Cleanup following rebase

DESCRIPTION

@@ -64,7 +64,6 @@ Imports:
     checkmate,
     Rcpp,
     RcppEigen,
-    jsonlite,
     data.table,
     glue,
     utils,

NAMESPACE

@@ -10,7 +10,6 @@ S3method(print,vaccination)
 export(as.intervention)
 export(as.vaccination)
 export(epidemic_size)
-export(get_model_names)
 export(get_parameter)
 export(get_transmission_rate)
 export(infection)
@@ -24,7 +23,6 @@ export(is_vaccination)
 export(model_default_cpp)
 export(model_default_r)
 export(model_ebola_r)
-export(model_library)
 export(model_vacamole_cpp)
 export(model_vacamole_r)
 export(new_infections)

R/RcppExports.R

@@ -41,16 +41,8 @@
 #' as specified in the initial conditions matrix (see [population()]).
 #' The second list element is a vector of timesteps.
 #' @keywords internal
-.model_default_cpp <- function(
-    initial_state, beta, alpha, gamma, contact_matrix, npi_time_begin,
-    npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu,
-    rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
-    .Call(
-        `_epidemics_model_default_cpp_internal`, initial_state, beta, alpha,
-        gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr,
-        vax_time_begin, vax_time_end, vax_nu, rate_interventions,
-        time_dependence, time_end, increment
-    )
+.model_default_cpp <- function(initial_state, beta, alpha, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
+    .Call(`_epidemics_model_default_cpp_internal`, initial_state, beta, alpha, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
 }
 
 #' @title Run an SEIR model with Erlang passage times
@@ -81,13 +73,8 @@
 #' This output is intended to be passed to [output_to_df()] to be converted
 #' into a data.frame for further analysis.
 #' @keywords internal
-.model_ebola_cpp <- function(
-    initial_state, population_size, beta, shape_E, rate_E,
-    shape_I, rate_I, time_end) {
-    .Call(
-        `_epidemics_model_ebola_cpp_internal`, initial_state,
-        population_size, beta, shape_E, rate_E, shape_I, rate_I, time_end
-    )
+.model_ebola_cpp <- function(initial_state, population_size, beta, shape_E, rate_E, shape_I, rate_I, time_end) {
+    .Call(`_epidemics_model_ebola_cpp_internal`, initial_state, population_size, beta, shape_E, rate_E, shape_I, rate_I, time_end)
 }
 
 #' @title Run the RIVM Vacamole model
@@ -145,17 +132,8 @@
 #' as specified in the initial conditions matrix (see [population()]).
 #' The second list element is a vector of timesteps.
 #' @keywords internal
-.model_vacamole_cpp <- function(
-    initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma,
-    contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin,
-    vax_time_end, vax_nu, rate_interventions, time_dependence,
-    time_end = 100.0, increment = 1.0) {
-    .Call(
-        `_epidemics_model_vacamole_cpp_internal`, initial_state, beta, beta_v,
-        alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix,
-        npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end,
-        vax_nu, rate_interventions, time_dependence, time_end, increment
-    )
+.model_vacamole_cpp <- function(initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
+    .Call(`_epidemics_model_vacamole_cpp_internal`, initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
 }
 
 #' @title Compute the discrete probability of the truncated Erlang distribution
@@ -165,3 +143,4 @@
 prob_discrete_erlang_cpp <- function(shape, rate) {
     .Call(`_epidemics_prob_discrete_erlang_cpp`, shape, rate)
 }
+

