Initial fully functioning package (#11)

* initial commit for CFR calculation

* removing duplicate/redudant functions for new approach

* editing README to include new use case for Ebola

* adding initial plot

* adding ggplot2 dependency and sourcing plotting functions

* changing README to reflect changes to script

* adding plot to README

* fixing plot in README

* fixing plot

* removing plot from README

* removing data.table dependency and adding package structure for existing
functions

* Add unit tests and related snapshots

* Remove scripts and plots dirs

* Add R CMD check, test-coverage, linter workflows

* Add Ebola 1976 outbreak data to package

* Add Ebola 1976 data file to extdata

* Add package infrastructure files

* Clean static_cfr + exs, output is named vector

* Clean rolling_cfr + exs, use data.table

* Simplify ccfr_uncertainty, output is named vec

* Input checks format_cfr, add full example

* Clean known_outcomes + example

* Update plot fun with input checking and namespacing

* Remove old snapshot

* Add datadelay package file

* Add revised documentation

* Update DESCR, epiparam to sgsts, rm lubridate/reshap2, add data.table

* Rm ggplot funs, add data.table funs to NAMESPACE

* Use README.Rmd, add example from scripts

* Add render-readme workflow

* Install epiparameter from Github

* Fix linter errors

* Ebola data uses Date class

* Allow deaths equal to cases

* Check delay_pmf only if passed

* Add Covid-19 USA example

* Add to gitignore

* Add {covidregionaldata} to suggests

* Use GH version of {covidregionaldata}

* Update snapshot for dataframe not datatable

* Correct rolling_cfr TESTS

* Add author, add rlang dep

* Rename ccfr_estimation to estimate_ccfr

* Input checking and full matching for known_outcomes

* Initialise output objs, reorder correction workflow

* Use .data pronoun from rlang

* Update documentation

* Correct README to use delay_pmf

* Update plot snapshot and package namespace script

* Update check workflows

* Style and add dependency R > 3.5.0

* Automatic readme update

* Vectorise likelihood calculation

* Add figures, fix style, fix examples

* Automatic readme update

* Correct convolution, fixes #17

* Correct likelihood calculation, fixes #18

* Rewrite `rolling_cfr` to avoid repeated `static_cfr` calls

* Minor corrections; update documentation

* Correct snapshots

* Update data documentation

* Update README figures

* Update static CFR print format

Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>

* Update print CFR snapshots

* Clarify rolling CFR as real-time CFR

Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>

* Automatic readme update

* Add usethis to suggests

Co-authored-by: thimotei <timothywilliamrussell@gmail.com>
Co-authored-by: GitHub Action <action@github.com>
Co-authored-by: Adam Kucharski <adam.kucharski@lshtm.ac.uk>

.Rbuildignore

@@ -1,2 +1,8 @@
-^datadelay\.Rproj$
+^.*\.Rproj$
 ^\.Rproj\.user$
+^LICENSE\.md$
+^\.github$
+^codecov\.yml$
+^README\.Rmd$
+^\.lintr$
+^data-raw$

.github/.gitignore

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

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# 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]
+  pull_request:
+    branches:
+      - "*"
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/lint-changed-files.yaml

@@ -0,0 +1,45 @@
+# 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:
+  pull_request:
+    branches: [main, master]
+
+name: lint-changed-files
+
+jobs:
+  lint-changed-files:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+            epiverse-trace/etdev
+          needs: check
+
+      - name: Add lintr options
+        run: |
+          cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("GET https://api.github.com/repos/${{ 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

