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cleaning up documentation for aquatic modules #189

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merged 2 commits into from
Oct 3, 2024
Merged

cleaning up documentation for aquatic modules #189

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1812a2e
Cleanup documentation; renaming functions
smitdave Oct 3, 2024
c7c527b
minor documentation changes
smitdave Oct 3, 2024
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26 changes: 12 additions & 14 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -218,10 +218,6 @@ S3method(list_MYZvars,SI)
S3method(list_MYZvars,basicM)
S3method(list_MYZvars,macdonald)
S3method(list_Xvars,SIS)
S3method(make_Linits,basicL)
S3method(make_Linits,trivial)
S3method(make_Lpar,basicL)
S3method(make_Lpar,trivial)
S3method(make_MYZinits,GeRM)
S3method(make_MYZinits,RM_dts)
S3method(make_MYZinits,SI)
Expand Down Expand Up @@ -255,8 +251,6 @@ S3method(make_function,sharkfin)
S3method(make_function,sigmoid)
S3method(make_function,sin)
S3method(make_function,sum)
S3method(make_indices_L,basicL)
S3method(make_indices_L,trivial)
S3method(make_indices_MYZ,GeRM)
S3method(make_indices_MYZ,RM_dts)
S3method(make_indices_MYZ,SI)
Expand All @@ -276,7 +270,6 @@ S3method(parse_MYZorbits,trivial)
S3method(parse_Xorbits,SIS)
S3method(parse_Xorbits,hMoI)
S3method(parse_Xorbits,trivial)
S3method(put_Lvars,trivial)
S3method(put_MYZvars,RM_dts)
S3method(put_MYZvars,SI)
S3method(put_Xvars,SIS)
Expand All @@ -302,13 +295,19 @@ S3method(set_Xpars,hMoI)
S3method(set_Xpars,trivial)
S3method(set_eir,cohort)
S3method(setup_EIP,fixedlag_dts)
S3method(setup_Linits,basicL)
S3method(setup_Linits,trivial)
S3method(setup_Lpar,basicL)
S3method(setup_Lpar,trivial)
S3method(setup_development,func)
S3method(setup_exposure_nb,dts)
S3method(setup_exposure_nb,xde)
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)
Expand Down Expand Up @@ -447,9 +446,6 @@ export(compute_calU)
export(compute_eggs_laid)
export(compute_kappa)
export(compute_local_frac)
export(create_Linits_basicL)
export(create_Lpar_basicL)
export(create_Lpar_trivial)
export(create_MYZinits_GeRM)
export(create_MYZinits_RM_dts)
export(create_MYZinits_SI)
Expand Down Expand Up @@ -520,8 +516,9 @@ export(list_Xvars)
export(list_vars)
export(make_EIR)
export(make_EIR_full)
export(make_Linits)
export(make_Lpar)
export(make_Linits_basicL)
export(make_Lpar_basicL)
export(make_Lpar_trivial)
export(make_MYZinits)
export(make_MYZpar)
export(make_Omega)
Expand All @@ -539,7 +536,6 @@ export(make_calU)
export(make_eggs_laid)
export(make_function)
export(make_indices)
export(make_indices_L)
export(make_indices_MYZ)
export(make_kappa)
export(make_local_frac)
Expand All @@ -560,7 +556,6 @@ export(parse_MYZorbits)
export(parse_Xorbits)
export(parse_orbits)
export(parse_y)
export(put_Lvars)
export(put_MYZvars)
export(put_Xvars)
export(reset_state)
Expand All @@ -579,6 +574,8 @@ export(setup_BLOOD_FEEDING)
export(setup_EGG_LAYING)
export(setup_EIP)
export(setup_Hpar_static)
export(setup_Linits)
export(setup_Lpar)
export(setup_TRANSMISSION)
export(setup_care_seeking_no_behavior)
export(setup_development)
Expand All @@ -592,6 +589,7 @@ 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)
Expand Down
26 changes: 14 additions & 12 deletions R/adult-interface.R
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Expand Up @@ -15,6 +15,20 @@ dMYZdt <- function(t, y, pars, s) {
UseMethod("dMYZdt", pars$MYZpar[[s]])
}


#' @title Derivatives for adult mosquitoes
#' @description This method dispatches on the type of `pars$MYZpar`.
#' @param t current simulation time
#' @param y state vector
#' @param pars a [list]
#' @param s the species index
#' @return the derivatives a [vector]
#' @export
Update_MYZt <- function(t, y, pars, s) {
UseMethod("Update_MYZt", pars$MYZpar[[s]])
}


#' @title Adult Mosquito - Baseline Bionomics
#' @description Compute adult mosquito bionomics as a
#' *changing baseline.*
Expand Down Expand Up @@ -84,18 +98,6 @@ MYZ_rates2probs = function(MYZpar, runtime){
UseMethod("MYZ_rates2probs", MYZpar)
}

#' @title Derivatives for adult mosquitoes
#' @description This method dispatches on the type of `pars$MYZpar`.
#' @param t current simulation time
#' @param y state vector
#' @param pars a [list]
#' @param s the species index
#' @return the derivatives a [vector]
#' @export
Update_MYZt <- function(t, y, pars, s) {
UseMethod("Update_MYZt", pars$MYZpar[[s]])
}

#' @title Compute the steady states as a function of the daily EIR
#' @description This method dispatches on the type of `MYZpar`.
#' @inheritParams xde_steady_state_MYZ
Expand Down
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