Merge branch 'develop' into rework-validate_forceasts

NAMESPACE

@@ -59,10 +59,15 @@ export(plot_score_table)
 export(plot_wis)
 export(quantile_score)
 export(quantile_to_interval)
+export(rules_binary)
+export(rules_point)
+export(rules_quantile)
+export(rules_sample)
 export(run_safely)
 export(sample_to_quantile)
 export(score)
 export(se_mean_sample)
+export(select_rules)
 export(set_forecast_unit)
 export(squared_error)
 export(summarise_scores)
@@ -86,6 +91,7 @@ importFrom(checkmate,assert_logical)
 importFrom(checkmate,assert_number)
 importFrom(checkmate,assert_numeric)
 importFrom(checkmate,assert_string)
+importFrom(checkmate,assert_subset)
 importFrom(checkmate,assert_vector)
 importFrom(checkmate,check_atomic_vector)
 importFrom(checkmate,check_data_frame)

NEWS.md

@@ -1,4 +1,4 @@
-# scoringutils 1.3
+# scoringutils 2.0.0
 
 This major update and addresses a variety of comments made by reviewers from the Journal of Statistical Software (see preprint of the manuscript [here](https://arxiv.org/abs/2205.07090)).
 
@@ -7,20 +7,21 @@ The update introduces breaking changes. If you want to keep using the older vers
 ## Package updates
 - In `score()`, required columns "true_value" and "prediction" were renamed and replaced by required columns "observed" and "predicted". Scoring functions now also use the function arguments "observed" and "predicted" everywhere consistently. 
 - The overall scoring workflow was updated. `score()` is now a generic function that dispatches the correct method based on the forecast type. forecast types currently supported are "binary", "point", "sample" and "quantile" with corresponding classes "forecast_binary", "forecast_point", "forecast_sample" and "forecast_quantile". An object of class `forecast_*` can be created using the function `as_forecast()`, which also replaces the previous function `check_forecasts()` (see more information below). 
-- Scoring functions received a consistent interface and input checks:
-  - metrics for binary forecasts:
+- Scoring rules (functions used for scoring) received a consistent interface and input checks:
+  - Scoring rules for binary forecasts:
     - `observed`: factor with exactly 2 levels
     - `predicted`: numeric, vector with probabilities
-  - metrics for point forecasts:
+  - Scoring rules for point forecasts:
     - `observed`: numeric vector
     - `predicted`: numeric vector
-  - metrics for sample-based forecasts:
+  - Scoring rules for sample-based forecasts:
     - `observed`: numeric, either a scalar or a vector
     - `predicted`: numeric, a vector (if `observed` is a scalar) or a matrix (if `observed` is a vector)
-  - metrics for quantile-based forecasts:
+  - Scoring rules for quantile-based forecasts:
     - `observed`: numeric, either a scalar or a vector
     - `predicted`: numeric, a vector (if `observed` is a scalar) or a matrix (if `observed` is a vector)
     - `quantile`: numeric, a vector with quantile-levels. Can alternatively be a matrix of the same shape as `predicted`.
+- Users can now supply their own scoring rules to `score()` as a list of functions. Default scoring rules can be accessed using the functions `rules_point()`, `rules_sample()`, `rules_quantile()` and `rules_binary()`, which return a list of scoring rules suitable for the respective forecast type.
 - `check_forecasts()` was replaced by a different workflow. There now is a function, `as_forecast()`, that determines forecast type of the data, constructs a forecasting object and validates it using the function `validate_forecast()` (a generic that dispatches the correct method based on the forecast type). Objects of class `forecast_binary`, `forecast_point`, `forecast_sample` and `forecast_quantile` have print methods that fulfill the functionality of `check_forecasts()`.
 - The functionality for computing pairwise comparisons was now split from `summarise_scores()`. Instead of doing pairwise comparisons as part of summarising scores, a new function, `add_pairwise_comparison()`, was introduced that takes summarised scores as an input and adds pairwise comparisons to it. 
 - `add_coverage()` was reworked completely. It's new purpose is now to add coverage information to the raw forecast data (essentially fulfilling some of the functionality that was previously covered by `score_quantile()`)

