZ.macdonald = function(Lambda, kappa, MYZpar){with(MYZpar,{ #' @title Add indices for adult mosquitoes to parameter list -#' @description Implements [make_indices_MYZ] for the macdonald model. -#' @inheritParams make_indices_MYZ +#' @description Implements [setup_MYZix] for the macdonald model. +#' @inheritParams setup_MYZix #' @return a [list] #' @importFrom utils tail #' @export -make_indices_MYZ.macdonald <- function(pars, s) {with(pars,{ +setup_MYZix.macdonald <- function(pars, s) {with(pars,{ M_ix <- seq(from = max_ix+1, length.out=nPatches) max_ix <- tail(M_ix, 1) diff --git a/R/adult-si.R b/R/adult-si.R index c7c99ea09..9186aaf04 100644 --- a/R/adult-si.R +++ b/R/adult-si.R @@ -355,12 +355,12 @@ put_MYZvars.SI <- function(MYZvars, y, pars, s){ } #' @title Add indices for adult mosquitoes to parameter list -#' @description Implements [make_indices_MYZ] for the `SI` model. -#' @inheritParams make_indices_MYZ +#' @description Implements [setup_MYZix] for the `SI` model. +#' @inheritParams setup_MYZix #' @return a [list] #' @importFrom utils tail #' @export -make_indices_MYZ.SI <- function(pars, s) {with(pars,{ +setup_MYZix.SI <- function(pars, s) {with(pars,{ M_ix <- seq(from = max_ix+1, length.out=nPatches) max_ix <- tail(M_ix, 1) diff --git a/R/adult-trivial.R b/R/adult-trivial.R index 4a3b879f5..687de9a81 100644 --- a/R/adult-trivial.R +++ b/R/adult-trivial.R @@ -201,11 +201,11 @@ setup_MYZinits.trivial = function(pars, s, MYZopts=NULL){ } #' @title Add indices for aquatic stage mosquitoes to parameter list -#' @description Implements [make_indices_MYZ] for trivial (forced emergence) model. -#' @inheritParams make_indices_MYZ +#' @description Implements [setup_MYZix] for trivial (forced emergence) model. +#' @inheritParams setup_MYZix #' @return none #' @export -make_indices_MYZ.trivial <- function(pars, s) { +setup_MYZix.trivial <- function(pars, s) { return(pars) } diff --git a/R/aquatic-basicL.R b/R/aquatic-basicL.R index 43935310a..39b909140 100644 --- a/R/aquatic-basicL.R +++ b/R/aquatic-basicL.R @@ -246,11 +246,11 @@ update_Linits.basicL <- function(pars, y, s) { #' @title Setup Variable Indices for `basicL` (**L** Component) #' @description Set the values of the indices for the **L** component variables #' for the `basicL` module -#' @inheritParams setup_indices_L +#' @inheritParams setup_Lix #' @return an **`xds`** object #' @importFrom utils tail #' @export -setup_indices_L.basicL <- function(pars, s) {with(pars,{ +setup_Lix.basicL <- function(pars, s) {with(pars,{ L_ix <- seq(from = max_ix+1, length.out = nHabitats) max_ix <- tail(L_ix, 1) diff --git a/R/aquatic-interface.R b/R/aquatic-interface.R index d06f3401e..cf56935ef 100644 --- a/R/aquatic-interface.R +++ b/R/aquatic-interface.R @@ -171,8 +171,8 @@ update_Linits <- function(pars, y, s) { #' @param s the species index #' @return an **`xds`** object #' @export -setup_indices_L <- function(pars, s) { - UseMethod("setup_indices_L", pars$Lpar[[s]]) +setup_Lix <- function(pars, s) { + UseMethod("setup_Lix", pars$Lpar[[s]]) } #' @title Parse **L** Component Outputs diff --git a/R/aquatic-trivial.R b/R/aquatic-trivial.R index 9f3e9a656..7ca207a63 100644 --- a/R/aquatic-trivial.R +++ b/R/aquatic-trivial.R @@ -154,11 +154,11 @@ update_Linits.trivial<- function(pars, y, s) { } #' @title Setup Variable Indices for `trivial` (**L** Component) -#' @description Implements [setup_indices_L] for trivial (forced emergence) model. -#' @inheritParams setup_indices_L +#' @description Implements [setup_Lix] for trivial (forced emergence) model. +#' @inheritParams setup_Lix #' @return an **`xds`** object #' @export -setup_indices_L.trivial <- function(pars, s) { +setup_Lix.trivial <- function(pars, s) { return(pars) } diff --git a/R/human-SIS.R b/R/human-SIS.R index 87b93cfd3..0a85fbd66 100644 --- a/R/human-SIS.R +++ b/R/human-SIS.R @@ -228,12 +228,12 @@ get_Xinits.SIS <- function(pars, i=1){pars$Xinits[[i]]} #' @title Add indices for human population to parameter list -#' @description Implements [setup_X_indices] for the SIS model. -#' @inheritParams setup_X_indices +#' @description Implements [setup_Xix] for the SIS model. +#' @inheritParams setup_Xix #' @return none #' @importFrom utils tail #' @export -setup_X_indices.SIS <- function(pars, i) {with(pars,{ +setup_Xix.SIS <- function(pars, i) {with(pars,{ S_ix <- seq(from = max_ix+1, length.out=nStrata[i]) max_ix <- tail(S_ix, 1) diff --git a/R/human-hMoI.R b/R/human-hMoI.R index 05fec3daf..412f41a2d 100644 --- a/R/human-hMoI.R +++ b/R/human-hMoI.R @@ -191,12 +191,12 @@ HTC.hMoI <- function(pars, i) { } #' @title Add indices for human population to parameter list -#' @description Implements [setup_X_indices] for the hybrid MoI model. -#' @inheritParams setup_X_indices +#' @description Implements [setup_Xix] for the hybrid MoI model. +#' @inheritParams setup_Xix #' @return none #' @importFrom utils tail #' @export -setup_X_indices.hMoI <- function(pars, i) {with(pars,{ +setup_Xix.hMoI <- function(pars, i) {with(pars,{ m1_ix <- seq(from = max_ix+1, length.out=nStrata[i]) max_ix <- tail(m1_ix, 1) diff --git a/R/human-interface.R b/R/human-interface.R index baddda81a..6a5fa01f5 100644 --- a/R/human-interface.R +++ b/R/human-interface.R @@ -108,8 +108,8 @@ setup_Xinits = function(pars, H, i, Xopts=list()){ #' @param i the host species index #' @return an **`xds`** object #' @export -setup_X_indices <- function(pars, i) { - UseMethod("setup_X_indices", pars$Xpar[[i]]) +setup_Xix <- function(pars, i) { + UseMethod("setup_Xix", pars$Xpar[[i]]) } #' @title Return the variables as a list diff --git a/R/human-trivial.R b/R/human-trivial.R index f92d49ccc..2d4ecc3c9 100644 --- a/R/human-trivial.R +++ b/R/human-trivial.R @@ -140,12 +140,12 @@ setup_Xinits.trivial = function(pars, H, i, Xopts=list()){ } #' @title Add indices for human population to parameter list -#' @description Implements [setup_X_indices] for the trivial model. -#' @inheritParams setup_X_indices +#' @description Implements [setup_Xix] for the trivial model. +#' @inheritParams setup_Xix #' @return none #' @importFrom utils tail #' @export -setup_X_indices.trivial <- function(pars, i) { +setup_Xix.trivial <- function(pars, i) { return(pars) } diff --git a/R/utils.R b/R/utils.R index 65d1bfa2d..45e69b47c 100644 --- a/R/utils.R +++ b/R/utils.R @@ -9,17 +9,17 @@ make_indices <- function(pars) { s = length(pars$Linits) if(s>0) for(ix in 1:s) - pars = setup_indices_L(pars, ix) + pars = setup_Lix(pars, ix) s = length(pars$MYZinits) if(s>0) for(ix in 1:s) - pars = make_indices_MYZ(pars, ix) + pars = setup_MYZix(pars, ix) i = length(pars$Xinits) if(i>0) for(ix in 1:i) - pars = setup_X_indices(pars, ix) + pars = setup_Xix(pars, ix) return(pars) } diff --git a/_pkgdown.yml b/_pkgdown.yml index 2c12055ea..5d124f660 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -272,7 +272,7 @@ reference: - get_MYZinits - set_MYZinits - update_MYZinits - - make_indices_MYZ + - setup_MYZix - parse_MYZorbits - subtitle: Visualization for Adult Mosquito desc: | @@ -334,7 +334,7 @@ reference: - make_MYZpar_trivial - xde_steady_state_MYZ.trivial - setup_MYZinits.trivial - - make_indices_MYZ.trivial + - setup_MYZix.trivial - parse_MYZorbits.trivial - get_MYZinits.trivial - update_MYZinits.trivial @@ -353,7 +353,7 @@ reference: - F_eggs.basicM - setup_MYZinits.basicM - make_MYZinits_basicM - - make_indices_MYZ.basicM + - setup_MYZix.basicM - list_MYZvars.basicM - get_MYZpars.basicM - set_MYZpars.basicM @@ -382,7 +382,7 @@ reference: - put_MYZvars.SI - setup_MYZinits.SI - make_MYZinits_SI - - make_indices_MYZ.SI + - setup_MYZix.SI - parse_MYZorbits.SI - get_MYZinits.SI - update_MYZinits.SI @@ -411,7 +411,7 @@ reference: - make_MYZinits_macdonald - get_MYZinits.macdonald - update_MYZinits.macdonald - - make_indices_MYZ.macdonald + - setup_MYZix.macdonald - parse_MYZorbits.macdonald - get_f.macdonald - get_q.macdonald @@ -439,7 +439,7 @@ reference: - make_MYZinits_GeRM - get_MYZinits.GeRM - update_MYZinits.GeRM - - make_indices_MYZ.GeRM + - setup_MYZix.GeRM - parse_MYZorbits.GeRM - get_f.GeRM - get_q.GeRM @@ -457,7 +457,7 @@ reference: - list_MYZvars.RM_dts - put_MYZvars.RM_dts - make_MYZinits_RM_dts - - make_indices_MYZ.RM_dts + - setup_MYZix.RM_dts - parse_MYZorbits.RM_dts - get_MYZinits.RM_dts - update_MYZinits.RM_dts @@ -478,7 +478,7 @@ reference: - list_Lvars - get_Lpars - set_Lpars - - setup_indices_L + - setup_Lix - parse_Lorbits - get_Linits - set_Linits @@ -500,7 +500,7 @@ reference: - get_Lpars.trivial - set_Lpars.trivial - set_Linits.trivial - - setup_indices_L.trivial + - setup_Lix.trivial - parse_Lorbits.trivial - update_Linits.trivial - subtitle: basicL @@ -521,7 +521,7 @@ reference: - get_Lpars.basicL - set_Lpars.basicL - set_Linits.basicL - - setup_indices_L.basicL + - setup_Lix.basicL - parse_Lorbits.basicL - update_Linits.basicL - title: Mosquito Bionomics @@ -571,7 +571,7 @@ reference: - dXdt - Update_Xt - setup_Xinits - - setup_X_indices + - setup_Xix - list_Xvars - get_Xpars - set_Xpars @@ -610,7 +610,7 @@ reference: - setup_Xpar.trivial - make_Xpar_trivial - setup_Xinits.trivial - - setup_X_indices.trivial + - setup_Xix.trivial - parse_Xorbits.trivial - get_Xinits.trivial - set_Xinits.trivial @@ -627,7 +627,7 @@ reference: - xde_steady_state_X.hMoI - setup_Xinits.hMoI - make_Xinits_hMoI - - setup_X_indices.hMoI + - setup_Xix.hMoI - F_X.hMoI - F_H.hMoI - F_b.hMoI @@ -652,7 +652,7 @@ reference: - make_Xpar_SIS - setup_Xinits.SIS - make_Xinits_SIS - - setup_X_indices.SIS + - setup_Xix.SIS - list_Xvars.SIS - get_Xpars.SIS - set_Xpars.SIS diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index b692cbcb9..4a101ca52 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: 2024-10-04T00:02Z +last_built: 2024-10-04T00:19Z 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 af11ac04c..818308061 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -767,7 +767,7 @@

