Update from devel branch to close it

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: hagis
 Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
     and Diversity
-Version: 3.1.11.9000
+Version: 3.1.12
 Authors@R: c(
     person("Austin G.", "McCoy", , "[email protected]", role = c("aut", "ccp"),
            comment = c(ORCID = "0000-0003-2483-4184")),
@@ -11,6 +11,8 @@ Authors@R: c(
            comment = c(ORCID = "0000-0002-0061-8359")),
     person("Martin", "Chilvers", , "[email protected]", role = c("aut", "ths"),
            comment = c(ORCID = "0000-0001-8832-1666")),
+    person("Jari", "Oksanen", , "[email protected]", role = "aut",
+           comment = "Contributed patch to update betadiversity vignette and fixed bug therein as well."),
     person("Zhian N.", "Kamvar", role = c("ctb", "rev"),
            comment = c(ORCID = "0000-0003-1458-7108")),
     person("Michigan Soybean Promotion Committee", role = "fnd"),
@@ -43,16 +45,14 @@ Suggests:
     knitr,
     rmarkdown,
     roxyglobals,
+    roxyglobals,
     testthat,
     vdiffr,
     vegan
 VignetteBuilder: 
     knitr
-Config/roxyglobals/filename: globals.R
-Config/roxyglobals/unique: FALSE
 Encoding: UTF-8
 Language: en-US
-LazyData: true
 Roxygen: list(markdown = TRUE, roclets = c("collate", "namespace", "rd",
     "roxyglobals::global_roclet"))
 RoxygenNote: 7.3.1

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/openplantpathology/hagis",
   "issueTracker": "https://github.com/openplantpathology/hagis/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "3.1.11.9000",
+  "version": "3.1.12",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -49,6 +49,12 @@
       "familyName": "Chilvers",
       "email": "[email protected]",
       "@id": "https://orcid.org/0000-0001-8832-1666"
+    },
+    {
+      "@type": "Person",
+      "givenName": "Jari",
+      "familyName": "Oksanen",
+      "email": "[email protected]"
     }
   ],
   "contributor": [
@@ -154,6 +160,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=roxyglobals"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "roxyglobals",
+      "name": "roxyglobals",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=roxyglobals"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "testthat",
@@ -249,7 +267,7 @@
   "applicationCategory": "Tools",
   "isPartOf": "https://openplantpathology.org",
   "keywords": ["plant-pathology", "pathotype", "pathogen-survey", "virulenceanalysis", "differentialset", "assessmentscale", "plant-disease", "pathotype-complexities", "population-diversities"],
-  "fileSize": "294.779KB",
+  "fileSize": "295.986KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",
@@ -320,13 +338,13 @@
       "name": "{hagis}: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity",
       "identifier": "10.5281/zenodo.2619820",
       "url": "https://openplantpathology.github.io/hagis/",
-      "description": "R package version 3.1.11.9000",
+      "description": "R package version 3.1.12",
       "@id": "https://doi.org/10.5281/zenodo.2619820",
       "sameAs": "https://doi.org/10.5281/zenodo.2619820"
     }
   ],
   "releaseNotes": "https://github.com/openplantpathology/hagis/blob/master/NEWS.md",
   "readme": "https://github.com/openplantpathology/hagis/blob/main/README.md",
-  "contIntegration": ["https://app.codecov.io/gh/openplantpathology/hagis", "https://github.com/openplantpathology/hagis/actions/workflows/test-coverage.yaml"],
+  "contIntegration": ["https://codecov.io/gh/openplantpathology/hagis", "https://github.com/openplantpathology/hagis/actions/workflows/test-coverage.yaml"],
   "developmentStatus": "https://www.repostatus.org/#active"
 }

vignettes/betadiversity.Rmd

@@ -166,8 +166,7 @@ ggplot(data = princoor.pathotype.data, aes(x = X, y = Y)) +
     legend.text = element_text(face = "bold", size = 10),
     legend.key.size = unit(1, 'lines')
   ) +
-  stat_ellipse(data = princoor.pathotype.data, aes(x = X, y = Y),
-               level = 0.95) +
+  stat_ellipse(data = princoor.pathotype.data, aes(x = X, y = Y), level = 0.95) +
   ggtitle("Pathotype Jaccard Distances PCOA")
 ```
 

vignettes/hagis.Rmd

@@ -31,7 +31,7 @@ library("hagis")
 head(P_sojae_survey)
 ```
 
-We see in the `gene` column that each gene is prepended with "Rps".
+We see in the `gene` column that each gene is pre-pended with "Rps".
 We can remove this to make the graphs cleaner and report the genes in tables as we would in a manuscript.
 Note that this will work for any string you enter as the first value, `pattern`.
 The second string, `replacement`, is the replacement value, the third, `x`, is where to look and make the changes.
@@ -266,8 +266,7 @@ Set the font to be a bold-face serif family font.
 
 ```{r change-plot-font}
 Rps.plot <- Rps.plot +
-  theme(text = element_text(face = "bold",
-                            family = "serif"))
+  theme(text = element_text(face = "bold", family = "serif"))
 
 Rps.plot
 ```
@@ -289,24 +288,22 @@ You can use named, *e.g.*, "red", "yellow", "blue", colors in R or you can use c
 Illustrated below is using Michigan State University (MSU) Green, hex code #18453b, using `theme_bw()` with a serif font.
 
 ```{r use-Colors}
-autoplot(Rps.summary,
-         type = "percentage",
-         color = "#18453b") +
+autoplot(Rps.summary, type = "percentage", color = "#18453b") +
   theme_bw() +
-  theme(text = element_text(face = "bold",
-                            family = "serif"))
+  theme(text = element_text(face = "bold", family = "serif"))
 ```
 
 ### Sorting the x-axis
 
 You can sort the x-axis of any graph produced using `autoplot()` in an `ascending` or `descending` order using the `order` parameter in `autoplot()`.
 
 ```{r sort-axis}
-autoplot(Rps.summary,
-          type = "percentage",
-          color = "#18453b",
-          order = "ascending") +
+autoplot(
+  Rps.summary,
+  type = "percentage",
+  color = "#18453b",
+  order = "ascending"
+) +
   theme_bw() +
-  theme(text = element_text(face = "bold",
-                            family = "serif"))
+  theme(text = element_text(face = "bold", family = "serif"))
 ```