changes enforced by CRAN

R/epinow-internal.R

@@ -20,7 +20,7 @@ update_horizon <- function(horizon, target_date, reported_cases) {
 #' Saves observed data to a target location if given.
 #' @inheritParams setup_target_folder
 #' @inheritParams epinow
-#' @return NULL
+#' @return No return value, called for side effects
 #' @export
 save_input <- function(reported_cases, target_folder) {
   if (!is.null(target_folder)) {
@@ -45,7 +45,7 @@ save_input <- function(reported_cases, target_folder) {
 #' @seealso estimate_infections
 #' @inheritParams setup_target_folder
 #' @inheritParams  estimate_infections
-#' @return NULL
+#' @return No return value, called for side effects
 #' @export
 save_estimate_infections <- function(estimates, target_folder = NULL,
                                      samples = TRUE, return_fit = TRUE) {
@@ -105,7 +105,7 @@ estimates_by_report_date <- function(estimates, CrIs = c(0.2, 0.5, 0.9),
 #' @param latest_folder Character string containing the path to the latest target folder.
 #' As produced by `setup_target_folder`.
 #' @inheritParams setup_target_folder
-#' @return NULL
+#' @return No return value, called for side effects
 #' @export
 copy_results_to_latest <- function(target_folder = NULL, latest_folder = NULL) {
   if (!is.null(target_folder)) {

R/estimate_infections.R

@@ -1,27 +1,40 @@
-#' Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth
+#' Estimate Infections, the Time-Varying Reproduction Number and the Rate of
+#' Growth
 #'
 #' @description `r lifecycle::badge("maturing")`
-#' Uses a non-parametric approach to reconstruct cases by date of infection from reported
-#' cases. It uses either a generative Rt model or non-parametric back calculation to estimate underlying
-#' latent infections and then maps these infections to observed cases via uncertain reporting delays and a flexible
-#' observation model. See the examples and function arguments for the details of all options. The default settings
-#' may not be sufficient for your use case so the number of warmup samples (`stan_args = list(warmup)`) may need to
-#' be increased as may the overall number of samples. Follow the links provided by any warnings messages to diagnose
-#' issues with the MCMC fit. It is recommended to explore several of the Rt estimation approaches supported as not all
-#' of them may be suited to users own use cases. See [here](https://gist.github.com/seabbs/163d0f195892cde685c70473e1f5e867)
-#' for an example of using `estimate_infections` within the `epinow` wrapper to estimate Rt for Covid-19 in a country from
-#' the ECDC data source.
-#' @param reported_cases A data frame of confirmed cases (confirm) by date (date). confirm must be integer and date must be
-#' in date format.
-#' @param generation_time A list containing the mean, standard deviation of the mean (mean_sd),
-#' standard deviation (sd), standard deviation of the standard deviation and the maximum allowed value for the
-#' generation time (assuming a gamma distribution).
-#' @param delays A call to `delay_opts()` defining delay distributions and options. See the documentation of `delay_opts()`
-#' and the examples below for details.
-#' @param horizon Numeric, defaults to 7. Number of days into the future to forecast.
-#' @param verbose Logical, defaults to `TRUE` when used interactively and otherwise `FALSE`. Should verbose debug progress messages be printed. Corresponds to the "DEBUG" level from
-#' `futile.logger`. See `setup_logging` for more detailed logging options.
+#' Uses a non-parametric approach to reconstruct cases by date of infection
+#' from reported cases. It uses either a generative Rt model or non-parametric
+#' back calculation to estimate underlying latent infections and then maps
+#' these infections to observed cases via uncertain reporting delays and a
+#' flexible observation model. See the examples and function arguments for th
+#' details of all options. The default settings may not be sufficient for your
+#' use case so the number of warmup samples (`stan_args = list(warmup)`) may
+#' need to be increased as may the overall number of samples. Follow the links
+#' provided by any warnings messages to diagnose issues with the MCMC fit. It
+#' is recommended to explore several of the Rt estimation approaches supported
+#' as not all of them may be suited to users own use cases. See
+#' [here](https://gist.github.com/seabbs/163d0f195892cde685c70473e1f5e867)
+#' for an example of using `estimate_infections` within the `epinow` wrapper to
+#' estimate Rt for Covid-19 in a country from the ECDC data source.
+#' 
+#' @param reported_cases A data frame of confirmed cases (confirm) by date
+#' (date). confirm must be integer and date must be in date format.
+#' @param generation_time A list containing the mean, standard deviation of the
+#' mean (mean_sd), standard deviation (sd), standard deviation of the standard
+#' deviation and the maximum allowed value for the generation time (assuming a
+#' gamma distribution).
+#' @param delays A call to `delay_opts()` defining delay distributions and
+#' options. See the documentation of `delay_opts()` and the examples below for
+#' details.
+#' @param horizon Numeric, defaults to 7. Number of days into the future to
+#' forecast.
+#' @param verbose Logical, defaults to `TRUE` when used interactively and otherwise `FALSE`. Should verbose debug progress messages be printed.
+#' Corresponds to the "DEBUG" level from `futile.logger`. See `setup_logging` 
+#' for more detailed logging options.
 #' @export
+#' @return A list of output including: posterior samples, summarised posterior
+#' samples, data used to fit the model, and the fit object itself.
+#' 
 #' @seealso epinow regional_epinow forecast_infections simulate_infections
 #' @inheritParams create_stan_args
 #' @inheritParams create_stan_data