Adult Mosquito Dynamics make_indices_MYZ()

+

setup_MYZix()

Add indices for adult mosquitoes to parameter list

@@ -967,7 +967,7 @@

trivial

make_indices_MYZ(<trivial>)

+

setup_MYZix(<trivial>)

Add indices for aquatic stage mosquitoes to parameter list

@@ -1031,7 +1031,7 @@

basicM <

Make inits for basicM adult mosquito model

-

make_indices_MYZ(<basicM>)

+

setup_MYZix(<basicM>)

Add indices for adult mosquitoes to parameter list

@@ -1135,7 +1135,7 @@

The “SI” model for infection make_indices_MYZ(<SI>)

+

setup_MYZix(<SI>)

Add indices for adult mosquitoes to parameter list

@@ -1239,7 +1239,7 @@

macdonald make_indices_MYZ(<macdonald>)

+

setup_MYZix(<macdonald>)

Add indices for adult mosquitoes to parameter list

@@ -1339,7 +1339,7 @@

GeRM

Update inits for GeRM adult mosquito model

-

make_indices_MYZ(<GeRM>)

+

setup_MYZix(<GeRM>)

Add indices for adult mosquitoes to parameter list

@@ -1399,7 +1399,7 @@

RM-Mosquito in discrete-time make_indices_MYZ(<RM_dts>)

+

setup_MYZix(<RM_dts>)

Add indices for adult mosquitoes to parameter list

@@ -1471,7 +1471,7 @@

Aquatic Mosquito Dynamics setup_indices_L()

+

setup_Lix()

Set the Values of the Indices for L Component Modules

@@ -1547,7 +1547,7 @@

trivial

setup_indices_L(<trivial>)

+

setup_Lix(<trivial>)

Setup Variable Indices for trivial (L Component)

@@ -1619,7 +1619,7 @@

basicL <

Set the Initial Values for basicL (L Component)

-

setup_indices_L(<basicL>)

+

setup_Lix(<basicL>)

Setup Variable Indices for basicL (L Component)

@@ -1771,7 +1771,7 @@

Human Infection Dynamics setup_X_indices()

+

setup_Xix()

Add indices for human population to parameter list

@@ -1915,7 +1915,7 @@

trivial

setup_X_indices(<trivial>)

+

setup_Xix(<trivial>)

Add indices for human population to parameter list

@@ -1971,7 +1971,7 @@

hMoI

Make inits for hybrid MoI human model

-

setup_X_indices(<hMoI>)

+

setup_Xix(<hMoI>)

Add indices for human population to parameter list

@@ -2059,7 +2059,7 @@

SIS

Make initial values for the SIS xde human model, with defaults

-

setup_X_indices(<SIS>)

