Major update

.Rbuildignore

@@ -11,4 +11,7 @@
 ^doc$
 ^Meta$
 ^_pkgdown\.yml$
-^\.devcontainer$
+^inst/manuscript/manuscript_cache$
+^\.lintr$
+^docs$
+^\.devcontainer$

.Rinstignore

@@ -0,0 +1,5 @@
+inst/manuscript/manuscript_cache/
+inst/manuscript/manuscript.log
+inst/manuscript/manuscript.pdf
+inst/manuscript/manuscript.tex
+inst/manuscript/manuscript_files/

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/CONTRIBUTING.md

@@ -0,0 +1,45 @@
+# Contributing to scoringutils
+
+This outlines how to propose a change to scoringutils. 
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("epiforecasts/scoringutils", fork = TRUE)`.
+
+*   Install all development dependences with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the scoringutils project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/workflows/lint.yaml

@@ -0,0 +1,49 @@
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("remotes"))
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("lintr")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}

.github/workflows/test-coverage.yaml

@@ -11,6 +11,8 @@ name: test-coverage
 jobs:
   test-coverage:
     runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 

.gitignore

@@ -6,3 +6,9 @@ inst/doc
 R/sandbox.R
 doc
 Meta
+inst/manuscript/manuscript_cache/
+inst/manuscript/manuscript.log
+inst/manuscript/manuscript.pdf
+inst/manuscript/manuscript.tex
+inst/manuscript/manuscript_files/
+docs

.lintr

@@ -0,0 +1,6 @@
+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))
+exclude: "# nolint"

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: scoringutils
 Title: Utilities for Scoring and Assessing Predictions
-Version: 0.1.8
+Version: 1.0.0
 Language: en-GB
 Authors@R: c(
     person(given = "Nikos",
@@ -21,22 +21,9 @@ Authors@R: c(
            role = c("ctb"),
            email = "johannes.bracher@kit.edu",
            comment = c(ORCID = "0000-0002-3777-1410")), 
-    person("Joel", "Hellewell",
-           email = "joel.hellewell@lshtm.ac.uk", 
-           role = c("ctb"),
-           comment = c(ORCID = "0000-0003-2683-0849")),
-    person(given = "Sophie Meakins",
-           role = c("ctb"),
-           email = "sophie.meakins@lshtm.ac.uk"),  
-    person("James", "Munday", 
-           email = "james.munday@lshtm.ac.uk", 
-           role = c("ctb")),
-    person("Katharine", "Sherratt", 
-           email = "katharine.sherratt@lshtm.ac.uk", 
-           role = c("ctb")),
     person("Sebastian", "Funk", 
             email = "sebastian.funk@lshtm.ac.uk", 
-            role = c("aut")))
+            role = c("ctb")))
 Description: 
     Combines a collection of metrics and proper scoring rules 
     (Tilmann Gneiting & Adrian E Raftery (2007) 
@@ -61,21 +48,26 @@ Encoding: UTF-8
 LazyData: true
 Imports: 
     data.table,
-    forcats,
+    ggdist (>= 3.1.0),
     ggplot2,
-    goftest,
     scoringRules,
     stats,
     methods
 Suggests: 
     testthat,
+    kableExtra,
+    magrittr,
     knitr,
     rmarkdown,
     vdiffr
-RoxygenNote: 7.1.1
+Config/Needs/website: 
+    r-lib/pkgdown,
+    amirmasoudabdol/preferably
+Config/testthat/edition: 3
+RoxygenNote: 7.1.2
 URL: https://github.com/epiforecasts/scoringutils, https://epiforecasts.io/scoringutils/
 BugReports: https://github.com/epiforecasts/scoringutils/issues
 VignetteBuilder: knitr
 Depends: 
-    R (>= 3.1)
+    R (>= 3.5)
 Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -2,51 +2,50 @@
 
 S3method(print,scoringutils_check)
 export(abs_error)
+export(add_coverage)
 export(ae_median_quantile)
 export(ae_median_sample)
+export(avail_forecasts)
 export(available_metrics)
-export(bias)
+export(bias_quantile)
+export(bias_range)
+export(bias_sample)
 export(brier_score)
 export(check_forecasts)
-export(correlation_plot)
-export(crps)
-export(dss)
-export(eval_forecasts)
-export(interval_coverage)
+export(correlation)
+export(crps_sample)
+export(dss_sample)
+export(find_duplicates)
 export(interval_score)
-export(logs)
+export(logs_binary)
+export(logs_sample)
+export(mad_sample)
 export(merge_pred_and_obs)
-export(mse)
 export(pairwise_comparison)
 export(pit)
-export(pit_df)
-export(pit_df_fast)
+export(pit_sample)
+export(plot_avail_forecasts)
+export(plot_correlation)
+export(plot_heatmap)
+export(plot_interval_coverage)
 export(plot_pairwise_comparison)
+export(plot_pit)
 export(plot_predictions)
-export(quantile_bias)
-export(quantile_coverage)
-export(quantile_to_long)
-export(quantile_to_range)
-export(quantile_to_range_long)
-export(quantile_to_wide)
-export(range_long_to_quantile)
-export(range_long_to_wide)
-export(range_plot)
-export(range_to_quantile)
-export(range_wide_to_long)
+export(plot_quantile_coverage)
+export(plot_ranges)
+export(plot_score_table)
+export(plot_wis)
+export(quantile_score)
 export(sample_to_quantile)
-export(sample_to_range)
-export(sample_to_range_long)
-export(score_heatmap)
-export(score_table)
-export(sharpness)
-export(show_avail_forecasts)
-export(wis_components)
+export(score)
+export(se_mean_sample)
+export(squared_error)
+export(summarise_scores)
+export(theme_scoringutils)
 importFrom(data.table,"%like%")
 importFrom(data.table,':=')
 importFrom(data.table,.I)
 importFrom(data.table,.N)
-importFrom(data.table,`%like%`)
 importFrom(data.table,`:=`)
 importFrom(data.table,as.data.table)
 importFrom(data.table,copy)
@@ -57,39 +56,48 @@ importFrom(data.table,melt)
 importFrom(data.table,rbindlist)
 importFrom(data.table,setDT)
 importFrom(data.table,setnames)
-importFrom(forcats,fct_relevel)
-importFrom(forcats,fct_rev)
+importFrom(ggdist,geom_lineribbon)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,aes_string)
 importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expand_limits)
 importFrom(ggplot2,facet_grid)
 importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_col)
 importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_linerange)
 importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_polygon)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_tile)
 importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_color_continuous)
 importFrom(ggplot2,scale_colour_manual)
+importFrom(ggplot2,scale_fill_gradient)
 importFrom(ggplot2,scale_fill_gradient2)
 importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,stat)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_light)
+importFrom(ggplot2,theme_minimal)
 importFrom(ggplot2,unit)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
-importFrom(goftest,ad.test)
 importFrom(methods,hasArg)
 importFrom(scoringRules,crps_sample)
 importFrom(scoringRules,dss_sample)
 importFrom(scoringRules,logs_sample)
+importFrom(stats,as.formula)
 importFrom(stats,cor)
 importFrom(stats,mad)
 importFrom(stats,median)