Merge pull request #2 from inbo/2023_voorlopig

2023 voorlopig

.github/CONTRIBUTING.md

@@ -0,0 +1,39 @@
+# CONTRIBUTING #
+
+### Fixing typos
+
+Small typos or grammatical errors in documentation may be edited directly using the GitHub web interface, so long as the changes are made in the _source_ file.
+E.g. edit a roxygen2 comment in a `.R` file below `R/`, not in an `.Rd` file below `man/`.
+
+### Prerequisites
+
+Before you make a substantial pull request, you should always file an issue and make sure someone from the team agrees that it’s a problem. 
+If you’ve found a bug, create an associated issue and illustrate the bug with a minimal [reproducible example](https://www.tidyverse.org/help/#reprex).
+
+### Pull request process
+
+*  We recommend that you create a Git branch for each pull request (PR).  
+*  Look at the GitHub Actions build status before and after making changes.
+The `README` should contain badges for any continuous integration services used by the package.  
+*  We require the tidyverse [style guide](http://style.tidyverse.org).
+You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2).  
+*  We use [testthat](https://cran.r-project.org/package=testthat). 
+Contributions with test cases included are easier to accept.  
+*  For user-facing changes, add a bullet to the top of `NEWS.md` below the current development version header describing the changes made followed by your GitHub username, and links to relevant issue(s)/PR(s).
+
+### Code of Conduct
+
+Please note that this project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). 
+By contributing to this project you agree to abide by its terms.
+
+### Prefer to Email? 
+
+Email the person listed as maintainer in the `DESCRIPTION` file of this repo.
+
+Though note that private discussions over email don't help others - of course
+email is totally warranted if it's a sensitive problem of any kind.
+
+### Thanks for contributing!
+
+This contributing guide is adapted from the tidyverse contributing guide available at https://raw.githubusercontent.com/r-lib/usethis/master/inst/templates/tidy-contributing.md 

.gitignore

@@ -1,14 +1,17 @@
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
 *.gpkg
 *.gpkg-shm
 *.gpkg-wal
 *.html
-*.json
 *.pbf
 *.zip
+.DS_Store
+.RData
+.Rhistory
+.Rproj.user
+.Ruserdata
+.httr-oauth
 cover.txt
+data/*
+docs
 open_ruimte/*
 output/*

.zenodo.json

@@ -0,0 +1,43 @@
+{
+  "title": "Sampling frame for partridge (Perdrix perdrix) in Flanders",
+  "version": "2023.1",
+  "description": "<p>Since 2008, partridge hunting in Flanders has been subject to a\nnumber of conditions. The first condition states compliance with an\naverage density of at least 3 breeding pairs per 100 ha of open space.\nThe Research Institute for Nature and Forest (<a\nhref=\"https://www.vlaanderen.be/inbo/en\">INBO<\/a>) is responsible for\nthe calculation of these densities and advises the Agency for Nature and\nForests (<a href=\"https://www.natuurenbos.be/\">ANB<\/a>) on this.<\/p>\n<p>This repository contains the source code to generate the layer with\nopen space within <a\nhref=\"https://doi.org/10.5281/zenodo.5584203\">hunting grounds<\/a> in\nFlanders. The selection is based on relevant categories of the <a\nhref=\"https://openstreetmap.org\">OpenStreetMap<\/a> information.<\/p>\n<p>We aim to make the layer reproducible by making the code publicly\navailable under an open source license. The code itself requires only\nfreeware open source software (<a\nhref=\"https://www.r-project.org/\">R<\/a> and <a\nhref=\"https://qgis.org\">QGIS<\/a>). The OpenStreetMap database updates\ncontinuously. Rerunning the code on the current database might yield a\ndifferent layer. Therefore we also republish the <a\nhref=\"https://doi.org/10.5281/zenodo.5792948\">snapshot<\/a> of the\nOpenStreetMap data we used. When we need to update the open space layer,\nwe will add an updated snapshot as a new version. Having both the code\nand the data available under version control, allows to recreate both\nthe most recent version as any older version.<\/p>",
+  "keywords": [
+    "hunting",
+    "monitoring",
+    "habitat"
+  ],
+  "upload_type": "software",
+  "license": "CC-BY-4.0",
+  "language": "eng",
+  "contributors": [
+    {
+      "name": "Onkelinx, Thierry",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0001-8804-4216",
+      "type": "ContactPerson"
+    },
+    {
+      "name": "Research Institute for Nature and Forest",
+      "type": "RightsHolder"
+    }
+  ],
+  "creators": [
+    {
+      "name": "Onkelinx, Thierry",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0001-8804-4216"
+    },
+    {
+      "name": "Carmen, Raïsa",
+      "affiliation": "Research Institute for Nature and Forest (INBO)",
+      "orcid": "0000-0003-1025-8702"
+    }
+  ],
+  "access_right": "open",
+  "communities": [
+    {
+      "identifier": "inbo"
+    }
+  ]
+}