+

setup_Xix(<SIS>)

Add indices for human population to parameter list

diff --git a/man/setup_indices_L.Rd b/man/setup_Lix.Rd similarity index 84% rename from man/setup_indices_L.Rd rename to man/setup_Lix.Rd index e65abc794..5cacf05b1 100644 --- a/man/setup_indices_L.Rd +++ b/man/setup_Lix.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/aquatic-interface.R -\name{setup_indices_L} -\alias{setup_indices_L} +\name{setup_Lix} +\alias{setup_Lix} \title{Set the Values of the Indices for \strong{L} Component Modules} \usage{ -setup_indices_L(pars, s) +setup_Lix(pars, s) } \arguments{ \item{pars}{an \strong{\code{xds}} object} diff --git a/man/setup_indices_L.basicL.Rd b/man/setup_Lix.basicL.Rd similarity index 80% rename from man/setup_indices_L.basicL.Rd rename to man/setup_Lix.basicL.Rd index 5d4b4a351..e9a9b241c 100644 --- a/man/setup_indices_L.basicL.Rd +++ b/man/setup_Lix.basicL.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/aquatic-basicL.R -\name{setup_indices_L.basicL} -\alias{setup_indices_L.basicL} +\name{setup_Lix.basicL} +\alias{setup_Lix.basicL} \title{Setup Variable Indices for \code{basicL} (\strong{L} Component)} \usage{ -\method{setup_indices_L}{basicL}(pars, s) +\method{setup_Lix}{basicL}(pars, s) } \arguments{ \item{pars}{an \strong{\code{xds}} object} diff --git a/man/setup_indices_L.trivial.Rd b/man/setup_Lix.trivial.Rd similarity index 64% rename from man/setup_indices_L.trivial.Rd rename to man/setup_Lix.trivial.Rd index 12b92220c..9f11745a7 100644 --- a/man/setup_indices_L.trivial.Rd +++ b/man/setup_Lix.trivial.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/aquatic-trivial.R -\name{setup_indices_L.trivial} -\alias{setup_indices_L.trivial} +\name{setup_Lix.trivial} +\alias{setup_Lix.trivial} \title{Setup Variable Indices for \code{trivial} (\strong{L} Component)} \usage{ -\method{setup_indices_L}{trivial}(pars, s) +\method{setup_Lix}{trivial}(pars, s) } \arguments{ \item{pars}{an \strong{\code{xds}} object} @@ -15,5 +15,5 @@ an \strong{\code{xds}} object } \description{ -Implements \link{setup_indices_L} for trivial (forced emergence) model. +Implements \link{setup_Lix} for trivial (forced emergence) model. } diff --git a/man/make_indices_MYZ.GeRM.Rd b/man/setup_MYZix.GeRM.Rd similarity index 63% rename from man/make_indices_MYZ.GeRM.Rd rename to man/setup_MYZix.GeRM.Rd index 6874bcb65..63eb2bdc0 100644 --- a/man/make_indices_MYZ.GeRM.Rd +++ b/man/setup_MYZix.GeRM.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-GeRM.R -\name{make_indices_MYZ.GeRM} -\alias{make_indices_MYZ.GeRM} +\name{setup_MYZix.GeRM} +\alias{setup_MYZix.GeRM} \title{Add indices for adult mosquitoes to parameter list} \usage{ -\method{make_indices_MYZ}{GeRM}(pars, s) +\method{setup_MYZix}{GeRM}(pars, s) } \arguments{ \item{pars}{a \link{list}} @@ -15,5 +15,5 @@ a \link{list} } \description{ -Implements \link{make_indices_MYZ} for the GeRM model. +Implements \link{setup_MYZix} for the GeRM model. } diff --git a/man/make_indices_MYZ.RM_dts.Rd b/man/setup_MYZix.RM_dts.Rd similarity index 62% rename from man/make_indices_MYZ.RM_dts.Rd rename to man/setup_MYZix.RM_dts.Rd index d276a1518..f5c54d218 100644 --- a/man/make_indices_MYZ.RM_dts.Rd +++ b/man/setup_MYZix.RM_dts.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-RM-dts.R -\name{make_indices_MYZ.RM_dts} -\alias{make_indices_MYZ.RM_dts} +\name{setup_MYZix.RM_dts} +\alias{setup_MYZix.RM_dts} \title{Add indices for adult mosquitoes to parameter list} \usage{ -\method{make_indices_MYZ}{RM_dts}(pars, s) +\method{setup_MYZix}{RM_dts}(pars, s) } \arguments{ \item{pars}{a \link{list}} @@ -15,5 +15,5 @@ a \link{list} } \description{ -Implements \link{make_indices_MYZ} for the RM_dts model. +Implements \link{setup_MYZix} for the RM_dts model. } diff --git a/man/make_indices_MYZ.Rd b/man/setup_MYZix.Rd similarity index 81% rename from man/make_indices_MYZ.Rd rename to man/setup_MYZix.Rd index d90211e74..2e3a3b93c 100644 --- a/man/make_indices_MYZ.Rd +++ b/man/setup_MYZix.