R/check-input-helpers.R

@@ -211,6 +211,7 @@ assure_model_column <- function(data) {
 #' @inherit document_check_functions params return
 #' @keywords internal_input_check
 check_number_per_forecast <- function(data, forecast_unit) {
+  data <- na.omit(data)
   # check whether there are the same number of quantiles, samples --------------
   data[, scoringutils_InternalNumCheck := length(predicted), by = forecast_unit]
   n <- unique(data$scoringutils_InternalNumCheck)

R/data.R

@@ -195,51 +195,3 @@
 #'
 #' @keywords info
 "metrics"
-
-#' Default metrics for binary forecasts.
-#'
-#' A named list with functions:
-#' - "brier_score" = [brier_score()]
-#' - "log_score" = [logs_binary()]
-#' @keywords info
-"metrics_binary"
-
-#' Default metrics for point forecasts.
-#'
-#' A named list with functions:
-#' - "ae_point" = [ae()][Metrics::ae()]
-#' - "se_point" = [se()][Metrics::se()]
-#' - "ape" = [ape()][Metrics::ape()]
-#' @keywords info
-"metrics_point"
-
-#' Default metrics for sample-based forecasts.
-#'
-#' A named list with functions:
-#' - "mad" = [mad_sample()]
-#' - "bias" = [bias_sample()]
-#' - "dss" = [dss_sample()]
-#' - "crps" = [crps_sample()]
-#' - "log_score" = [logs_sample()]
-#' - "mad" = [mad_sample()]
-#' - "ae_median" = [ae_median_sample()]
-#' - "se_mean" = [se_mean_sample()]
-#' @keywords info
-"metrics_sample"
-
-#' Default metrics for quantile-based forecasts.
-#'
-#' A named list with functions:
-#' - "wis" = [wis]
-#' - "overprediction" = [overprediction()]
-#' - "underprediction" = [underprediction()]
-#' - "dispersion" = [dispersion()]
-#' - "bias" = [bias_quantile()]
-#' - "coverage_50" = [interval_coverage_quantile()]
-#' - "coverage_90" = \(...) \{
-#'      run_safely(..., range = 90, fun = [interval_coverage_quantile])
-#'   \}
-#' - "coverage_deviation" = [interval_coverage_dev_quantile()],
-#' - "ae_median" = [ae_median_quantile()]
-#' @keywords info
-"metrics_quantile"

