Merge pull request #93 from mitre/t86-cran-install-docs

Updated docs w/CRAN install, added CRAN badge to README, bumped version, NEWS, etc., closes #86

.github/workflows/pkgdown.yaml

@@ -1,49 +1,47 @@
+# Workflow from example at:
+# https://github.com/r-lib/actions/blob/v2-branch/examples/pkgdown.yaml
+# updated 2022-09
 on:
   push:
-    branches:
-      - main
-    tags:
-      -'*'
+    branches: [main]
+  pull_request:
+    branches: [main]
+  release:
+    types: [published]
+  workflow_dispatch:
 
 name: pkgdown
 
 jobs:
   pkgdown:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-pandoc@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}
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
 
-      - name: Restore R package cache
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@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-
+            extra-packages: any::pkgdown, local::.
+            needs: website
 
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          install.packages("pkgdown", type = "binary")
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Install package
-        run: R CMD INSTALL .
-
-      - name: Deploy package
-        run: |
-          git config --local user.email "actions@github.com"
-          git config --local user.name "GitHub Actions"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE, branch = "gh-pages")'
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@4.1.4
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: growthcleanr
 Type: Package
 Title: Data Cleaner for Anthropometric Measurements
-Version: 2.0.1
+Version: 2.0.2
 Authors@R: c(
     person("Daymont","Carrie", email = "cdaymont@pennstatehealth.psu.edu", role = "aut"),
     person("Grundmeier","Robert", role = "aut"),

NEWS.md

@@ -1,4 +1,18 @@
-# growthcleanr 2.0.1 - 2021-07-21
+# growthcleanr 2.0.2 - 2022-09-13
+
+## Added
+
+- Package now available on CRAN: https://cran.r-project.org/package=growthcleanr
+
+## Changed
+
+- Several updates for CRAN deployment: improved example/test runtimes, text
+  corrections (#82); switched examples to use `donttest`, added CRAN comments
+  file, updated `.Rbuildignore` (#84)
+- Documentation updated with CRAN install (#86), fixed links (#85)
+- Updated GitHub check workflow (#80) and pkgdown workflow
+
+# growthcleanr 2.0.1 - 2022-08-29
 
 ## Changed
 
@@ -84,8 +98,8 @@
 
 ## Changed
 
-- Improved experimental carry forward adjustment handling of strings of
-  CF values, output handling, and documentation; renamed "Missing" values
+- Improved experimental carry forward adjustment handling of strings of CF
+  values, output handling, and documentation; renamed "Missing" values
 - Updated DESCRIPTION, imports, documentation to address testing issue (#12)
 - Switched to R-native argparser library to support script options
 - Switched to GitHub Actions for continuous integration / testing (thanks
@@ -118,8 +132,8 @@
 
 ## Added
 
-- New tests in `tests/testthat/test-utils.R` and `tests/testthat/test-cdc.R`
-  to support newly added functions
+- New tests in `tests/testthat/test-utils.R` and `tests/testthat/test-cdc.R` to
+  support newly added functions
 
 ## Changed
 
@@ -169,8 +183,8 @@
 - Several updates to improve performance, including eliminating use of
   data.table in ewma function.
 - Updated README with link to paper, detailed introduction, more installation
-  details, examples, notes on handling large datasets, lists of parameters
-  and exclusions.
+  details, examples, notes on handling large datasets, lists of parameters and
+  exclusions.
 
 # growthcleanr 1.0.0 - 2018-09-11
 

README.Rmd

@@ -17,15 +17,15 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 
+[![CRAN status](https://www.r-pkg.org/badges/version/growthcleanr) ](https://cran.r-project.org/package=growthcleanr)
 [![R build status](https://github.com/carriedaymont/growthcleanr/workflows/R-CMD-check/badge.svg) ](https://github.com/carriedaymont/growthcleanr/actions)
 
 <!-- badges: end -->
 
 R package for cleaning data from Electronic Health Record systems, focused on
 cleaning height and weight measurements.
 
-<a name="cite"></a>
-This package implements the
+<a name="cite"></a> This package implements the
 [Daymont et al. algorithm](https://academic.oup.com/jamia/article/24/6/1080/3767271),
 as specified in Supplemental File 3 within the
 [Supplementary Material](https://academic.oup.com/jamia/article/24/6/1080/3767271#97610899)
@@ -43,24 +43,32 @@ for calculating percentiles and Z-scores of pediatric growth observations and
 utilities for working with both functions. As of summer 2021, it also supports
 cleaning anthropometric measurements for adults up to age 65. The adult
 algorithm has not yet been published in a peer-reviewed publication, but is
-described in detail at [Adult
-algorithm](https://carriedaymont.github.io/growthcleanr/articles/adult-algorithm.html).
+described in detail at
+[Adult algorithm](https://carriedaymont.github.io/growthcleanr/articles/adult-algorithm.html).
+
+## Installation
+
+To install the stable version from CRAN:
+
+```{r, eval = FALSE}
+install.packages("growthcleanr")
+```
 