CITATION.cff

@@ -0,0 +1,46 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it using these metadata.
+title: Sampling frame for partridge (Perdrix perdrix) in Flanders
+authors:
+- given-names: Thierry
+  family-names: Onkelinx
+  affiliation: Research Institute for Nature and Forest (INBO)
+  orcid: 0000-0001-8804-4216
+- given-names: Raïsa
+  family-names: Carmen
+  affiliation: Research Institute for Nature and Forest (INBO)
+  orcid: 0000-0003-1025-8702
+keywords:
+- hunting
+- monitoring
+- habitat
+contact:
+- given-names: Thierry
+  family-names: Onkelinx
+  affiliation: Research Institute for Nature and Forest (INBO)
+  orcid: 0000-0001-8804-4216
+doi: 10.5281/zenodo.5814813
+license: CC-BY-4.0
+repository-code: https://github.com/inbo/patrijs-steekproefkader
+type: software
+abstract: |-
+  Since 2008, partridge hunting in Flanders has been subject to a number of conditions.
+  The first condition states compliance with an average density of at least 3 breeding pairs per 100 ha of open space.
+  The Research Institute for Nature and Forest ([INBO](https://www.vlaanderen.be/inbo/en)) is responsible for the calculation of these densities and advises the Agency for Nature and Forests ([ANB](https://www.natuurenbos.be/)) on this.
+
+  This repository contains the source code to generate the layer with open space within [hunting grounds](https://doi.org/10.5281/zenodo.5584203) in Flanders.
+  The selection is based on relevant categories of the [OpenStreetMap](https://openstreetmap.org) information.
+
+  We aim to make the layer reproducible by making the code publicly available under an open source license.
+  The code itself requires only freeware open source software ([R](https://www.r-project.org/) and [QGIS](https://qgis.org)).
+  The OpenStreetMap database updates continuously.
+  Rerunning the code on the current database might yield a different layer.
+  Therefore we also republish the [snapshot](https://doi.org/10.5281/zenodo.5792948) of the OpenStreetMap data we used.
+  When we need to update the open space layer, we will add an updated snapshot as a new version.
+  Having both the code and the data available under version control, allows to recreate both the most recent version as any older version.
+identifiers:
+- type: doi
+  value: 10.5281/zenodo.5814813
+- type: url
+  value: https://inbo.github.io/patrijs-steekproefkader/
+version: '2023.1'

README.md

@@ -1,5 +1,31 @@
+<!-- badges: start -->
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5814813.svg)](https://doi.org/10.5281/zenodo.5814813)
+[![website](https://img.shields.io/badge/website-https%3A%2F%2Finbo.github.io%2Fpatrijs--steekproefkader%2F-c04384)](https://inbo.github.io/patrijs-steekproefkader/)
+![GitHub](https://img.shields.io/github/license/inbo/patrijs-steekproefkader)
+![GitHub release (latest by date)](https://img.shields.io/github/v/release/inbo/patrijs-steekproefkader)
+![GitHub Release Date](https://img.shields.io/github/release-date/inbo/patrijs-steekproefkader)
+![GitHub Workflow Status](https://img.shields.io/github/workflow/status/inbo/patrijs-steekproefkader/check-source)
+![GitHub repo size](https://img.shields.io/github/repo-size/inbo/patrijs-steekproefkader)
+<!-- badges: end -->
+
 # Sampling frame for partridge (_Perdrix perdrix_) in Flanders
 