.github/workflows/render_readme.yml

@@ -0,0 +1,63 @@
+# Name of the workflow
+name: render-readme
+
+# Controls when the action will run. Triggers include:
+# 
+# - button trigger from github action page
+# - on changes to readme.Rmd
+
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - 'README.Rmd'
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  render-readme:
+    runs-on: macos-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repos
+        uses: actions/checkout@v2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Setup pandoc
+        uses: r-lib/actions/setup-pandoc@v2
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rmarkdown, local::.
+
+      - name: Compile the readme
+        run: |
+          tf <- tempfile(fileext = ".Rmd")
+          writeLines(
+            knitr::knit_expand(
+              "README.Rmd", 
+              packagename = read.dcf("DESCRIPTION", "Package"), 
+              gh_repo = Sys.getenv("GITHUB_REPOSITORY")
+            ), 
+            tf
+          )
+          rmarkdown::render(tf, output_file = "README.md", output_dir = ".")
+        shell: Rscript {0}
+
+      - name: Commit files
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add README.md
+          # Also add README figures if they exist
+          if [ -d man/figures ]
+          then
+            git add man/figures/
+          fi
+          git diff-index --quiet HEAD || git commit -m "Automatic readme update"
+          git push origin || echo "No changes to push"

.github/workflows/test-coverage.yaml

@@ -0,0 +1,51 @@
+# 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]
+  pull_request:
+    branches:
+      - "*"
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - 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::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -1 +1,9 @@
 .Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+docs
+inst/doc
+/doc/
+/Meta/

.lintr

@@ -0,0 +1,11 @@
+linters: linters_with_tags(
+    tags = NULL, # include all linters
+    object_name_linter = NULL,
+    undesirable_function_linter = NULL,
+    implicit_integer_linter = NULL,
+    extraction_operator_linter = NULL,
+    todo_comment_linter = NULL,
+    function_argument_linter = NULL,
+    # Use minimum R declared in DESCRIPTION or fall back to current R version
+    backport_linter(if (length(x <- etdev::extract_min_r_version())) x else getRversion())
+  )

DESCRIPTION

@@ -1,12 +1,50 @@
 Package: datadelay
 Title: Delay Functions for Epidemic Data
 Version: 0.1
-Authors@R: 
-    person("Adam", "Kucharski", , "adam.kucharski@lshtm.ac.uk", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-8814-9421"))
+Authors@R: c(
+    person(
+        given = "Adam",
+        family = "Kucharski",
+        email = "adam.kucharski@lshtm.ac.uk", 
+        role = c("aut", "cre"),
+        comment = c(ORCID = "0000-0001-8814-9421")
+        ),
+    person(
+          given = "Tim",
+          family = "Russell",
+          email = "timothy.russell@lshtm.ac.uk", 
+          role = c("aut"),
+          comment = c(ORCID = "0000-0001-5610-6080")
+        ),
+    person(
+          given = "Pratik",
+          family = "Gupte",
+          role = c("aut"),
+          email = "pratik.gupte@lshtm.ac.uk",
+          comment = c(ORCID = "0000-0001-5294-7819")
+        )
+    )
 Description: Delay functions for routine surveillance data.
-License: `use_mit_license()`, `use_gpl3_license()` or friends to pick a
-    license
+License: MIT + file LICENSE
+URL: https://github.com/epiverse-trace/datadelay
+BugReports: https://github.com/epiverse-trace/datadelay/issues
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.2
+Imports:
+    data.table,
+    ggplot2,
+    patchwork,
+    rlang
+Suggests: 
+    testthat (>= 3.0.0),
+    epiparameter,
+    covidregionaldata,
+    usethis
+Remotes:
+    epiverse-trace/epiparameter,
+    epiforecasts/covidregionaldata
+Config/testthat/edition: 3
+Depends: 
+    R (>= 3.5.0)
+LazyData: true

NAMESPACE

@@ -1,4 +1,18 @@
 # Generated by roxygen2: do not edit by hand
 
-export(cases_to_infections)
-export(cfr_calculation)
+export(estimate_ccfr)
+export(format_cfr_neatly)
+export(known_outcomes)
+export(plot_data_and_cfr)
+export(rolling_cfr)
+export(static_cfr)
+importFrom(data.table,":=")
+importFrom(data.table,.BY)
+importFrom(data.table,.EACHI)
+importFrom(data.table,.GRP)
+importFrom(data.table,.I)
+importFrom(data.table,.N)
+importFrom(data.table,.NGRP)
+importFrom(data.table,.SD)
+importFrom(data.table,data.table)
+importFrom(rlang,.data)