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-interface.R -\name{make_indices_MYZ} -\alias{make_indices_MYZ} +\name{setup_MYZix} +\alias{setup_MYZix} \title{Add indices for adult mosquitoes to parameter list} \usage{ -make_indices_MYZ(pars, s) +setup_MYZix(pars, s) } \arguments{ \item{pars}{a \link{list}} diff --git a/man/make_indices_MYZ.si.Rd b/man/setup_MYZix.SI.Rd similarity index 63% rename from man/make_indices_MYZ.si.Rd rename to man/setup_MYZix.SI.Rd index 80be3ccfa..c2eda1592 100644 --- a/man/make_indices_MYZ.si.Rd +++ b/man/setup_MYZix.SI.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-SI.R -\name{make_indices_MYZ.SI} -\alias{make_indices_MYZ.SI} +\name{setup_MYZix.SI} +\alias{setup_MYZix.SI} \title{Add indices for adult mosquitoes to parameter list} \usage{ -\method{make_indices_MYZ}{SI}(pars, s) +\method{setup_MYZix}{SI}(pars, s) } \arguments{ \item{pars}{a \link{list}} @@ -15,5 +15,5 @@ a \link{list} } \description{ -Implements \link{make_indices_MYZ} for the \code{SI} model. +Implements \link{setup_MYZix} for the \code{SI} model. } diff --git a/man/make_indices_MYZ.basicM.Rd b/man/setup_MYZix.basicM.Rd similarity index 61% rename from man/make_indices_MYZ.basicM.Rd rename to man/setup_MYZix.basicM.Rd index c41584caf..c3a0c0386 100644 --- a/man/make_indices_MYZ.basicM.Rd +++ b/man/setup_MYZix.basicM.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-basicM.R -\name{make_indices_MYZ.basicM} -\alias{make_indices_MYZ.basicM} +\name{setup_MYZix.basicM} +\alias{setup_MYZix.basicM} \title{Add indices for adult mosquitoes to parameter list} \usage{ -\method{make_indices_MYZ}{basicM}(pars, s) +\method{setup_MYZix}{basicM}(pars, s) } \arguments{ \item{pars}{a \link{list}} @@ -15,5 +15,5 @@ none } \description{ -Implements \link{make_indices_MYZ} for the basic M model. +Implements \link{setup_MYZix} for the basic M model. } diff --git a/man/make_indices_MYZ.macdonald.Rd b/man/setup_MYZix.macdonald.Rd similarity index 61% rename from man/make_indices_MYZ.macdonald.Rd rename to man/setup_MYZix.macdonald.Rd index 3b7efc254..f89d9eaef 100644 --- a/man/make_indices_MYZ.macdonald.Rd +++ b/man/setup_MYZix.macdonald.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-macdonald.R -\name{make_indices_MYZ.macdonald} -\alias{make_indices_MYZ.macdonald} +\name{setup_MYZix.macdonald} +\alias{setup_MYZix.macdonald} \title{Add indices for adult mosquitoes to parameter list} \usage{ -\method{make_indices_MYZ}{macdonald}(pars, s) +\method{setup_MYZix}{macdonald}(pars, s) } \arguments{ \item{pars}{a \link{list}} @@ -15,5 +15,5 @@ a \link{list} } \description{ -Implements \link{make_indices_MYZ} for the macdonald model. +Implements \link{setup_MYZix} for the macdonald model. } diff --git a/man/make_indices_MYZ.trivial.Rd b/man/setup_MYZix.trivial.Rd similarity index 59% rename from man/make_indices_MYZ.trivial.Rd rename to man/setup_MYZix.trivial.Rd index 93260e0f9..3428a6f8e 100644 --- a/man/make_indices_MYZ.trivial.Rd +++ b/man/setup_MYZix.trivial.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/adult-trivial.R -\name{make_indices_MYZ.trivial} -\alias{make_indices_MYZ.trivial} +\name{setup_MYZix.trivial} +\alias{setup_MYZix.trivial} \title{Add indices for aquatic stage mosquitoes to parameter list} \usage{ -\method{make_indices_MYZ}{trivial}(pars, s) +\method{setup_MYZix}{trivial}(pars, s) } \arguments{ \item{pars}{a \link{list}} @@ -15,5 +15,5 @@ none } \description{ -Implements \link{make_indices_MYZ} for trivial (forced emergence) model. +Implements \link{setup_MYZix} for trivial (forced emergence) model. } diff --git a/man/setup_X_indices.Rd b/man/setup_Xix.Rd similarity index 83% rename from man/setup_X_indices.Rd rename to man/setup_Xix.Rd index 79981a1cb..786eb2214 100644 --- a/man/setup_X_indices.Rd +++ b/man/setup_Xix.