diff --git a/DESCRIPTION b/DESCRIPTION index d1f7ada04..72bf718be 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -41,7 +41,7 @@ Authors@R: c( email = "michaelchirico4@gmail.com", comment = c(ORCID = "0000-0003-0787-087X"))) Description: - scoringutils facilitates the evaluation of forecasts in a convenient + Facilitate the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and diff --git a/R/class-forecast-binary.R b/R/class-forecast-binary.R index d76057828..73d96eb80 100644 --- a/R/class-forecast-binary.R +++ b/R/class-forecast-binary.R @@ -98,7 +98,7 @@ score.forecast_binary <- function(forecast, metrics = get_metrics(forecast), ... #' @param ... unused #' @return A list of scoring functions. #' @export -#' @family `get_metrics` functions +#' @family get_metrics functions #' @keywords handle-metrics #' @examples #' get_metrics(example_binary) @@ -142,6 +142,6 @@ get_metrics.forecast_binary <- function(x, select = NULL, exclude = NULL, ...) { #' \item{predicted}{predicted value} #' } # nolint start -#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} # nolint end "example_binary" diff --git a/R/class-forecast-nominal.R b/R/class-forecast-nominal.R index 6b0bc1724..5f89aad48 100644 --- a/R/class-forecast-nominal.R +++ b/R/class-forecast-nominal.R @@ -115,7 +115,7 @@ score.forecast_nominal <- function(forecast, metrics = get_metrics(forecast), .. #' For nominal forecasts, the default scoring rule is: #' - "log_score" = [logs_nominal()] #' @export -#' @family `get_metrics` functions +#' @family get_metrics functions #' @keywords handle-metrics #' @examples #' get_metrics(example_nominal) @@ -150,6 +150,6 @@ get_metrics.forecast_nominal <- function(x, select = NULL, exclude = NULL, ...) #' \item{horizon}{forecast horizon in weeks} #' } # nolint start -#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} # nolint end "example_nominal" diff --git a/R/class-forecast-point.R b/R/class-forecast-point.R index 9b06d75be..15b54e3d2 100644 --- a/R/class-forecast-point.R +++ b/R/class-forecast-point.R @@ -102,7 +102,7 @@ score.forecast_point <- function(forecast, metrics = get_metrics(forecast), ...) #' @inheritSection illustration-input-metric-binary-point Input format #' @inheritParams get_metrics.forecast_binary #' @export -#' @family `get_metrics` functions +#' @family get_metrics functions #' @keywords handle-metrics #' @examples #' get_metrics(example_point, select = "ape") @@ -160,6 +160,6 @@ get_metrics.forecast_point <- function(x, select = NULL, exclude = NULL, ...) { #' \item{horizon}{forecast horizon in weeks} #' } # nolint start -#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} # nolint end "example_point" diff --git a/R/class-forecast-quantile.R b/R/class-forecast-quantile.R index 94972fece..409a4532f 100644 --- a/R/class-forecast-quantile.R +++ b/R/class-forecast-quantile.R @@ -153,7 +153,7 @@ score.forecast_quantile <- function(forecast, metrics = get_metrics(forecast), . #' @inheritSection illustration-input-metric-quantile Input format #' @inheritParams get_metrics.forecast_binary #' @export -#' @family `get_metrics` functions +#' @family get_metrics functions #' @keywords handle-metrics #' @importFrom purrr partial #' @examples @@ -252,6 +252,6 @@ get_pit_histogram.forecast_quantile <- function(forecast, num_bins = NULL, #' \item{horizon}{forecast horizon in weeks} #' } # nolint start -#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} # nolint end "example_quantile" diff --git a/R/class-forecast-sample.R b/R/class-forecast-sample.R index a0983bd7d..a02a80388 100644 --- a/R/class-forecast-sample.R +++ b/R/class-forecast-sample.R @@ -144,7 +144,7 @@ score.forecast_sample <- function(forecast, metrics = get_metrics(forecast), ... #' @inheritSection illustration-input-metric-sample Input format #' @inheritParams get_metrics.forecast_binary #' @export -#' @family `get_metrics` functions +#' @family get_metrics functions #' @keywords handle-metrics #' @examples #' get_metrics(example_sample_continuous, exclude = "mad") @@ -238,7 +238,7 @@ get_pit_histogram.forecast_sample <- function(forecast, num_bins = 10, #' \item{sample_id}{id for the corresponding sample} #' } # nolint start -#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} # nolint end "example_sample_continuous" @@ -266,6 +266,6 @@ get_pit_histogram.forecast_sample <- function(forecast, num_bins = 10, #' \item{sample_id}{id for the corresponding sample} #' } # nolint start -#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +#' @source \url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} # nolint end "example_sample_discrete" diff --git a/R/class-scores.R b/R/class-scores.R index 6cc72be9b..d103c0536 100644 --- a/R/class-scores.R +++ b/R/class-scores.R @@ -108,7 +108,7 @@ assert_scores <- function(scores) { #' Character vector with the names of the scoring rules that were used #' for scoring. #' @keywords handle-metrics -#' @family `get_metrics` functions +#' @family get_metrics functions #' @export get_metrics.scores <- function(x, error = FALSE, ...) { assert_data_frame(x) diff --git a/R/metrics-quantile.R b/R/metrics-quantile.R index ddb14f35a..3ef8589c4 100644 --- a/R/metrics-quantile.R +++ b/R/metrics-quantile.R @@ -556,23 +556,22 @@ interpolate_median <- function(predicted, quantile_level) { } -#' @title Absolute error of the median (quantile-based version) -#' @description +#' Absolute error of the median (quantile-based version) +#' #' Compute the absolute error of the median calculated as #' \deqn{ -#' \textrm{abs}(\textrm{observed} - \textrm{median prediction}) -#' }{ -#' abs(observed - median_prediction) +#' |observed - median prediction| #' } -#' The median prediction is the predicted value for which quantile_level == 0.5, -#' the function therefore requires 0.5 to be among the quantile levels in -#' `quantile_level`. +#' The median prediction is the predicted value for which quantile_level == 0.5. +#' The function requires 0.5 to be among the quantile levels in `quantile_level`. +#' #' @inheritParams wis #' @inheritSection illustration-input-metric-quantile Input format #' @return Numeric vector of length N with the absolute error of the median. #' @seealso [ae_median_sample()] #' @importFrom stats median #' @importFrom cli cli_warn +#' @keywords metric #' @examples #' observed <- rnorm(30, mean = 1:30) #' predicted_values <- replicate(3, rnorm(30, mean = 1:30)) @@ -580,7 +579,6 @@ interpolate_median <- function(predicted, quantile_level) { #' observed, predicted_values, quantile_level = c(0.2, 0.5, 0.8) #' ) #' @export -#' @keywords metric ae_median_quantile <- function(observed, predicted, quantile_level) { assert_input_quantile(observed, predicted, quantile_level) if (!any(quantile_level == 0.5)) { diff --git a/R/metrics-sample.R b/R/metrics-sample.R index 23308a05b..1d1776381 100644 --- a/R/metrics-sample.R +++ b/R/metrics-sample.R @@ -119,28 +119,26 @@ bias_sample <- function(observed, predicted) { #' #' @description #' Absolute error of the median calculated as -#' -#' \deqn{% -#' \textrm{abs}(\textrm{observevd} - \textrm{median\_prediction}) -#' }{% -#' abs(observed - median_prediction) +#' \deqn{ +#' |observed - median\_prediction| #' } +#' where the median prediction is calculated as the median of the predictive +#' samples. #' #' @param observed A vector with observed values of size n #' @param predicted nxN matrix of predictive samples, n (number of rows) being #' the number of data points and N (number of columns) the number of Monte #' Carlo samples. Alternatively, `predicted` can just be a vector of size n. #' @inheritSection illustration-input-metric-sample Input format -#' @return vector with the scoring values +#' @return Numeric vector of length n with the absolute errors of the median. #' @seealso [ae_median_quantile()] #' @importFrom stats median +#' @keywords metric #' @examples #' observed <- rnorm(30, mean = 1:30) #' predicted_values <- matrix(rnorm(30, mean = 1:30)) #' ae_median_sample(observed, predicted_values) #' @export -#' @keywords metric - ae_median_sample <- function(observed, predicted) { assert_input_sample(observed, predicted) median_predictions <- apply( diff --git a/R/metrics.R b/R/metrics.R index f94735b8a..c7f1323ea 100644 --- a/R/metrics.R +++ b/R/metrics.R @@ -60,7 +60,7 @@ select_metrics <- function(metrics, select = NULL, exclude = NULL) { #' See [as_forecast()] for more information on `forecast` objects and [score()] #' for more information on `scores` objects. #' -#' @family `get_metrics` functions +#' @family get_metrics functions #' @keywords handle-metrics #' @export get_metrics <- function(x, ...) { diff --git a/R/pairwise-comparisons.R b/R/pairwise-comparisons.R index d42969f1c..d04103307 100644 --- a/R/pairwise-comparisons.R +++ b/R/pairwise-comparisons.R @@ -565,17 +565,18 @@ permutation_test <- function(scores1, } -#' @title Add relative skill scores based on pairwise comparisons -#' @description +#' Add relative skill scores based on pairwise comparisons +#' #' Adds a columns with relative skills computed by running #' pairwise comparisons on the scores. #' For more information on #' the computation of relative skill, see [get_pairwise_comparisons()]. #' Relative skill will be calculated for the aggregation level specified in #' `by`. +#' #' @inheritParams get_pairwise_comparisons #' @export -#' @keywords keyword scoring +#' @keywords scoring add_relative_skill <- function( scores, compare = "model", diff --git a/README.Rmd b/README.Rmd index 9f424ceea..a73c86a4d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -35,17 +35,17 @@ devel <- length(unclass(package_version(version))[[1]]) > 3 if (devel) { cat( "**Note**: ", - "[This documentation](https://epiforecasts.io/scoringutils/dev) refers to the development version of `scoringutils`. ", + "[This documentation](https://epiforecasts.io/scoringutils/dev/) refers to the development version of `scoringutils`. ", "You can also view the [documentation of the stable version]", - "(https://epiforecasts.io/scoringutils).", + "(https://epiforecasts.io/scoringutils/).", sep = "" ) } else { cat( "**Note**: ", - "[This documentation](https://epiforecasts.io/scoringutils) refers to the stable version of `scoringutils`. ", + "[This documentation](https://epiforecasts.io/scoringutils/) refers to the stable version of `scoringutils`. ", "You can also view the [documentation of the development version]", - "(https://epiforecasts.io/scoringutils/dev).", + "(https://epiforecasts.io/scoringutils/dev/).", sep = "" ) } @@ -163,7 +163,7 @@ The development of `scoringutils` was funded via the Health Protection Research -All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropenscilabs/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome! +All contributions to this project are gratefully acknowledged using the [`allcontributors` package](https://github.com/ropensci/allcontributors) following the [all-contributors](https://allcontributors.org) specification. Contributions of any kind are welcome! ### Code diff --git a/README.md b/README.md index 126e1da23..8facb2777 100644 --- a/README.md +++ b/README.md @@ -12,10 +12,11 @@ version](https://img.shields.io/github/r-package/v/epiforecasts/scoringutils) downloads](http://cranlogs.r-pkg.org/badges/grand-total/scoringutils)](https://cran.r-project.org/package=scoringutils) -**Note**: [This documentation](https://epiforecasts.io/scoringutils/dev) -refers to the development version of `scoringutils`. You can also view -the [documentation of the stable -version](https://epiforecasts.io/scoringutils). +**Note**: [This +documentation](https://epiforecasts.io/scoringutils/dev/) refers to the +development version of `scoringutils`. You can also view the +[documentation of the stable +version](https://epiforecasts.io/scoringutils/). The `scoringutils` package facilitates the process of evaluating forecasts in R, using a convenient and flexible `data.table`-based @@ -253,14 +254,15 @@ Health. ## Contributors + + All contributions