R/default-scoring-rules.R

@@ -0,0 +1,169 @@
+#' @title Select Scoring Rules From A List of Possible Scoring Rules
+#' @description Helper function to return only the scoring rules selected by
+#' the user from a list of possible scoring rules.
+#' @param rules A list of scoring rules.
+#' @param select A character vector of scoring rules to select from the list.
+#' If `select` is `NULL` (the default), all possible scoring rules are returned.
+#' @param exclude A character vector of scoring rules to exclude from the list.
+#' If `select` is not `NULL`, this argument is ignored.
+#' @return A list of scoring rules.
+#' @keywords metric
+#' @importFrom checkmate assert_subset assert_list
+#' @export
+#' @examples
+#' select_rules(
+#'   rules = rules_binary(),
+#'   select = "brier_score"
+#' )
+#' select_rules(
+#'   rules = rules_binary(),
+#'   exclude = "log_score"
+#' )
+select_rules <- function(rules, select = NULL, exclude = NULL) {
+  assert_character(x = c(select, exclude), null.ok = TRUE)
+  assert_list(rules, names = "named")
+  allowed <- names(rules)
+
+  if (is.null(select) && is.null(exclude)) {
+    return(rules)
+  } else if (is.null(select)) {
+    assert_subset(exclude, allowed)
+    select <- allowed[!allowed %in% exclude]
+    return(rules[select])
+  } else {
+    assert_subset(select, allowed)
+    return(rules[select])
+  }
+}
+
+
+#' @title Scoring Rules for Binary Forecasts
+#' @description Helper function that returns a named list of default
+#' scoring rules suitable for binary forecasts.
+#'
+#' The default scoring rules are:
+#' - "brier_score" = [brier_score()]
+#' - "log_score" = [logs_binary()]
+#' @inherit select_rules params return
+#' @export
+#' @keywords metric
+#' @examples
+#' rules_binary()
+#' rules_binary(select = "brier_score")
+#' rules_binary(exclude = "log_score")
+rules_binary <- function(select = NULL, exclude = NULL) {
+  all <- list(
+    brier_score = brier_score,
+    log_score = logs_binary
+  )
+  selected <- select_rules(all, select, exclude)
+  return(selected)
+}
+
+
+#' @title Scoring Rules for Point Forecasts
+#' @description Helper function that returns a named list of default
+#' scoring rules suitable for point forecasts.
+#'
+#' The default scoring rules are:
+#' - "ae_point" = [ae()][Metrics::ae()]
+#' - "se_point" = [se()][Metrics::se()]
+#' - "ape" = [ape()][Metrics::ape()]
+#' @inherit select_rules params return
+#' @export
+#' @keywords metric
+#' @examples
+#' rules_point()
+#' rules_point(select = "ape")
+rules_point <- function(select = NULL, exclude = NULL) {
+  all <- list(
+    ae_point = Metrics::ae,
+    se_point = Metrics::se,
+    ape = Metrics::ape
+  )
+  selected <- select_rules(all, select, exclude)
+  return(selected)
+}
+
+
+#' @title Scoring Rules for Sample-Based Forecasts
+#' @description Helper function that returns a named list of default
+#' scoring rules suitable for forecasts in a sample-based format
+#'
+#' The default scoring rules are:
+#' - "mad" = [mad_sample()]
+#' - "bias" = [bias_sample()]
+#' - "dss" = [dss_sample()]
+#' - "crps" = [crps_sample()]
+#' - "log_score" = [logs_sample()]
+#' - "mad" = [mad_sample()]
+#' - "ae_median" = [ae_median_sample()]
+#' - "se_mean" = [se_mean_sample()]
+#' @inherit select_rules params return
+#' @export
+#' @keywords metric
+#' @examples
+#' rules_sample()
+#' rules_sample(select = "mad")
+rules_sample <- function(select = NULL, exclude = NULL) {
+  all <- list(
+    bias = bias_sample,
+    dss = dss_sample,
+    crps = crps_sample,
+    log_score = logs_sample,
+    mad = mad_sample,
+    ae_median = ae_median_sample,
+    se_mean = se_mean_sample
+  )
+  selected <- select_rules(all, select, exclude)
+  return(selected)
+}
+
+
+#' @title Scoring Rules for Quantile-Based Forecasts
+#' @description Helper function that returns a named list of default
+#' scoring rules suitable for forecasts in a quantile-based format
+#'
+#' The default scoring rules are:
+#' - "wis" = [wis]
+#' - "overprediction" = [overprediction()]
+#' - "underprediction" = [underprediction()]
+#' - "dispersion" = [dispersion()]
+#' - "bias" = [bias_quantile()]
+#' - "coverage_50" = [interval_coverage_quantile()]
+#' - "coverage_90" = function(...) \{
+#'      run_safely(..., range = 90, fun = [interval_coverage_quantile])
+#'   \}
+#' - "coverage_deviation" = [interval_coverage_dev_quantile()],
+#' - "ae_median" = [ae_median_quantile()]
+#'
+#' Note: The `coverage_90` scoring rule is created as a wrapper around
+#' [interval_coverage_quantile()], making use of the function [run_safely()].
+#' This construct allows the function to deal with arbitrary arguments in `...`,
+#' while making sure that only those that [interval_coverage_quantile()] can
+#' accept get passed on to it. `range = 90` is set in the function definition,
+#' as passing an argument `range = 90` to [score()] would mean it would also
+#' get passed to `coverage_50`.
+#' @inherit select_rules params return
+#' @export
+#' @keywords metric
+#' @examples
+#' rules_quantile()
+#' rules_quantile(select = "wis")
+rules_quantile <- function(select = NULL, exclude = NULL) {
+  all <- list(
+    wis = wis,
+    overprediction = overprediction,
+    underprediction = underprediction,
+    dispersion = dispersion,
+    bias = bias_quantile,
+    coverage_50 = interval_coverage_quantile,
+    coverage_90 = function(...) {
+      run_safely(..., range = 90, fun = interval_coverage_quantile)
+    },
+    coverage_deviation = interval_coverage_dev_quantile,
+    ae_median = ae_median_quantile
+  )
+  selected <- select_rules(all, select, exclude)
+  return(selected)
+}

