Merge pull request #8 from jasenfinch/devel

v0.4.2

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

@@ -1,10 +1,14 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
 on:
   push:
     branches:
+      - main
       - master
       - devel
   pull_request:
     branches:
+      - main
       - master
 
 name: R-CMD-check
@@ -21,21 +25,22 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
-          - {os: macOS-latest, r: 'devel'}
-          - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
 
       - name: Query dependencies
         run: |
@@ -46,20 +51,19 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        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 system dependencies
         if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
       - name: Install dependencies
         run: |
@@ -70,16 +74,18 @@ jobs:
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
-          
+
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0} 
-        
+
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          path: check

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: pdi
 Type: Package
 Title: Phenotypic Index Measures for Oak Decline Severity
-Version: 0.4.1
+Version: 0.4.2
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"),  comment = c(ORCID = "0000-0002-6070-7476"))
-Description: Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest.
+Description: Oak declines are complex disease syndromes and consist of many visual indicators that include aspects of tree size, crown condition and trunk condition. This can cause difficulty in the manual classification of symptomatic and non-symptomatic trees from what is in reality a broad spectrum of oak tree health condition. Two phenotypic oak decline indexes have been developed to quantitatively describe and differentiate oak decline syndromes in Quercus robur. This package provides a toolkit to generate these decline indexes from phenotypic descriptors using the machine learning algorithm random forest. The methodology for generating these indexes is outlined in Finch et al. (2121) <doi:10.1016/j.foreco.2021.118948>.
 URL: https://jasenfinch.github.io/pdi
 BugReports: https://github.com/jasenfinch/pdi/issues
 License: GPL-3

NEWS.md

@@ -0,0 +1,5 @@
+# pdi 0.4.2
+
+* Added a `NEWS.md` file to track changes to the package.
+
+* Added methodology manuscript reference and [link](https://doi.org/10.1016/j.foreco.2021.118948).

README.md

@@ -17,14 +17,30 @@ Two oak decline indexes have been developed to quantitatively describe and diffe
 
 This package provides the tools generate these decline indexes using machine learning algorithm random forest.
 
-Install the package from GitHub:
+The methodology is outlined in the article:
 
+[Finch, J.P., Brown, N., Beckmann, M., Denman, S. and Draper, J., 2021. Index measures for oak decline severity using phenotypic descriptors. Forest Ecology and Management, 485, p.118948.](https://doi.org/10.1016/j.foreco.2021.118948)
+
+### Installation
+
+The package can be installed from CRAN using:
+
+``` r
+install.packages('pdi')
 ```
+
+Or this development version of the package can be installed from GitHub:
+
+``` r
 devtools::install_github('jasenfinch/pdi',build_vignettes = TRUE)
 ```
 
-See the vignette for how to generate a phenotypic decline index (PDI) for oak decline severity using example data:
+### Learn more
 
-```
-vignette('pdi-example',package = 'pdi')
-```
+The package documentation can be browsed online at <https://jasenfinch.github.io/pdi/>. 
+
+If this is your first time using `pdi` see the [Generating phenotypic decline indexes using the pdi package](https://jasenfinch.github.io/pdi/articles/pdi-example.html) vignette for information on how to get started.
+
+If you believe you've found a bug in `pdi`, please file a bug (and, if
+possible, a [reproducible example](https://reprex.tidyverse.org)) at
+<https://github.com/jasenfinch/pdi/issues>.

_pkgdown.yml

@@ -1 +1 @@
-destination: docs
+url: https://jasenfinch.github.io/pdi/