R/check_args_default.R

@@ -5,7 +5,7 @@
 #' @description Check and prepare the four main arguments to
 #' [model_default_cpp()] for use with [.model_default_cpp()].
 #'
-#' `.check_args_epidemic_default()` adds an empty `<intervention>` and
+#' `.check_args_model_default()` adds an empty `<intervention>` and
 #' `<vaccination>` object if these are missing from the model arguments.
 #'
 #' `.prepare_args_epidemics_default()` prepares arguments for
@@ -18,12 +18,12 @@
 #'
 #' @return
 #'
-#' `.check_args_epidemic_default()` invisibly returns the model arguments passed
+#' `.check_args_model_default()` invisibly returns the model arguments passed
 #' in `mod_args`. If the model arguments did not previously contain elements
 #' named `intervention` and `vaccination`, these are added as dummy objects of
 #' the corresponding classes.
 #'
-#' `.prepare_args_epidemic_default()` returns a list of model arguments suitable
+#' `.prepare_args_model_default()` returns a list of model arguments suitable
 #' for [.model_default_cpp()]. This is a named list consisting of:
 #'
 #'  - `initial_state`: the initial conditions modified to represent absolute
@@ -51,7 +51,7 @@
 #' is incremented.
 #'
 #' @keywords internal
-.check_args_epidemic_default <- function(mod_args) {
+.check_args_model_default <- function(mod_args) {
   # check that arguments list has expected names
   checkmate::assert_names(
     names(mod_args),
@@ -148,7 +148,7 @@
 #' @name check_prepare_default_args
 #' @rdname check_prepare_default_args
 #' @keywords internal
-.prepare_args_epidemic_default <- function(mod_args) {
+.prepare_args_model_default <- function(mod_args) {
   # prepare the contact matrix and the initial conditions
   # scale the contact matrix by the maximum real eigenvalue
   contact_matrix <- get_parameter(mod_args[["population"]], "contact_matrix")

R/check_args_ebola.R

@@ -6,10 +6,10 @@
 #' [model_ebola_cpp()] for use with [.model_ebola_cpp()].
 #' @return
 #'
-#' `.check_args_epidemic_ebola()` invisibly returns the model arguments passed
+#' `.check_args_model_ebola()` invisibly returns the model arguments passed
 #' in `mod_args`.
 #'
-#' `.prepare_args_epidemic_ebola()` returns a list of model arguments suitable
+#' `.prepare_args_model_ebola()` returns a list of model arguments suitable
 #' for [.model_ebola_cpp()]. This is a named list consisting of:
 #'
 #' - `initial_state`: the initial conditions modified to represent absolute
@@ -29,7 +29,7 @@
 #' - `time_end`: the time at which the simulation ends.
 #'
 #' @keywords internal
-.check_args_epidemic_ebola <- function(mod_args) {
+.check_args_model_ebola <- function(mod_args) {
   # check that arguments list has expected names
   checkmate::assert_names(
     names(mod_args),
@@ -60,7 +60,7 @@
 #' @name check_prepare_ebola_args
 #' @rdname check_prepare_ebola_args
 #' @keywords internal
-.prepare_args_epidemic_ebola <- function(mod_args) {
+.prepare_args_model_ebola <- function(mod_args) {
   # prepare initial conditions by scaling with demography
   # we take the ceiling to ensure that models with only one
   # infectious individual can be accommodated

R/check_args_vacamole.R

@@ -5,7 +5,7 @@
 #' @description Check and prepare the four main arguments to
 #' [model_vacamole_cpp()] for use with [.model_vacamole_cpp()].
 #'
-#' `.check_args_epidemic_vacamole()` adds an empty `<intervention>` object if
+#' `.check_args_model_vacamole()` adds an empty `<intervention>` object if
 #' this is missing from the model arguments.
 #'
 #' `.prepare_args_epidemics_vacamole()` prepares arguments for
@@ -18,12 +18,12 @@
 #'
 #' @return
 #'
-#' `.check_args_epidemic_vacamole()` invisibly returns the model arguments
+#' `.check_args_model_vacamole()` invisibly returns the model arguments
 #' passed in `mod_args`. If the model arguments did not previously contain
 #' elements named `intervention` this is added as dummy objects of the
 #' corresponding classes.
 #'
-#' `.prepare_args_epidemic_vacamole()` returns a list of model arguments
+#' `.prepare_args_model_vacamole()` returns a list of model arguments
 #' suitable for [.model_vacamole_cpp()]. This is a named list consisting of:
 #'
 #'  - `initial_state`: the initial conditions modified to represent absolute
@@ -65,7 +65,7 @@
 #' is incremented.
 #'
 #' @keywords internal
-.check_args_epidemic_vacamole <- function(mod_args) {
+.check_args_model_vacamole <- function(mod_args) {
   # check that arguments list has expected names
   checkmate::assert_names(
     names(mod_args),
@@ -172,7 +172,7 @@
 #' @name check_prepare_vacamole_args
 #' @rdname check_prepare_vacamole_args
 #' @keywords internal
-.prepare_args_epidemic_vacamole <- function(mod_args) {
+.prepare_args_model_vacamole <- function(mod_args) {
   # prepare the contact matrix and the initial conditions
   # scale the contact matrix by the maximum real eigenvalue
   contact_matrix <- get_parameter(mod_args[["population"]], "contact_matrix")