R/score.R

@@ -16,8 +16,8 @@
 #' @inheritSection forecast_types Forecast unit
 #' @param data A data.frame or data.table with predicted and observed values.
 #' @param metrics A named list of scoring functions. Names will be used as
-#' column names in the output. See [metrics_point()], [metrics_binary()],
-#' `metrics_quantile()`, and [metrics_sample()] for more information on the
+#' column names in the output. See [rules_point()], [rules_binary()],
+#' [rules_quantile()], and [rules_sample()] for more information on the
 #' default metrics used.
 #' @param ... additional arguments
 #' @return A data.table with unsummarised scores. This will generally be
@@ -78,7 +78,7 @@ score.default <- function(data, ...) {
 #' @importFrom stats na.omit
 #' @rdname score
 #' @export
-score.forecast_binary <- function(data, metrics = metrics_binary, ...) {
+score.forecast_binary <- function(data, metrics = rules_binary(), ...) {
   data <- validate_forecast(data)
   data <- na.omit(data)
   metrics <- validate_metrics(metrics)
@@ -99,7 +99,7 @@ score.forecast_binary <- function(data, metrics = metrics_binary, ...) {
 #' @importFrom stats na.omit
 #' @rdname score
 #' @export
-score.forecast_point <- function(data, metrics = metrics_point, ...) {
+score.forecast_point <- function(data, metrics = rules_point(), ...) {
   data <- validate_forecast(data)
   data <- na.omit(data)
   metrics <- validate_metrics(metrics)
@@ -117,7 +117,7 @@ score.forecast_point <- function(data, metrics = metrics_point, ...) {
 #' @importFrom stats na.omit
 #' @rdname score
 #' @export
-score.forecast_sample <- function(data, metrics = metrics_sample, ...) {
+score.forecast_sample <- function(data, metrics = rules_sample(), ...) {
   data <- validate_forecast(data)
   data <- na.omit(data)
   forecast_unit <- get_forecast_unit(data)
@@ -155,7 +155,7 @@ score.forecast_sample <- function(data, metrics = metrics_sample, ...) {
 #' @importFrom data.table `:=` as.data.table rbindlist %like%
 #' @rdname score
 #' @export
-score.forecast_quantile <- function(data, metrics = metrics_quantile, ...) {
+score.forecast_quantile <- function(data, metrics = rules_quantile(), ...) {
   data <- validate_forecast(data)
   data <- na.omit(data)
   forecast_unit <- get_forecast_unit(data)

R/utils.R

@@ -133,7 +133,7 @@ strip_attributes <- function(object, attributes) {
 
 #' @title Run a function safely
 #' @description This is a wrapper function designed to run a function safely
-#' when it is not completely clear what arguments coulld be passed to the
+#' when it is not completely clear what arguments could be passed to the
 #' function.
 #'
 #' All named arguments in `...` that are not accepted by `fun` are removed.

R/z_globalVariables.R

@@ -44,10 +44,10 @@ globalVariables(c(
   "metric",
   "metrics_select",
   "metrics",
-  "metrics_binary",
-  "metrics_point",
-  "metrics_quantile",
-  "metrics_sample",
+  "rules_binary",
+  "rules_point",
+  "rules_quantile",
+  "rules_sample",
   "model",
   "n_obs",
   "n_obs wis_component_name",