 ## Summary
 
-The `growthcleanr` package processes data prepared in a specific format to identify
-biologically implausible height and weight measurements. It bases these evaluations on
-techniques which use patient-specific longitudinal analysis and variations from
-published growth trajectory charts for pediatric subjects. These techniques are
-performed in a specific order which refines and improves results throughout the
-process.
+The `growthcleanr` package processes data prepared in a specific format to
+identify biologically implausible height and weight measurements. It bases these
+evaluations on techniques which use patient-specific longitudinal analysis and
+variations from published growth trajectory charts for pediatric subjects. These
+techniques are performed in a specific order which refines and improves results
+throughout the process.
 
-Results from `growthcleanr` include a flag for each measurement indicating whether it
-is to be included or excluded based on plausibility, with a variety of specific types
-of exclusions identified distinctly. These flags can be analyzed further by researchers
-studying anthropometric EHR data to determine which measurements to include or exclude
-in their own studies. No values are deleted or otherwise removed; each is only flagged
-in a new column.
+Results from `growthcleanr` include a flag for each measurement indicating
+whether it is to be included or excluded based on plausibility, with a variety
+of specific types of exclusions identified distinctly. These flags can be
+analyzed further by researchers studying anthropometric EHR data to determine
+which measurements to include or exclude in their own studies. No values are
+deleted or otherwise removed; each is only flagged in a new column.
 
 To start running `growthcleanr`, an R installation with a variety of additional
 packages is required, as is a growth measurement dataset prepared for use in
@@ -73,33 +81,31 @@ The rest of this documentation includes:
 - [Quickstart](https://carriedaymont.github.io/growthcleanr/articles/quickstart.html),
   a brief tour of using growthcleanr, including data preparation
 - [Installation](https://carriedaymont.github.io/growthcleanr/articles/usage.html),
+  options for installing growthcleanr, with notes on specific platforms and
+  source-level installation for developers
+- [Usage](https://carriedaymont.github.io/growthcleanr/articles/usage.html),
   examples of cleaning data, multiple options, example data
 
 ### Advanced topics:
 
-- [Configuration
-  options](https://carriedaymont.github.io/growthcleanr/articles/configuration.html),
+- [Configuration options](https://carriedaymont.github.io/growthcleanr/articles/configuration.html),
   changing growthcleanr operational settings
-- [Understanding growthcleanr
-  output](https://carriedaymont.github.io/growthcleanr/articles/output.html), the
-  exclusion types growthcleanr identifies
-- [Adult
-  algorithm](https://carriedaymont.github.io/growthcleanr/articles/adult-algorithm.html),
+- [Understanding growthcleanr output](https://carriedaymont.github.io/growthcleanr/articles/output.html),
+  the exclusion types growthcleanr identifies
+- [Adult algorithm](https://carriedaymont.github.io/growthcleanr/articles/adult-algorithm.html),
   a detailed description of how growthcleanr assesses observations from adult
   subjects
-- [Computing BMI percentiles and
-  Z-scores](https://carriedaymont.github.io/growthcleanr/articles/utilities.html),
+- [Computing BMI percentiles and Z-scores](https://carriedaymont.github.io/growthcleanr/articles/utilities.html),
   additional functions for common data transforms and determining percentiles
   and Z-scores using the CDC method
-- [Working with large
-  datasets](https://carriedaymont.github.io/growthcleanr/articles/large-data-sets.html),
+- [Working with large datasets](https://carriedaymont.github.io/growthcleanr/articles/large-data-sets.html),
   notes and suggestions for running `growthcleanr` with large data sources
 - [Next steps](https://carriedaymont.github.io/growthcleanr/articles/next-steps.html),
   notes on potential enhancements to the pediatric and adult algorithms
 
 ## Changes
 
 For a detailed history of released versions, see the
-[Changelog](https://carriedaymont.github.io/growthcleanr/news/index.html) or`NEWS.md`.
-Tagged releases, starting with 1.2.3 in January 2021, are listed [at
-GitHub](https://github.com/carriedaymont/growthcleanr/releases).
+[Changelog](https://carriedaymont.github.io/growthcleanr/news/index.html)
+or`NEWS.md`. Tagged releases, starting with 1.2.3 in January 2021, are listed
+[at GitHub](https://github.com/carriedaymont/growthcleanr/releases).

