Merge pull request #106 from b-cubed-eu/documentation-issues-102-104

Documentation issues 102 104

.zenodo.json

@@ -1,9 +1,9 @@
 {
   "title": "gcube: Simulating Biodiversity Data Cubes",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "license": "MIT",
   "upload_type": "software",
-  "description": "<p>Simulation framework for biodiversity data cubes.<\/p>",
+  "description": "<p>This R package provides a simulation framework for biodiversity data cubes. This can start from simulating multiple species distributed in a landscape over a temporal scope. In a second phase, the simulation of a variety of observation processes and effort can generate actual occurrence datasets. Based on their (simulated) spatial uncertainty, occurrences can then be designated to a grid to form a data cube.<\/p>",
   "keywords": [
     "simulation",
     "data cubes",

CITATION.cff

@@ -17,12 +17,19 @@ contact:
   family-names: Langeraert
   affiliation: Research Institute for Nature and Forest (INBO)
   orcid: 0000-0002-5900-8109
-doi: ~
+doi: 10.5281/zenodo.14038996
 license: MIT
 repository-code: https://github.com/b-cubed-eu/gcube/
 type: software
-abstract: "Simulation framework for biodiversity data cubes."
+abstract: "This R package provides a simulation framework for biodiversity data cubes.
+  This can start from simulating multiple species distributed in a landscape over
+  a temporal scope. In a second phase, the simulation of a variety of observation
+  processes and effort can generate actual occurrence datasets. Based on their (simulated)
+  spatial uncertainty, occurrences can then be designated to a grid to form a data
+  cube."
 identifiers:
+- type: doi
+  value: 10.5281/zenodo.14038996
 - type: url
   value: https://b-cubed-eu.github.io/gcube/
-version: 1.1.0
+version: 1.1.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gcube
 Title: Simulating Biodiversity Data Cubes
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: c(
     person("Ward", "Langeraert", , "ward.langeraert@inbo.be", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-5900-8109", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -33,10 +33,17 @@ Authors@R: c(
     person("Research Institute for Nature and Forest (INBO)", , , "info@inbo.be", role = "cph"),
     person("European Union's Horizon Europe Research and Innovation Programme (ID No 101059592)", role = "fnd")
   )
-Description: Simulation framework for biodiversity data cubes.
+Description: This R package provides a simulation framework for
+    biodiversity data cubes. This can start from simulating multiple
+    species distributed in a landscape over a temporal scope. In a second
+    phase, the simulation of a variety of observation processes and effort
+    can generate actual occurrence datasets. Based on their (simulated)
+    spatial uncertainty, occurrences can then be designated to a grid to
+    form a data cube.
 License: MIT + file LICENSE
 URL: https://github.com/b-cubed-eu/gcube,
-    https://b-cubed-eu.github.io/gcube/
+    https://b-cubed-eu.github.io/gcube/,
+    https://doi.org/10.5281/zenodo.14038996
 BugReports: https://github.com/b-cubed-eu/gcube/issues
 Imports:
     assertthat,

NEWS.md

@@ -1,3 +1,9 @@
+# gcube 1.1.1
+
+* Add more elaborate package description #102.
+* Uniform naming of articles and start headings at h2 #103.
+* Add DOI to citation file #104.
+
 # gcube 1.1.0
 
 * Publish release on Zenodo.

_pkgdown.yml

@@ -36,7 +36,7 @@ articles:
     - articles/grid-designation-process
   - title: "Multi-species approach"
     contents:
-    - articles/multi_species_approach
+    - articles/multi-species-approach
 
 reference:
   - title: "Core gcube workflow functions"

codemeta.json

@@ -2,19 +2,19 @@
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
   "identifier": "gcube",
-  "description": "Simulation framework for biodiversity data cubes.",
+  "description": "gcube is an R package that provides a simulation framework for biodiversity data cubes. This can start from simulating multiple species distributed in a landscape over a temporal scope. In a second phase, the simulation of a variety of observation processes and effort can generate actual occurrence datasets. Based on their (simulated) spatial uncertainty, occurrences can then be designated to a grid to form a data cube.",
   "name": "gcube: Simulating Biodiversity Data Cubes",
-  "relatedLink": "https://b-cubed-eu.github.io/gcube/",
+  "relatedLink": ["https://b-cubed-eu.github.io/gcube/", "https://doi.org/10.5281/zenodo.14038996"],
   "codeRepository": "https://github.com/b-cubed-eu/gcube",
   "issueTracker": "https://github.com/b-cubed-eu/gcube/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.4.1 (2024-06-14 ucrt)",
+  "runtimePlatform": "R version 4.4.2 (2024-10-31 ucrt)",
   "author": [
     {
       "@type": "Person",
@@ -334,7 +334,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "557.447KB",
+  "fileSize": "558.437KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -346,13 +346,16 @@
           "familyName": "Langeraert"
         }
       },
-      "name": "gcube: Simulating Biodiversity Data Cubes. Version 1.1.0",
-      "url": "https://b-cubed-eu.github.io/gcube/"
+      "name": "gcube: Simulating Biodiversity Data Cubes. Version 1.1.1",
+      "identifier": "10.5281/zenodo.14038996",
+      "url": "https://b-cubed-eu.github.io/gcube/",
+      "@id": "https://doi.org/10.5281/zenodo.14038996",
+      "sameAs": "https://doi.org/10.5281/zenodo.14038996"
     }
   ],
   "releaseNotes": "https://github.com/b-cubed-eu/gcube/blob/master/NEWS.md",
   "readme": "https://github.com/b-cubed-eu/gcube/blob/main/README.md",
   "contIntegration": ["https://github.com/b-cubed-eu/gcube/actions/workflows/check_on_different_r_os.yml", "https://app.codecov.io/gh/b-cubed-eu/gcube/"],
   "developmentStatus": "https://www.repostatus.org/#active",
-  "keywords": ["r", "r-package"]
+  "keywords": ["r", "r-package", "biodiversity-informatics", "data-cubes", "simulations"]
 }

inst/CITATION

@@ -2,12 +2,13 @@ citHeader("To cite `gcube` in publications please use:")
 # begin checklist entry
 bibentry(
   bibtype = "Manual",
-  title = "gcube: Simulating Biodiversity Data Cubes. Version 1.1.0",
+  title = "gcube: Simulating Biodiversity Data Cubes. Version 1.1.1",
   author = c( author = c(person(given = "Ward", family = "Langeraert"))),
   year = 2024,
   url = "https://b-cubed-eu.github.io/gcube/",
-  abstract = "Simulation framework for biodiversity data cubes.",
-  textVersion = "Langeraert, Ward (2024) gcube: Simulating Biodiversity Data Cubes. Version 1.1.0. https://b-cubed-eu.github.io/gcube/",
+  abstract = "This R package provides a simulation framework for biodiversity data cubes. This can start from simulating multiple species distributed in a landscape over a temporal scope. In a second phase, the simulation of a variety of observation processes and effort can generate actual occurrence datasets. Based on their (simulated) spatial uncertainty, occurrences can then be designated to a grid to form a data cube.",
+  textVersion = "Langeraert, Ward (2024) gcube: Simulating Biodiversity Data Cubes. Version 1.1.1. https://b-cubed-eu.github.io/gcube/",
   keywords = "simulation; data cubes; B-Cubed; biodiversity; Monte-Carlo",
+  doi = "10.5281/zenodo.14038996",
 )
 # end checklist entry