to this project are gratefully acknowledged using the -[`allcontributors` -package](https://github.com/ropenscilabs/allcontributors) following the -[all-contributors](https://allcontributors.org) specification. -Contributions of any kind are welcome! +[`allcontributors` package](https://github.com/ropensci/allcontributors) +following the [all-contributors](https://allcontributors.org) +specification. Contributions of any kind are welcome! ### Code @@ -291,5 +293,7 @@ Contributions of any kind are welcome! kathsherratt + + diff --git a/man/add_relative_skill.Rd b/man/add_relative_skill.Rd index 62bf180ad..84cb88048 100644 --- a/man/add_relative_skill.Rd +++ b/man/add_relative_skill.Rd @@ -44,5 +44,4 @@ the computation of relative skill, see \code{\link[=get_pairwise_comparisons]{ge Relative skill will be calculated for the aggregation level specified in \code{by}. } -\keyword{keyword} \keyword{scoring} diff --git a/man/ae_median_quantile.Rd b/man/ae_median_quantile.Rd index 7314c7b70..20c40a9e2 100644 --- a/man/ae_median_quantile.Rd +++ b/man/ae_median_quantile.Rd @@ -25,13 +25,10 @@ Numeric vector of length N with the absolute error of the median. \description{ Compute the absolute error of the median calculated as \deqn{ - \textrm{abs}(\textrm{observed} - \textrm{median prediction}) -}{ - abs(observed - median_prediction) + |observed - median prediction| } -The median prediction is the predicted value for which quantile_level == 0.5, -the function therefore requires 0.5 to be among the quantile levels in -\code{quantile_level}. +The median prediction is the predicted value for which quantile_level == 0.5. +The function requires 0.5 to be among the quantile levels in \code{quantile_level}. } \section{Input format}{ \if{html}{ diff --git a/man/ae_median_sample.Rd b/man/ae_median_sample.Rd index a23b898f3..2e2d4b292 100644 --- a/man/ae_median_sample.Rd +++ b/man/ae_median_sample.Rd @@ -14,16 +14,15 @@ the number of data points and N (number of columns) the number of Monte Carlo samples. Alternatively, \code{predicted} can just be a vector of size n.} } \value{ -vector with the scoring values +Numeric vector of length n with the absolute errors of the median. } \description{ Absolute error of the median calculated as - -\deqn{% - \textrm{abs}(\textrm{observevd} - \textrm{median\_prediction}) -}{% - abs(observed - median_prediction) +\deqn{ + |observed - median\_prediction| } +where the median prediction is calculated as the median of the predictive +samples. } \section{Input format}{ \if{html}{ diff --git a/man/example_binary.Rd b/man/example_binary.Rd index 6d2a28ed7..dfe83e81f 100644 --- a/man/example_binary.Rd +++ b/man/example_binary.Rd @@ -20,7 +20,7 @@ following columns: } } \source{ -\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} } \usage{ example_binary diff --git a/man/example_nominal.Rd b/man/example_nominal.Rd index e07914840..71d18635a 100644 --- a/man/example_nominal.Rd +++ b/man/example_nominal.Rd @@ -21,7 +21,7 @@ following columns: } } \source{ -\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} } \usage{ example_nominal diff --git a/man/example_point.Rd b/man/example_point.Rd index a8872f0f8..a6f325e17 100644 --- a/man/example_point.Rd +++ b/man/example_point.Rd @@ -20,7 +20,7 @@ following columns: } } \source{ -\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} } \usage{ example_point diff --git a/man/example_quantile.Rd b/man/example_quantile.Rd index 6bbe1df3b..d16a04d18 100644 --- a/man/example_quantile.Rd +++ b/man/example_quantile.Rd @@ -21,7 +21,7 @@ following columns: } } \source{ -\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} } \usage{ example_quantile diff --git a/man/example_sample_continuous.Rd b/man/example_sample_continuous.Rd index 1e9a72273..3a447f3cd 100644 --- a/man/example_sample_continuous.Rd +++ b/man/example_sample_continuous.Rd @@ -21,7 +21,7 @@ following columns: } } \source{ -\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} } \usage{ example_sample_continuous