README.md

@@ -5,6 +5,8 @@
 
 <!-- badges: start -->
 
+[![CRAN
+status](https://www.r-pkg.org/badges/version/growthcleanr)](https://cran.r-project.org/package=growthcleanr)
 [![R build
 status](https://github.com/carriedaymont/growthcleanr/workflows/R-CMD-check/badge.svg)](https://github.com/carriedaymont/growthcleanr/actions)
 
@@ -36,6 +38,14 @@ up to age 65. The adult algorithm has not yet been published in a
 peer-reviewed publication, but is described in detail at [Adult
 algorithm](https://carriedaymont.github.io/growthcleanr/articles/adult-algorithm.html).
 
+## Installation
+
+To install the stable version from CRAN:
+
+``` r
+install.packages("growthcleanr")
+```
+
 ## Summary
 
 The `growthcleanr` package processes data prepared in a specific format
@@ -62,38 +72,37 @@ The rest of this documentation includes:
 
 ### Getting started:
 
--   [Quickstart](https://carriedaymont.github.io/growthcleanr/articles/quickstart.html),
-    a brief tour of using growthcleanr, including data preparation
--   [Installation](https://carriedaymont.github.io/growthcleanr/articles/installation.html),
-    options for installing growthcleanr, with notes on specific platforms and source-level
-    installation for developers
--   [Usage](https://carriedaymont.github.io/growthcleanr/articles/usage.html),
-    examples of cleaning data, multiple options, example data
+- [Quickstart](https://carriedaymont.github.io/growthcleanr/articles/quickstart.html),
+  a brief tour of using growthcleanr, including data preparation
+- [Installation](https://carriedaymont.github.io/growthcleanr/articles/usage.html),
+  options for installing growthcleanr, with notes on specific platforms
+  and source-level installation for developers
+- [Usage](https://carriedaymont.github.io/growthcleanr/articles/usage.html),
+  examples of cleaning data, multiple options, example data
 
 ### Advanced topics:
 
--   [Configuration
-    options](https://carriedaymont.github.io/growthcleanr/articles/configuration.html),
-    changing growthcleanr operational settings
--   [Understanding growthcleanr
-    output](https://carriedaymont.github.io/growthcleanr/articles/output.html),
-    the exclusion types growthcleanr identifies
--   [Adult
-    algorithm](https://carriedaymont.github.io/growthcleanr/articles/adult-algorithm.html),
-    a detailed description of how growthcleanr assesses observations
-    from adult subjects
--   [Computing BMI percentiles and
-    Z-scores](https://carriedaymont.github.io/growthcleanr/articles/utilities.html),
-    additional functions for common data transforms and determining
-    percentiles and Z-scores using the CDC method
--   [Working with large
-    datasets](https://carriedaymont.github.io/growthcleanr/articles/large-data-sets.html),
-    notes and suggestions for running `growthcleanr` with large data
-    sources
--   [Next
-    steps](https://carriedaymont.github.io/growthcleanr/articles/next-steps.html),
-    notes on potential enhancements to the pediatric and adult
-    algorithms
+- [Configuration
+  options](https://carriedaymont.github.io/growthcleanr/articles/configuration.html),
+  changing growthcleanr operational settings
+- [Understanding growthcleanr
+  output](https://carriedaymont.github.io/growthcleanr/articles/output.html),
+  the exclusion types growthcleanr identifies
+- [Adult
+  algorithm](https://carriedaymont.github.io/growthcleanr/articles/adult-algorithm.html),
+  a detailed description of how growthcleanr assesses observations from
+  adult subjects
+- [Computing BMI percentiles and
+  Z-scores](https://carriedaymont.github.io/growthcleanr/articles/utilities.html),
+  additional functions for common data transforms and determining
+  percentiles and Z-scores using the CDC method
+- [Working with large
+  datasets](https://carriedaymont.github.io/growthcleanr/articles/large-data-sets.html),
+  notes and suggestions for running `growthcleanr` with large data
+  sources
+- [Next
+  steps](https://carriedaymont.github.io/growthcleanr/articles/next-steps.html),
+  notes on potential enhancements to the pediatric and adult algorithms
 
 ## Changes
 

cran-comments.md

@@ -1,3 +1,13 @@
+# CRAN submission growthcleanr 2.0.2 (1)
+
+## R CMD check results
+There were no ERRORs, WARNINGs, or NOTEs.
+
+## Downstream dependencies
+There are currently no downstream dependencies for this package.
+
+# Previous Submissions
+
 # CRAN submission growthcleanr 2.0.1 (6)
 
 ## R CMD check results
@@ -28,8 +38,6 @@ I have gone through all functions in package and affected functions have been ad
 ## Downstream dependencies
 There are currently no downstream dependencies for this package.
 
-# Previous Submissions
-
 # CRAN submission growthcleanr 2.0.1 (5)
 
 ## R CMD check results