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/human-interface.R -\name{setup_X_indices} -\alias{setup_X_indices} +\name{setup_Xix} +\alias{setup_Xix} \title{Add indices for human population to parameter list} \usage{ -setup_X_indices(pars, i) +setup_Xix(pars, i) } \arguments{ \item{pars}{an \strong{\code{xds}} object} diff --git a/man/setup_X_indices.SIS.Rd b/man/setup_Xix.SIS.Rd similarity index 65% rename from man/setup_X_indices.SIS.Rd rename to man/setup_Xix.SIS.Rd index e8825e77e..d79fe4ba8 100644 --- a/man/setup_X_indices.SIS.Rd +++ b/man/setup_Xix.SIS.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/human-SIS.R -\name{setup_X_indices.SIS} -\alias{setup_X_indices.SIS} +\name{setup_Xix.SIS} +\alias{setup_Xix.SIS} \title{Add indices for human population to parameter list} \usage{ -\method{setup_X_indices}{SIS}(pars, i) +\method{setup_Xix}{SIS}(pars, i) } \arguments{ \item{pars}{an \strong{\code{xds}} object} @@ -15,5 +15,5 @@ none } \description{ -Implements \link{setup_X_indices} for the SIS model. +Implements \link{setup_Xix} for the SIS model. } diff --git a/man/setup_X_indices.hMoI.Rd b/man/setup_Xix.hMoI.Rd similarity index 64% rename from man/setup_X_indices.hMoI.Rd rename to man/setup_Xix.hMoI.Rd index b536b78d7..07859c462 100644 --- a/man/setup_X_indices.hMoI.Rd +++ b/man/setup_Xix.hMoI.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/human-hMoI.R -\name{setup_X_indices.hMoI} -\alias{setup_X_indices.hMoI} +\name{setup_Xix.hMoI} +\alias{setup_Xix.hMoI} \title{Add indices for human population to parameter list} \usage{ -\method{setup_X_indices}{hMoI}(pars, i) +\method{setup_Xix}{hMoI}(pars, i) } \arguments{ \item{pars}{an \strong{\code{xds}} object} @@ -15,5 +15,5 @@ none } \description{ -Implements \link{setup_X_indices} for the hybrid MoI model. +Implements \link{setup_Xix} for the hybrid MoI model. } diff --git a/man/setup_X_indices.trivial.Rd b/man/setup_Xix.trivial.Rd similarity index 63% rename from man/setup_X_indices.trivial.Rd rename to man/setup_Xix.trivial.Rd index 4d00b3dfd..d024fa531 100644 --- a/man/setup_X_indices.trivial.Rd +++ b/man/setup_Xix.trivial.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/human-trivial.R -\name{setup_X_indices.trivial} -\alias{setup_X_indices.trivial} +\name{setup_Xix.trivial} +\alias{setup_Xix.trivial} \title{Add indices for human population to parameter list} \usage{ -\method{setup_X_indices}{trivial}(pars, i) +\method{setup_Xix}{trivial}(pars, i) } \arguments{ \item{pars}{an \strong{\code{xds}} object} @@ -15,5 +15,5 @@ none } \description{ -Implements \link{setup_X_indices} for the trivial model. +Implements \link{setup_Xix} for the trivial model. } From b3692caf92ed67a90402ae44582bcf2c207dbb78 Mon Sep 17 00:00:00 2001 From: David Smith Date: Thu, 3 Oct 2024 17:40:41 -0700 Subject: [PATCH 2/2] removed detritus removed MBionomics.static removed LBionomics.static --- NAMESPACE | 2 - R/aquatic-basicL.R | 22 ++++---- R/bionomics.R | 18 ------- _pkgdown.yml | 36 +++++++------ docs/pkgdown.yml | 2 +- docs/reference/index.html | 104 ++++++++++++++++++-------------------- man/LBionomics.static.Rd | 23 --------- man/MBionomics.static.Rd | 23 --------- 8 files changed, 77 insertions(+), 153 deletions(-) delete mode 100644 man/LBionomics.static.Rd delete mode 100644 man/MBionomics.static.Rd diff --git a/NAMESPACE b/NAMESPACE index 908a65309..b1e266181 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -96,7 +96,6 @@ S3method(IRSEffectSizes,none) S3method(LBaseline,basicL) S3method(LBaseline,trivial) S3method(LBionomics,basicL) -S3method(LBionomics,static) S3method(LBionomics,trivial) S3method(LSM,none) S3method(MBaseline,GeRM) @@ -108,7 +107,6 @@ S3method(MBionomics,GeRM) S3method(MBionomics,SI) S3method(MBionomics,basicM) S3method(MBionomics,macdonald) -S3method(MBionomics,static) S3method(MBionomics,trivial) S3method(MassHealth,none) S3method(OtherBloodHosts,static) diff --git a/R/aquatic-basicL.R b/R/aquatic-basicL.R index 39b909140..68cd17a15 100644 --- a/R/aquatic-basicL.R +++ b/R/aquatic-basicL.R @@ -243,6 +243,17 @@ update_Linits.basicL <- function(pars, y, s) { return(pars) } + +#' @title