+[Onkelinx, Thierry![ORCID logo](https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png)](https://orcid.org/0000-0001-8804-4216)[^aut][^cre][^INBO];
+[Carmen, Raïsa![ORCID logo](https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png)](https://orcid.org/0000-0003-1025-8702)[^aut][^INBO];
+Research Institute for Nature and Forest[^cph][^fnd]
+
+[^aut]: author
+[^cre]: contact person
+[^cph]: copyright holder
+[^fnd]: funder
+[^INBO]: Research Institute for Nature and Forest (INBO)
+
+**keywords**: hunting; monitoring; habitat
+
+<!-- version: 2023.01 -->
+<!-- community: inbo -->
+
+<!-- description: start -->
 Since 2008, partridge hunting in Flanders has been subject to a number of conditions.
 The first condition states compliance with an average density of at least 3 breeding pairs per 100 ha of open space.
 The Research Institute for Nature and Forest ([INBO](https://www.vlaanderen.be/inbo/en)) is responsible for the calculation of these densities and advises the Agency for Nature and Forests ([ANB](https://www.natuurenbos.be/)) on this.
@@ -14,3 +40,37 @@ Rerunning the code on the current database might yield a different layer.
 Therefore we also republish the [snapshot](https://doi.org/10.5281/zenodo.5792948) of the OpenStreetMap data we used.
 When we need to update the open space layer, we will add an updated snapshot as a new version.
 Having both the code and the data available under version control, allows to recreate both the most recent version as any older version.
+<!-- description: end -->
+
+## Available maps for field work
+
+### Areal photograph as background
+
+- **West-Flanders**: https://doi.org/10.5281/zenodo.5812597
+- **East-Flanders**: https://doi.org/10.5281/zenodo.5814972
+- **Antwerp**: https://doi.org/10.5281/zenodo.5815049
+- **Limburg**: https://doi.org/10.5281/zenodo.5815083
+- **Flemish Brabant**: https://doi.org/10.5281/zenodo.5815089
+
+### OpenStreetMap as background
+
+- **West-Flanders**: https://doi.org/10.5281/zenodo.5815407
+- **East-Flanders**: https://doi.org/10.5281/zenodo.5815400
+- **Antwerp**: https://doi.org/10.5281/zenodo.5815392
+- **Limburg**: https://doi.org/10.5281/zenodo.5815379
+- **Flemish Brabant**: https://doi.org/10.5281/zenodo.5815209
+
+### Cartoweb as background
+
+- **West-Flanders**: https://doi.org/10.5281/zenodo.5827428
+- **East-Flanders**: https://doi.org/10.5281/zenodo.5831528
+- **Antwerp**: https://doi.org/10.5281/zenodo.5827467
+- **Limburg**: https://doi.org/10.5281/zenodo.5827491
+- **Flemish Brabant**: https://doi.org/10.5281/zenodo.5827509
+
+## Other maps
+
+- **open area for partridge**: https://doi.org/10.5281/zenodo.5814833
+- **sampling units**: https://doi.org/10.5281/zenodo.5814900
+- **hunting grounds**: https://doi.org/10.5281/zenodo.5584203
+- **OpenStreetMap snapshot**: https://doi.org/10.5281/zenodo.5792948

checklist.yml

@@ -3,3 +3,30 @@ package: no
 allowed:
   warnings: []
   notes: []
+required:
+- CITATION
+- checklist
+- filename conventions
+- license
+- lintr
+- spelling
+spelling:
+  default: en-GB
+  ignore:
+  - .github
+  - LICENSE.md
+  - output
+  - renv
+  - source/create_map
+  other:
+    nl-BE:
+    - source/density/detectie.Rmd
+    - source/density/detectie2.Rmd
+    - source/rapport/01_inleiding.Rmd
+    - source/rapport/1_alternatief.Rmd
+    - source/rapport/2_relevant.Rmd
+    - source/rapport/3_telblok.Rmd
+    - source/rapport/4_map_roulette.Rmd
+    - source/rapport/5_reproduceerbaar.Rmd
+    - source/rapport/index.Rmd
+    - source/rapport/zzz_references_and_appendix.Rmd

data/downloads/checksum.csv

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downloads/checksum.yml → data/downloads/checksum.yml

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