Merge pull request #958 from epiforecasts/cran-release

Fix notes related to CRAN checks
epiforecasts · Oct 30, 2024 · ca235be · ca235be
2 parents 2649232 + bfd0b5c
commit ca235be
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -41,7 +41,7 @@ Authors@R: c(
            email = "[email protected]",
            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
@@ -98,7 +98,7 @@ score.forecast_binary <- function(forecast, metrics = get_metrics(forecast), ...
 #' @param ... unused
 #' @returns 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -556,31 +556,29 @@ 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
 #' @returns 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))
 #' ae_median_quantile(
 #'   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
@@ -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
-#' @returns vector with the scoring values
+#' @returns 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
@@ -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
@@ -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
@@ -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
 <!-- prettier-ignore-start -->
 <!-- markdownlint-disable -->
 
-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
@@ -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)
 <!-- badges: end -->
 
-**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-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+
 <!-- prettier-ignore-start -->
+
 <!-- markdownlint-disable -->
 
 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!
 <a href="https://github.com/epiforecasts/scoringutils/issues?q=is%3Aissue+commenter%3Akathsherratt">kathsherratt</a>
 
 <!-- markdownlint-enable -->
+
 <!-- prettier-ignore-end -->
+
 <!-- ALL-CONTRIBUTORS-LIST:END -->
diff --git a/man/add_relative_skill.Rd b/man/add_relative_skill.Rd
diff --git a/man/ae_median_quantile.Rd b/man/ae_median_quantile.Rd
diff --git a/man/ae_median_sample.Rd b/man/ae_median_sample.Rd
diff --git a/man/example_binary.Rd b/man/example_binary.Rd
diff --git a/man/example_nominal.Rd b/man/example_nominal.Rd
diff --git a/man/example_point.Rd b/man/example_point.Rd
diff --git a/man/example_quantile.Rd b/man/example_quantile.Rd
diff --git a/man/example_sample_continuous.Rd b/man/example_sample_continuous.Rd
diff --git a/man/example_sample_discrete.Rd b/man/example_sample_discrete.Rd