diff --git a/NEWS.md b/NEWS.md index 0fb6b386d..8b26fcd40 100644 --- a/NEWS.md +++ b/NEWS.md @@ -44,6 +44,7 @@ This release contains some bug fixes, minor new features, and the initial stages ## Documentation - Added a link to the recent CSTE workshop on using `EpiNow2` to the case studies vignette. By @seabbs in #441 and reviewed by @sbfnk. +* Removed references to the no longer existing `forecast_infections` function. # EpiNow2 1.3.5 diff --git a/R/epinow.R b/R/epinow.R index 78744975f..619d10efc 100644 --- a/R/epinow.R +++ b/R/epinow.R @@ -1,14 +1,13 @@ #' Real-time Rt Estimation, Forecasting and Reporting #' #' @description `r lifecycle::badge("maturing")` -#' This function wraps the functionality of `estimate_infections()` and -#' `forecast_infections()` in order to estimate Rt and cases by date of -#' infection, forecast into these infections into the future. It also contains -#' additional functionality to convert forecasts to date of report and produce -#' summary output useful for reporting results and interpreting them. See -#' [here](https://gist.github.com/seabbs/163d0f195892cde685c70473e1f5e867) for -#' an example of using `epinow` to estimate Rt for Covid-19 in a country from -#' the ECDC data source. +#' This function wraps the functionality of `estimate_infections()` in order +#' to estimate Rt and cases by date of infection and forecast these infections +#' into the future. In addition to the functionality of +#' `estimate_infections()` it produces additional summary output useful for +#' reporting results and interpreting them as well as error catching and +#' reporting, making it particularly useful for production use e.g. running at +#' set intervals on a deidcated server. #' #' @param output A character vector of optional output to return. Supported #' options are samples ("samples"), plots ("plots"), the run time ("timing"), @@ -21,11 +20,11 @@ #' #' @param plot_args A list of optional arguments passed to `plot.epinow()`. #' -#' @return A list of output from estimate_infections, forecast_infections, -#' report_cases, and report_summary. +#' @return A list of output from estimate_infections with additional elements +#' summarising results and reporting errors if they have occurred. #' @author Sam Abbott #' @export -#' @seealso estimate_infections simulate_infections forecast_infections +#' @seealso estimate_infections simulate_infections #' @seealso regional_epinow #' @inheritParams setup_target_folder #' @inheritParams estimate_infections diff --git a/R/regional_epinow.R b/R/regional_epinow.R index 3001faa80..5367fa7d5 100644 --- a/R/regional_epinow.R +++ b/R/regional_epinow.R @@ -50,7 +50,7 @@ #' @return A list of output stratified at the top level into regional output #' and across region output summary output #' @export -#' @seealso epinow estimate_infections forecast_infections +#' @seealso epinow estimate_infections #' @seealso setup_future regional_summary #' @importFrom future.apply future_lapply #' @importFrom data.table as.data.table setDT copy setorder diff --git a/man/epinow.Rd b/man/epinow.Rd index 357d2b523..eec1ea961 100644 --- a/man/epinow.Rd +++ b/man/epinow.Rd @@ -109,19 +109,17 @@ Corresponds to the "DEBUG" level from \code{futile.logger}. See \code{setup_logg for more detailed logging options.} } \value{ -A list of output from estimate_infections, forecast_infections, -report_cases, and report_summary. +A list of output from estimate_infections with additional elements +summarising results and reporting errors if they have occurred. } \description{ -\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#maturing}{\figure{lifecycle-maturing.svg}{options: alt='[Maturing]'}}}{\strong{[Maturing]}} -This function wraps the functionality of \code{estimate_infections()} and -\code{forecast_infections()} in order to estimate Rt and cases by date of -infection, forecast into these infections into the future. It also contains -additional functionality to convert forecasts to date of report and produce -summary output useful for reporting results and interpreting them. See -\href{https://gist.github.com/seabbs/163d0f195892cde685c70473e1f5e867}{here} for -an example of using \code{epinow} to estimate Rt for Covid-19 in a country from -the ECDC data source. +\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#maturing}{\figure{lifecycle-maturing.svg}{options: alt='[Maturing]'}}}{\strong{[Maturing]}} This function wraps the +functionality of \code{estimate_infections()} in order to estimate Rt and cases +by date of infection and forecast these infections into the future. In +addition to the functionality of \code{estimate_infections()} it produces +additional summary output useful for reporting results and interpreting +them as well as error catching and reporting, making it particularly useful +for production use e.g. running at set intervals on a deidcated server. } \examples{ \donttest{ @@ -165,7 +163,7 @@ options(old_opts) } } \seealso{ -estimate_infections simulate_infections forecast_infections +estimate_infections simulate_infections regional_epinow } diff --git a/man/regional_epinow.Rd b/man/regional_epinow.Rd index a022d977e..671f530c5 100644 --- a/man/regional_epinow.Rd +++ b/man/regional_epinow.Rd @@ -173,7 +173,7 @@ options(old_opts) } } \seealso{ -epinow estimate_infections forecast_infections +epinow estimate_infections setup_future regional_summary }