Set **L** Component Initial Values +#' @param pars an **`xds`** object +#' @param s the vector species index +#' @param Lopts a named list +#' @return an `xds` object +#' @export +set_Linits <- function(pars, s=1, Lopts=list()) { + UseMethod("set_Linits", pars$Lpar[[s]]) +} + #' @title Setup Variable Indices for `basicL` (**L** Component) #' @description Set the values of the indices for the **L** component variables #' for the `basicL` module @@ -274,17 +285,6 @@ parse_Lorbits.basicL <- function(outputs, pars, s) { return(list(L=L)) } - -#' @title Set **L** Component Initial Values -#' @param pars an **`xds`** object -#' @param s the vector species index -#' @param Lopts a named list -#' @return an `xds` object -#' @export -set_Linits <- function(pars, s=1, Lopts=list()) { - UseMethod("set_Linits", pars$Lpar[[s]]) -} - #' @title Compute the Steady State of `dLdt.basicL` (**L** Component) #' @description Given an egg deposition rate `eta,` #' return a steady state value for the equations in [dLdt.basicL] diff --git a/R/bionomics.R b/R/bionomics.R index 8bd42b4d5..9b6ebb68a 100644 --- a/R/bionomics.R +++ b/R/bionomics.R @@ -36,21 +36,3 @@ Bionomics <- function(t, y, pars){ } return(pars) } - -#' @title Set mosquito bionomics to baseline -#' @description Implements [MBionomics] for models with no forcing -#' @inheritParams MBionomics -#' @return an `xds` object -#' @export -MBionomics.static <- function(t, y, pars, s) { - return(pars) -} - -#' @title Set mosquito bionomics to baseline -#' @description Implements [LBionomics] for models with no forcing -#' @inheritParams LBionomics -#' @return the model as a [list] -#' @export -LBionomics.static <- function(t, y, pars, s) { - return(pars) -} diff --git a/_pkgdown.yml b/_pkgdown.yml index 5d124f660..4b0214bf0 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -466,50 +466,48 @@ reference: Generic methods for the aquatic (immature) mosquito component. contents: - dLdt - - xde_steady_state_L - - setup_Lpar - Update_Lt - - dts_steady_state_L + - F_emerge - LBionomics - LBaseline - - LBionomics.static - - F_emerge - - setup_Linits - - list_Lvars + - setup_Lpar - get_Lpars - set_Lpars + - setup_Linits + - list_Lvars + - update_Linits + - set_Linits + - get_Linits - setup_Lix - parse_Lorbits - - get_Linits - - set_Linits - - update_Linits + - xde_steady_state_L + - dts_steady_state_L - subtitle: trivial desc: | Specialized methods for the exogeneously forced trivial model of aquatic mosquito dynamics. contents: - - LBionomics.trivial - - LBaseline.trivial - - xde_steady_state_L.trivial - - F_emerge.trivial - dLdt.trivial - Update_Lt.trivial + - F_emerge.trivial + - LBionomics.trivial + - LBaseline.trivial - setup_Lpar.trivial - make_Lpar_trivial - - setup_Linits.trivial - - list_Lvars.trivial - get_Lpars.trivial - set_Lpars.trivial + - setup_Linits.trivial + - list_Lvars.trivial - set_Linits.trivial + - update_Linits.trivial - setup_Lix.trivial - parse_Lorbits.trivial - - update_Linits.trivial + - xde_steady_state_L.trivial - subtitle: basicL desc: | Specialized methods for a basicL competition model of aquatic mosquito dynamics. contents: - dLdt.basicL - Update_Lt.basicL - - xde_steady_state_L.basicL - setup_Lpar.basicL - make_Lpar_basicL - LBionomics.basicL @@ -524,12 +522,12 @@ reference: - setup_Lix.basicL - parse_Lorbits.basicL - update_Linits.basicL + - xde_steady_state_L.basicL - title: Mosquito Bionomics desc: | Methods to compute or update mosquito bionomic parameters contents: - Bionomics - - MBionomics.static - subtitle: Functional Responses desc: | Compute bionomic parameters as functional responses to resource availability diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4a101ca52..4e12ebd14 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: 2024-10-04T00:19Z +last_built: 2024-10-04T00:38Z 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 818308061..ef4d79f2e 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1422,22 +1422,14 @@