diff --git a/man/example_sample_discrete.Rd b/man/example_sample_discrete.Rd index 75569fca4..040e9390a 100644 --- a/man/example_sample_discrete.Rd +++ b/man/example_sample_discrete.Rd @@ -21,7 +21,7 @@ following columns: } } \source{ -\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} +\url{https://github.com/european-modelling-hubs/covid19-forecast-hub-europe_archive/commit/a42867b1ea152c57e25b04f9faa26cfd4bfd8fa6/} } \usage{ example_sample_discrete diff --git a/man/get_metrics.Rd b/man/get_metrics.Rd index 14cf188dc..9c3f2192b 100644 --- a/man/get_metrics.Rd +++ b/man/get_metrics.Rd @@ -30,7 +30,7 @@ See \code{\link[=as_forecast]{as_forecast()}} for more information on \code{fore for more information on \code{scores} objects. } \seealso{ -Other \code{get_metrics} functions: +Other get_metrics functions: \code{\link{get_metrics.forecast_binary}()}, \code{\link{get_metrics.forecast_nominal}()}, \code{\link{get_metrics.forecast_point}()}, @@ -38,5 +38,5 @@ Other \code{get_metrics} functions: \code{\link{get_metrics.forecast_sample}()}, \code{\link{get_metrics.scores}()} } -\concept{\code{get_metrics} functions} +\concept{get_metrics functions} \keyword{handle-metrics} diff --git a/man/get_metrics.forecast_binary.Rd b/man/get_metrics.forecast_binary.Rd index ea7440fb4..98de45ae6 100644 --- a/man/get_metrics.forecast_binary.Rd +++ b/man/get_metrics.forecast_binary.Rd @@ -45,7 +45,7 @@ get_metrics(example_binary, select = "brier_score") get_metrics(example_binary, exclude = "log_score") } \seealso{ -Other \code{get_metrics} functions: +Other get_metrics functions: \code{\link{get_metrics}()}, \code{\link{get_metrics.forecast_nominal}()}, \code{\link{get_metrics.forecast_point}()}, @@ -53,5 +53,5 @@ Other \code{get_metrics} functions: \code{\link{get_metrics.forecast_sample}()}, \code{\link{get_metrics.scores}()} } -\concept{\code{get_metrics} functions} +\concept{get_metrics functions} \keyword{handle-metrics} diff --git a/man/get_metrics.forecast_nominal.Rd b/man/get_metrics.forecast_nominal.Rd index 8d6f556b6..45a35d08f 100644 --- a/man/get_metrics.forecast_nominal.Rd +++ b/man/get_metrics.forecast_nominal.Rd @@ -28,7 +28,7 @@ For nominal forecasts, the default scoring rule is: get_metrics(example_nominal) } \seealso{ -Other \code{get_metrics} functions: +Other get_metrics functions: \code{\link{get_metrics}()}, \code{\link{get_metrics.forecast_binary}()}, \code{\link{get_metrics.forecast_point}()}, @@ -36,5 +36,5 @@ Other \code{get_metrics} functions: \code{\link{get_metrics.forecast_sample}()}, \code{\link{get_metrics.scores}()} } -\concept{\code{get_metrics} functions} +\concept{get_metrics functions} \keyword{handle-metrics} diff --git a/man/get_metrics.forecast_point.Rd b/man/get_metrics.forecast_point.Rd index e47d56118..df83ce610 100644 --- a/man/get_metrics.forecast_point.Rd +++ b/man/get_metrics.forecast_point.Rd @@ -76,7 +76,7 @@ Making and Evaluating Point Forecasts, Gneiting, Tilmann, 2011, Journal of the American Statistical Association. } \seealso{ -Other \code{get_metrics} functions: +Other get_metrics functions: \code{\link{get_metrics}()}, \code{\link{get_metrics.forecast_binary}()}, \code{\link{get_metrics.forecast_nominal}()}, @@ -84,5 +84,5 @@ Other \code{get_metrics} functions: \code{\link{get_metrics.forecast_sample}()}, \code{\link{get_metrics.scores}()} } -\concept{\code{get_metrics} functions} +\concept{get_metrics functions} \keyword{handle-metrics} diff --git a/man/get_metrics.forecast_quantile.Rd b/man/get_metrics.forecast_quantile.Rd index fc3f248d4..10197406e 100644 --- a/man/get_metrics.forecast_quantile.Rd +++ b/man/get_metrics.forecast_quantile.Rd @@ -56,7 +56,7 @@ mean it would also get passed to \code{interval_coverage_50}. get_metrics(example_quantile, select = "wis") } \seealso{ -Other \code{get_metrics} functions: +Other get_metrics functions: \code{\link{get_metrics}()}, \code{\link{get_metrics.forecast_binary}()}, \code{\link{get_metrics.forecast_nominal}()}, @@ -64,5 +64,5 @@ Other \code{get_metrics} functions: \code{\link{get_metrics.forecast_sample}()}, \code{\link{get_metrics.scores}()} } -\concept{\code{get_metrics} functions} +\concept{get_metrics functions} \keyword{handle-metrics} diff --git a/man/get_metrics.forecast_sample.Rd b/man/get_metrics.forecast_sample.Rd index e51b65e41..422724893 100644 --- a/man/get_metrics.forecast_sample.Rd +++ b/man/get_metrics.forecast_sample.Rd @@ -48,7 +48,7 @@ For sample-based forecasts, the default scoring rules are: get_metrics(example_sample_continuous, exclude = "mad") } \seealso{ -Other \code{get_metrics} functions: +Other get_metrics functions: \code{\link{get_metrics}()}, \code{\link{get_metrics.forecast_binary}()}, \code{\link{get_metrics.forecast_nominal}()}, @@ -56,5 +56,5 @@ Other \code{get_metrics} functions: \code{\link{get_metrics.forecast_quantile}()}, \code{\link{get_metrics.scores}()} } -\concept{\code{get_metrics} functions} +\concept{get_metrics functions} \keyword{handle-metrics} diff --git a/man/get_metrics.scores.Rd b/man/get_metrics.scores.Rd index 944371f01..c011e9e72 100644 --- a/man/get_metrics.scores.Rd +++ b/man/get_metrics.scores.Rd @@ -46,7 +46,7 @@ order does not matter). } } \seealso{ -Other \code{get_metrics} functions: +Other get_metrics functions: \code{\link{get_metrics}()}, \code{\link{get_metrics.forecast_binary}()}, \code{\link{get_metrics.forecast_nominal}()}, @@ -54,5 +54,5 @@ Other \code{get_metrics} functions: \code{\link{get_metrics.forecast_quantile}()}, \code{\link{get_metrics.forecast_sample}()} } -\concept{\code{get_metrics} functions} +\concept{get_metrics functions} \keyword{handle-metrics} diff --git a/man/scoringutils-package.Rd b/man/scoringutils-package.Rd index 94b0d9172..328d649c6 100644 --- a/man/scoringutils-package.Rd +++ b/man/scoringutils-package.Rd @@ -6,7 +6,7 @@ \alias{scoringutils-package} \title{scoringutils: Utilities for Scoring and Assessing Predictions} \description{ -scoringutils facilitates the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The package mostly focuses on the evaluation of probabilistic forecasts and allows evaluating several different forecast types and input formats. Find more information about the package in the Vignettes as well as in the accompanying paper, \doi{10.48550/arXiv.2205.07090}. +Facilitate the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The package mostly focuses on the evaluation of probabilistic forecasts and allows evaluating several different forecast types and input formats. Find more information about the package in the Vignettes as well as in the accompanying paper, \doi{10.48550/arXiv.2205.07090}. } \seealso{ Useful links: diff --git a/vignettes/Deprecated-visualisations.Rmd b/vignettes/Deprecated-visualisations.Rmd index 492e241b3..78a3dafe3 100644 --- a/vignettes/Deprecated-visualisations.Rmd +++ b/vignettes/Deprecated-visualisations.Rmd @@ -18,7 +18,7 @@ knitr::opts_chunk$set( ) ``` -This Vignette provides the code for visualisations that were previously part of `scoringutils` but have been removed with `scoringutils` version `2.0`. For alternative ways to implemenent data visualisations, we refer to the `hubVis` [package](https://github.com/Infectious-Disease-Modeling-Hubs/hubVis). +This Vignette provides the code for visualisations that were previously part of `scoringutils` but have been removed with `scoringutils` version `2.0`. For alternative ways to implemenent data visualisations, we refer to the `hubVis` [package](https://github.com/hubverse-org/hubVis). The example data used is the data shipped with the `scoringutils` package. It consists of short-term forecasts of COVID-19 cases and deaths for several European countries, submitted to the European COVID-19 Forecast Hub. Every week, forecasters submitted 1 to 4 week ahead forecasts (the "forecast horizon", here restricted to 1 to 3 week ahead). The dates for which a forecast was made are called `target_end_date`. See e.g. `?example_quantile` for more information.