update branch from master

.devcontainer/library-scripts/common-debian.sh

@@ -102,7 +102,6 @@ if [ "${PACKAGES_ALREADY_INSTALLED}" != "true" ]; then
         libkrb5-3 \
         libgssapi-krb5-2 \
         libicu[0-9][0-9] \
-        liblttng-ust0 \
         libstdc++6 \
         zlib1g \
         locales \

.github/workflows/lint.yaml

@@ -1,30 +1,49 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  push:
-    branches: [main, master, develop]
   pull_request:
-    branches: [main, master, develop]
+    branches:
+      - main
+      - master
+      - develop
+  workflow_dispatch:
 
-name: lint
+name: lint-changed-files
 
 jobs:
-  lint:
+  lint-changed-files:
     runs-on: ubuntu-latest
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::lintr
-          needs: lint
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+          needs: check
+
+      - name: Add lintr options
+        run: |
+          cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
 
-      - name: Lint
-        run: lintr::lint_package()
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
+          changed_files <- purrr::map_chr(files, "filename")
+          all_files <- list.files(recursive = TRUE)
+          exclusions_list <- as.list(setdiff(all_files, changed_files))
+          lintr::lint_package(exclusions = exclusions_list)
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.lintr

@@ -1,7 +1,16 @@
-linters: with_defaults(
-    line_length_linter = line_length_linter(120),
-    cyclocomp_linter = cyclocomp_linter(complexity_limit = 20L),
-    object_usage_linter = NULL)
-exclusions: c(list.files(path = "tests/", recursive = T, full.names = T),
- list.files(path = "inst/", recursive = T, full.names = T))
+linters: linters_with_tags(
+    tags = NULL, # include all linters
+    implicit_integer_linter = NULL,
+    extraction_operator_linter = NULL,
+    undesirable_function_linter = NULL,
+    function_argument_linter = NULL,
+    object_name_linter = NULL,
+    line_length_linter(120),
+    cyclocomp_linter(20L)
+  )
+exclusions: c(
+    list.files("tests", recursive = TRUE, full.names = TRUE),
+    list.files("inst", recursive = TRUE, full.names = TRUE),
+    "vignettes/metric-details.Rmd"
+  )
 exclude: "# nolint"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scoringutils
 Title: Utilities for Scoring and Assessing Predictions
-Version: 1.1.0
+Version: 1.1.4
 Language: en-GB
 Authors@R: c(
     person(given = "Nikos",
@@ -23,7 +23,7 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-3777-1410")), 
     person("Sebastian", "Funk", 
             email = "[email protected]", 
-            role = c("ctb")))
+            role = c("aut")))
 Description: 
     Provides a collection of metrics and proper scoring rules 
     (Tilmann Gneiting & Adrian E Raftery (2007) 
@@ -41,7 +41,8 @@ Description:
     Scoring metrics can be used either through a convenient data.frame format, 
     or can be applied as individual functions in a vector / matrix format. 
     All functionality has been implemented with a focus on performance and is 
-    robustly tested. 
+    robustly tested. Find more information about scoringutils in the 
+    accompanying paper (Bosse et al., 2022) <arXiv:2205.07090v1>. 
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -66,7 +67,7 @@ Config/Needs/website:
     amirmasoudabdol/preferably
 Config/testthat/edition: 3
 RoxygenNote: 7.2.3
-URL: https://epiforecasts.io/scoringutils/, https://github.com/epiforecasts/scoringutils
+URL: https://doi.org/10.48550/arXiv.2205.07090, https://epiforecasts.io/scoringutils/, https://github.com/epiforecasts/scoringutils
 BugReports: https://github.com/epiforecasts/scoringutils/issues
 VignetteBuilder: knitr
 Depends: 

NAMESPACE

@@ -3,7 +3,6 @@
 S3method(print,scoringutils_check)
 export(abs_error)
 export(add_coverage)
-export(add_transformation)
 export(ae_median_quantile)
 export(ae_median_sample)
 export(avail_forecasts)
@@ -18,6 +17,7 @@ export(crps_sample)
 export(dss_sample)
 export(find_duplicates)
 export(interval_score)
+export(log_shift)
 export(logs_binary)
 export(logs_sample)
 export(mad_sample)
@@ -46,6 +46,7 @@ export(squared_error)
 export(summarise_scores)
 export(summarize_scores)
 export(theme_scoringutils)
+export(transform_forecasts)
 importFrom(data.table,"%like%")
 importFrom(data.table,':=')
 importFrom(data.table,.I)
@@ -102,6 +103,7 @@ importFrom(ggplot2,ylab)
 importFrom(lifecycle,deprecated)
 importFrom(methods,hasArg)
 importFrom(rlang,enexprs)
+importFrom(rlang,warn)
 importFrom(scoringRules,crps_sample)
 importFrom(scoringRules,dss_sample)
 importFrom(scoringRules,logs_sample)