diff --git a/R/check_args_default.R b/R/check_args_default.R index 442b6029..2203a19e 100644 --- a/R/check_args_default.R +++ b/R/check_args_default.R @@ -1,8 +1,9 @@ -#' @title Prepare arguments to default epidemic function +#' @title Prepare arguments to default model function #' @name prepare_default_args #' @rdname prepare_default_args #' -#' @description Prepare arguments to for [.model_default_cpp()]. +#' @description Prepare arguments to [model_default_cpp()] for +#' [.model_default_cpp()]. #' #' @param mod_args A named list of the population, and epidemic modifiers. #' diff --git a/R/check_args_diphtheria.R b/R/check_args_diphtheria.R index afbfa173..782f8ad9 100644 --- a/R/check_args_diphtheria.R +++ b/R/check_args_diphtheria.R @@ -3,7 +3,7 @@ #' @rdname prepare_diphtheria_args #' #' @description Prepare arguments to [model_diphtheria_cpp()] for -#' [.model_default_cpp()]. +#' [.model_diphtheria_cpp()]. #' #' @param mod_args A named list of the population, and epidemic modifiers. #' @@ -50,7 +50,7 @@ #' @keywords internal #' @details #' `.check_prepare_args_diphtheria()` prepares arguments for -#' [.model_diphtheria_cpp()], which is the C++ function that solves the default +#' [.model_diphtheria_cpp()], which is the C++ function that solves the #' ODE system using a Boost _odeint_ solver, by converting the arguments #' collected in `mod_args` into simpler structures such as lists and numeric or #' integer vectors that can be interpreted as C++ types such as `Rcpp::List`, diff --git a/man/prepare_default_args.Rd b/man/prepare_default_args.Rd index fd2a7449..e619d6ab 100644 --- a/man/prepare_default_args.Rd +++ b/man/prepare_default_args.Rd @@ -3,7 +3,7 @@ \name{prepare_default_args} \alias{prepare_default_args} \alias{.check_prepare_args_default} -\title{Prepare arguments to default epidemic function} +\title{Prepare arguments to default model function} \usage{ .check_prepare_args_default(mod_args) } @@ -34,7 +34,8 @@ is incremented. } } \description{ -Prepare arguments to for \code{\link[=.model_default_cpp]{.model_default_cpp()}}. +Prepare arguments to \code{\link[=model_default_cpp]{model_default_cpp()}} for +\code{\link[=.model_default_cpp]{.model_default_cpp()}}. } \details{ \code{.check_prepare_args_default()} prepares arguments for diff --git a/man/prepare_diphtheria_args.Rd b/man/prepare_diphtheria_args.Rd new file mode 100644 index 00000000..1eff777d --- /dev/null +++ b/man/prepare_diphtheria_args.Rd @@ -0,0 +1,56 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/check_args_diphtheria.R +\name{prepare_diphtheria_args} +\alias{prepare_diphtheria_args} +\alias{.check_prepare_args_diphtheria} +\title{Prepare arguments to diphtheria model function} +\usage{ +.check_prepare_args_diphtheria(mod_args) +} +\arguments{ +\item{mod_args}{A named list of the population, and epidemic modifiers.} +} +\value{ +A list of model arguments suitable for \code{\link[=.model_diphtheria_cpp]{.model_diphtheria_cpp()}}. +This is a named list consisting of: +\itemize{ +\item \code{initial_state}: the initial conditions modified to represent absolute +rather than proportional values; +\item \code{transmissibility}, \code{transmissibility_vax}: two numbers representing the +transmission rate +of the infection for unvaccinated or single-dose vaccinated, and two-dose +vaccinated individuals, respectively; +\item \code{infectiousness_rate}: a single number for the transition rate from the +'exposed' and 'exposed_vaccinated' to the 'infectious' and +'infectious_vaccinated' compartments; +\item \code{recovery_rate}: a single number for the recovery rate from the infection; +\item \code{reporting_rate}: a single number for the proportion of infectious cases +reported; +\item \code{prop_hosp}: a single number for the proportion of reported cases that +need hospitalisation; +\item \code{hosp_entry_rate}, \code{hosp_exit_rate}: two numbers representing the rate of +entry and exit from the 'hospitalised' compartment; +\item \code{rate_interventions}: an Rcpp List giving the interventions on model +parameters; +\item \code{time_dependence}: an Rcpp List giving the time-dependent effects on model +parameters in the form of R functions; +\item \code{pop_change_times} and \code{pop_change_values}: the times and values of changes +in the population of susceptibles; +\item \code{time_end}, \code{increment}: two numbers for the time at which to end the +simulation, and the value by which the simulation time +is incremented. +} +} +\description{ +Prepare arguments to \code{\link[=model_diphtheria_cpp]{model_diphtheria_cpp()}} for +\code{\link[=.model_default_cpp]{.model_default_cpp()}}. +} +\details{ +\code{.check_prepare_args_diphtheria()} prepares arguments for +\code{\link[=.model_diphtheria_cpp]{.model_diphtheria_cpp()}}, which is the C++ function that solves the default +ODE system using a Boost \emph{odeint} solver, by converting the arguments +collected in \code{mod_args} into simpler structures such as lists and numeric or +integer vectors that can be interpreted as C++ types such as \code{Rcpp::List}, +\code{Rcpp::NumericVector}, or \code{Eigen::MatrixXd}. +} +\keyword{internal}