Merge pull request #189 from dd-harp/dev

cleaning up documentation for aquatic modules

NAMESPACE

@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)
@@ -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)

R/adult-interface.R

@@ -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.*
@@ -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