R/opts.R

@@ -524,22 +524,6 @@ opts_list <- function(opts, reported_cases, ...) {
 #' call to an `_opts()` function.
 #' @param region A character string indicating a region of interest.
 #' @return A list of options
-#' @examples
-#' # uses example case vector
-#' cases <- example_confirmed[1:40]
-#' cases <- data.table::rbindlist(list(
-#'   data.table::copy(cases)[, region := "testland"],
-#'   cases[, region := "realland"]
-#' ))
-#'
-#' # regional options
-#' regional_opts <- opts_list(rt_opts(), cases)
-#' EpiNow2:::filter_opts(regional_opts, "realland")
-#' # default only
-#' EpiNow2:::filter_opts(rt_opts(), "realland")
-#' # settings are NULL in one regions
-#' regional_opts <- update_list(regional_opts, list(realland = NULL))
-#' EpiNow2:::filter_opts(regional_opts, "realland")
 filter_opts <- function(opts, region) {
   if (region %in% names(opts)) {
     out <- opts[[region]]

R/setup.R

@@ -57,7 +57,7 @@ setup_logging <- function(threshold = "INFO", file = NULL,
 #' @param mirror_epinow Logical, defaults to FALSE. Should internal logging be
 #' returned from `epinow` to the console.
 #' @inheritParams setup_target_folder
-#' @return NULL
+#' @return No return value, called for side effects
 #' @export
 #' @importFrom purrr walk
 #' @examples

R/simulate_infections.R

@@ -4,8 +4,9 @@
 #' This function simulates infections using an existing fit to observed cases but with a modified
 #' time-varying reproduction number. This can be used to explore forecast models or past counterfactuals.
 #' Simulations can be run in parallel using `future::plan`.
-#' @param estimates The \code{estimates} element of an \code{epinow} run that has been done with
-#' output = "fit", or the result of \code{estimate_infections} with \code{return_fit} set to TRUE.
+#' @param estimates The \code{estimates} element of an \code{epinow} run that
+#' has been done with output = "fit", or the result of
+#' \code{estimate_infections} with \code{return_fit} set to TRUE.
 #' @param model A compiled stan model as returned by `rstan::stan_model`.
 #' @param R A numeric vector of reproduction numbers; these will overwrite the reproduction numbers
 #'  contained in \code{estimates}, except elements set to NA. If it is longer than the time series
@@ -25,6 +26,8 @@
 #' @importFrom progressr with_progress progressor
 #' @importFrom data.table rbindlist as.data.table
 #' @importFrom lubridate days
+#' @return A list of output as returned by [estimate_infections()] but based on
+#' results from the specified scenario rather than fitting.
 #' @export
 #' @examples
 #' \donttest{

R/utilities.R

@@ -8,7 +8,7 @@
 #' to the current directory.
 #' @importFrom purrr walk
 #' @importFrom futile.logger flog.info
-#' @return NULL
+#' @return No return value, called for side effects
 #' @export
 clean_nowcasts <- function(date = NULL, nowcast_dir = ".") {
   if (is.null(date)) {
@@ -157,9 +157,6 @@ allocate_delays <- function(delay_var, no_delays) {
 #' empty if missing.
 #' @param n Numeric, number of samples to assign an empty array
 #' @return A list of parameters some allocated to be empty
-#' @examples
-#' data <- list(x = 1, y = 2, z = 30)
-#' EpiNow2:::allocate_empty(data, params = c("x", "t"))
 allocate_empty <- function(data, params, n = 0) {
   for (param in params) {
     if (!exists(param, data)) {
@@ -181,22 +178,6 @@ allocate_empty <- function(data, params, n = 0) {
 #' of futile.logger for details. Supported options are "info" and "debug"
 #' @return A logical vector of named output arguments
 #' @importFrom  futile.logger flog.info flog.debug
-#' @examples
-#' # select nothing
-#' EpiNow2:::match_output_arguments(supported_args = c("fit", "plots", "samples"))
-#'
-#' # select just plots
-#' EpiNow2:::match_output_arguments("plots", supported_args = c("fit", "plots", "samples"))
-#'
-#' # select plots and samples
-#' EpiNow2:::match_output_arguments(c("plots", "samples"),
-#'   supported_args = c("fit", "plots", "samples")
-#' )
-#'
-#' # lazily select arguments
-#' EpiNow2:::match_output_arguments("p",
-#'   supported_args = c("fit", "plots", "samples")
-#' )
 match_output_arguments <- function(input_args = c(),
                                    supported_args = c(),
                                    logger = NULL,
@@ -245,7 +226,7 @@ match_output_arguments <- function(input_args = c(),
 #' @param files A character vector indicating the target files
 #' @param target_dir A character string indicating the target directory for the file
 #' @param ... Additional arguments passed to `rstan::expose_stan_functions`.
-#' @return NULL
+#' @return No return value, called for side effects
 #' @export
 #' @importFrom rstan expose_stan_functions stanc
 #' @importFrom purrr map_chr