normalise DESCRIPTION file

openplantpathology · May 3, 2024 · aea21b3 · aea21b3
1 parent 360fe00
commit aea21b3
Show file tree

Hide file tree

Showing 3 changed files with 58 additions and 84 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,75 +1,61 @@
 Package: hagis
-Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity
+Title: Analysis of Plant Pathogen Pathotype Complexities, Distributions
+    and Diversity
 Version: 3.1.11.9000
 Authors@R: c(
-  person(given = "Austin G.",
-         family = "McCoy",
-         role = c("aut", "ccp"),
-         email = "[email protected]",
-         comment = c(ORCID = "0000-0003-2483-4184")),
-  person(given = "Zachary",
-         family = "Noel",
-         role =  c("aut", "ccp"),
-         email = "[email protected]",
-         comment = c(ORCID = "0000-0001-6375-8300")),
-  person(given = "Adam H.",
-         family = "Sparks",
-         role = c("aut", "cre"),
-         email = "[email protected]",
-         comment = c(ORCID = "0000-0002-0061-8359")),
-  person(given = "Martin",
-         family = "Chilvers", 
-         role = c("aut", "ths"),
-         email = "[email protected] ",
-         comment = c(ORCID = "0000-0001-8832-1666")),
-  person(given = "Zhian N.",
-         family = "Kamvar",
-         role = c("ctb", "rev"),
-         comment = c(ORCID = "0000-0003-1458-7108")),
-  person("Michigan Soybean Promotion Committee",
-         role = "fnd"),
-  person("Project GREEEN",
-         role = "fnd"),
-  person("North Central Soybean Research Program",
-         role = "fnd"),
-  person("GRDC Project DAQ00186",
-         role = "fnd")
+    person("Austin G.", "McCoy", , "[email protected]", role = c("aut", "ccp"),
+           comment = c(ORCID = "0000-0003-2483-4184")),
+    person("Zachary", "Noel", , "[email protected]", role = c("aut", "ccp"),
+           comment = c(ORCID = "0000-0001-6375-8300")),
+    person("Adam H.", "Sparks", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-0061-8359")),
+    person("Martin", "Chilvers", , "[email protected]", role = c("aut", "ths"),
+           comment = c(ORCID = "0000-0001-8832-1666")),
+    person("Zhian N.", "Kamvar", role = c("ctb", "rev"),
+           comment = c(ORCID = "0000-0003-1458-7108")),
+    person("Michigan Soybean Promotion Committee", role = "fnd"),
+    person("Project GREEEN", role = "fnd"),
+    person("North Central Soybean Research Program", role = "fnd"),
+    person("GRDC Project DAQ00186", role = "fnd")
   )
 Description: Analysis of plant pathogen pathotype survey data.  Functions
-  provided calculate distribution of susceptibilities, distribution of
-  complexities with statistics, pathotype frequency distribution, as well as
-  diversity indices for pathotypes.  This package is meant to be a direct
-  replacement for Herrmann, Löwer and Schachtel's (1999)
-  <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS',
-  previously used for pathotype analysis.
-Depends: R (>= 3.4.0)
-Imports: 
-  data.table,
-  ggplot2,
-  pander,
-  stats,
-  utils
+    provided calculate distribution of susceptibilities, distribution of
+    complexities with statistics, pathotype frequency distribution, as
+    well as diversity indices for pathotypes.  This package is meant to be
+    a direct replacement for Herrmann, Löwer and Schachtel's (1999)
+    <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet,
+    'HaGiS', previously used for pathotype analysis.
 License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
+URL: https://github.com/openplantpathology/hagis,
+    https://openplantpathology.github.io/hagis/
+BugReports: https://github.com/openplantpathology/hagis/issues
+Depends: 
+    R (>= 3.4.0)
+Imports: 
+    data.table,
+    ggplot2,
+    pander,
+    stats,
+    utils
 Suggests:
     ape,
     dplyr,
     knitr,
     rmarkdown,
+    roxyglobals,
     testthat,
-    vegan,
-    vdiffr,
-    roxyglobals
-VignetteBuilder: knitr
-RoxygenNote: 7.3.1
+    vdiffr
+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"))