R/model_default.R

@@ -124,8 +124,8 @@ model_default_cpp <- function(population,
   # prepare checked arguments for function
   # this necessary as check_args adds intervention and vaccination
   # if missing
-  model_arguments <- .prepare_args_epidemic_default(
-    .check_args_epidemic_default(model_arguments)
+  model_arguments <- .prepare_args_model_default(
+    .check_args_model_default(model_arguments)
   )
 
   # get compartment names
@@ -272,8 +272,8 @@ model_default_r <- function(population,
   # prepare checked arguments for function
   # this necessary as check_args adds intervention and vaccination
   # if missing
-  model_arguments <- .prepare_args_epidemic_default(
-    .check_args_epidemic_default(model_arguments)
+  model_arguments <- .prepare_args_model_default(
+    .check_args_model_default(model_arguments)
   )
 
   # get compartment names

R/model_ebola.R

@@ -494,8 +494,8 @@ model_ebola_cpp <- function(population, infection,
   # prepare checked arguments for function
   # this necessary as check_args adds intervention and vaccination
   # if missing
-  model_arguments <- .prepare_args_epidemic_ebola(
-    .check_args_epidemic_ebola(model_arguments)
+  model_arguments <- .prepare_args_model_ebola(
+    .check_args_model_ebola(model_arguments)
   )
 
   # get compartment names

R/model_vacamole.R

@@ -110,12 +110,12 @@
 #'
 #' @export
 model_vacamole_cpp <- function(population,
-                                  infection,
-                                  intervention = NULL,
-                                  vaccination,
-                                  time_dependence = NULL,
-                                  time_end = 100,
-                                  increment = 1) {
+                               infection,
+                               intervention = NULL,
+                               vaccination,
+                               time_dependence = NULL,
+                               time_end = 100,
+                               increment = 1) {
   # check class on required inputs
   checkmate::assert_class(population, "population")
   checkmate::assert_class(infection, "infection")
@@ -157,8 +157,8 @@ model_vacamole_cpp <- function(population,
   # prepare checked arguments for function
   # this necessary as check_args adds intervention and vaccination
   # if missing
-  model_arguments <- .prepare_args_epidemic_vacamole(
-    .check_args_epidemic_vacamole(model_arguments)
+  model_arguments <- .prepare_args_model_vacamole(
+    .check_args_model_vacamole(model_arguments)
   )
 
   # get compartment names
@@ -296,12 +296,12 @@ model_vacamole_cpp <- function(population,
 #'
 #' @export
 model_vacamole_r <- function(population,
-                                infection,
-                                intervention = NULL,
-                                vaccination,
-                                time_dependence = NULL,
-                                time_end = 100,
-                                increment = 1) {
+                             infection,
+                             intervention = NULL,
+                             vaccination,
+                             time_dependence = NULL,
+                             time_end = 100,
+                             increment = 1) {
   # check class on required inputs
   checkmate::assert_class(population, "population")
   checkmate::assert_class(infection, "infection")
@@ -345,8 +345,8 @@ model_vacamole_r <- function(population,
   # prepare checked arguments for function
   # this necessary as check_args adds intervention and vaccination
   # if missing
-  model_arguments <- .prepare_args_epidemic_vacamole(
-    .check_args_epidemic_vacamole(model_arguments)
+  model_arguments <- .prepare_args_model_vacamole(
+    .check_args_model_vacamole(model_arguments)
   )
 
   # get compartment names