Aquatic Mosquito Dynamics dLdt()

Derivatives for an L Component Module

- -

xde_steady_state_L()

- -

Compute steady states for L Component Modules

- -

setup_Lpar()

- -

Set up Lpar for L Component modules

Update_Lt()

Update State Variables for an L Component Module

-

dts_steady_state_L()

+

F_emerge()

-

Compute steady States for L Component Modules

+

Compute Emergent Adults

LBionomics()

@@ -1447,13 +1439,17 @@

Aquatic Mosquito Dynamics LBionomics(<static>)

+

setup_Lpar()

+ +

Set up Lpar for L Component modules

+ +

get_Lpars()

-

Set mosquito bionomics to baseline

+

Get parameters for the L Component module

-

F_emerge()

+

set_Lpars()

-

Compute Emergent Adults

+

Set L Component Parameters

setup_Linits()

@@ -1463,13 +1459,17 @@

Aquatic Mosquito Dynamics get_Lpars()

+

update_Linits()

-

Get parameters for the L Component module

+

Update L Component Initial Values

-

set_Lpars()

+

set_Linits()

-

Set L Component Parameters

+

Set L Component Initial Values

+ +

get_Linits()

+ +

Get Initial Values for the L Component

setup_Lix()

@@ -1479,45 +1479,37 @@

Aquatic Mosquito Dynamics get_Linits()

- -

Get Initial Values for the L Component

- -

set_Linits()

+

xde_steady_state_L()

-

Set L Component Initial Values

+

Compute steady states for L Component Modules

-

update_Linits()

+

dts_steady_state_L()

-

Update L Component Initial Values

+

Compute steady States for L Component Modules

trivial

Specialized methods for the exogeneously forced trivial model of aquatic mosquito dynamics.

-

LBionomics(<trivial>)

- -

Bionomics for trivial (L Component)

- -

LBaseline(<trivial>)

+

dLdt(<trivial>)

-

Baseline Bionomics for trivial (L Component)

+

Derivatives for trivial (L Component)

-

xde_steady_state_L(<trivial>)

+

Update_Lt(<trivial>)

-

Compute the Steady State of dLdt.trivial (L Component)

+

Update State Variables for trivial (L Component)

F_emerge(<trivial>)

Compute Emergent Adults for trivial (L Component)

-

dLdt(<trivial>)

+

LBionomics(<trivial>)

-

Derivatives for trivial (L Component)

+

Bionomics for trivial (L Component)

-

Update_Lt(<trivial>)

+

LBaseline(<trivial>)

-

Update State Variables for trivial (L Component)

+

Baseline Bionomics for trivial (L Component)

setup_Lpar(<trivial>)

@@ -1526,14 +1518,6 @@

trivial make_Lpar_trivial()

Make Lpar for trivial (L Component)

- -

setup_Linits(<trivial>)

- -

Setup Initial Values for the L Component trivial Module

- -

list_Lvars(<trivial>)

- -

List L Component Variables for trivial

get_Lpars(<trivial>)

@@ -1542,10 +1526,22 @@

trivial set_Lpars(<trivial>)

Set L Component parameters for trivial

+ +

setup_Linits(<trivial>)

+ +

Setup Initial Values for the L Component trivial Module

+ +

list_Lvars(<trivial>)

+ +

List L Component Variables for trivial

set_Linits(<trivial>)

Set the Initial Values for trivial (L Component)

+ +

update_Linits(<trivial>)

+ +

Update Initial Values for basicL from a state vector y

setup_Lix(<trivial>)

@@ -1555,9 +1551,9 @@

trivial

update_Linits(<trivial>)

+

xde_steady_state_L(<trivial>)

-

Update Initial Values for basicL from a state vector y

+

Compute the Steady State of dLdt.trivial (L Component)

basicL

Specialized methods for a basicL competition model of aquatic mosquito dynamics.

@@ -1570,10 +1566,6 @@

basicL <

Update_Lt(<basicL>)

Update State Variables for basicL (L Component)

- -

xde_steady_state_L(<basicL>)

- -

Compute the Steady State of dLdt.basicL (L Component)

setup_Lpar(<basicL>)

@@ -1630,6 +1622,10 @@

basicL <

update_Linits(<basicL>)

Update Initial Values for basicL from a state vector y

+ +

xde_steady_state_L(<basicL>)

+ +

Compute the Steady State of dLdt.basicL (L Component)

Mosquito Bionomics

Methods to compute or update mosquito bionomic parameters

@@ -1638,10 +1634,6 @@

Mosquito Bionomics Bionomics()

Set bionomic parameter rates relative to baseline

- -

MBionomics(<static>)

- -

Set mosquito bionomics to baseline

Functional Responses

Compute bionomic parameters as functional responses to resource availability

diff --git a/man/LBionomics.static.Rd b/man/LBionomics.static.Rd deleted file mode 100644 index 8fb105da3..000000000 --- a/man/LBionomics.static.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R -\name{LBionomics.static} -\alias{LBionomics.static} -\title{Set mosquito bionomics to baseline} -\usage{ -\method{LBionomics}{static}(t, y, pars, s) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{an \code{xds} object} - -\item{s}{the species index} -} -\value{ -the model as a \link{list} -} -\description{ -Implements \link{LBionomics} for models with no forcing -} diff --git a/man/MBionomics.static.Rd b/man/MBionomics.static.Rd deleted file mode 100644 index 3915a4370..000000000 --- a/man/MBionomics.static.Rd +++ /dev/null @@ -1,23 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/bionomics.R -\name{MBionomics.static} -\alias{MBionomics.static} -\title{Set mosquito bionomics to baseline} -\usage{ -\method{MBionomics}{static}(t, y, pars, s) -} -\arguments{ -\item{t}{current simulation time} - -\item{y}{state vector} - -\item{pars}{an \code{xds} object} - -\item{s}{the species index} -} -\value{ -an \code{xds} object -} -\description{ -Implements \link{MBionomics} for models with no forcing -}