-Language: en-US
-URL: https://github.com/openplantpathology/hagis, https://openplantpathology.github.io/hagis/
-BugReports: https://github.com/openplantpathology/hagis/issues
+RoxygenNote: 7.3.1
 X-schema.org-applicationCategory: Tools
-X-schema.org-keywords: plant-pathology, pathotype, pathogen-survey, virulence analysis, differential set, assessment scale
 X-schema.org-isPartOf: https://openplantpathology.org
-Config/roxyglobals/filename: globals.R
-Config/roxyglobals/unique: FALSE
+X-schema.org-keywords: plant-pathology, pathotype, pathogen-survey,
+    virulence analysis, differential set, assessment scale
diff --git a/codemeta.json b/codemeta.json
@@ -3,7 +3,7 @@
   "@type": "SoftwareSourceCode",
   "identifier": "hagis",
   "description": "Analysis of plant pathogen pathotype survey data. Functions provided calculate distribution of susceptibilities, distribution of complexities with statistics, pathotype frequency distribution, as well as diversity indices for pathotypes. This package is meant to be a direct replacement for Herrmann, Löwer and Schachtel's (1999) <doi:10.1046/j.1365-3059.1999.00325.x> Habgood-Gilmour Spreadsheet, 'HaGiS', previously used for pathotype analysis.",
-  "name": "hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions and Diversity",
+  "name": "hagis: Analysis of Plant Pathogen Pathotype Complexities, Distributions\n    and Diversity",
   "relatedLink": ["https://openplantpathology.github.io/hagis/", "https://CRAN.R-project.org/package=hagis"],
   "codeRepository": "https://github.com/openplantpathology/hagis",
   "issueTracker": "https://github.com/openplantpathology/hagis/issues",
@@ -14,7 +14,7 @@
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.3.1 (2023-06-16)",
+  "runtimePlatform": "R version 4.4.0 (2024-04-24)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -47,7 +47,7 @@
       "@type": "Person",
       "givenName": "Martin",
       "familyName": "Chilvers",
-      "email": "[email protected] ",
+      "email": "[email protected]",
       "@id": "https://orcid.org/0000-0001-8832-1666"
     }
   ],
@@ -62,7 +62,7 @@
       "@type": "Person",
       "givenName": "Martin",
       "familyName": "Chilvers",
-      "email": "[email protected] ",
+      "email": "[email protected]",
       "@id": "https://orcid.org/0000-0001-8832-1666"
     }
   ],
@@ -144,27 +144,27 @@
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "testthat",
-      "name": "testthat",
+      "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=testthat"
+      "sameAs": "https://CRAN.R-project.org/package=roxyglobals"
     },
     {
       "@type": "SoftwareApplication",
-      "identifier": "vegan",
-      "name": "vegan",
+      "identifier": "testthat",
+      "name": "testthat",
       "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=vegan"
+      "sameAs": "https://CRAN.R-project.org/package=testthat"
     },
     {
       "@type": "SoftwareApplication",
@@ -177,18 +177,6 @@
         "url": "https://cran.r-project.org"
       },
       "sameAs": "https://CRAN.R-project.org/package=vdiffr"
-    },
-    {
-      "@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"
     }
   ],
   "softwareRequirements": {
@@ -248,8 +236,8 @@
   },
   "applicationCategory": "Tools",
   "isPartOf": "https://openplantpathology.org",
-  "keywords": ["plant-pathology", "pathotype", "pathogen-survey", "virulenceanalysis", "differentialset", "assessmentscale", "plant-disease", "plant-pathogens", "r", "pathogen-complexity", "pathogen-distribution", "pathogen-diversity", "phythophthora", "assessment-scale", "differential-set", "virulence-analysis"],
-  "fileSize": "295.481KB",
+  "keywords": ["plant-pathology", "pathotype", "pathogen-survey", "virulenceanalysis", "differentialset", "assessmentscale", "plant-disease", "pathotype-complexities", "population-diversities"],
+  "fileSize": "294.41KB",
   "citation": [
     {
       "@type": "ScholarlyArticle",

diff --git a/man/hagis-package.Rd b/man/hagis-package.Rd