diff --git a/.dockerignore b/.dockerignore
new file mode 100644
index 00000000..9cd7a9ca
--- /dev/null
+++ b/.dockerignore
@@ -0,0 +1,5 @@
+.git
+.Rproj.user
+publish
+src
+renv/library
diff --git a/.github/workflows/test_refs_PR.yml b/.github/workflows/test_refs_PR.yml
new file mode 100644
index 00000000..7444555c
--- /dev/null
+++ b/.github/workflows/test_refs_PR.yml
@@ -0,0 +1,25 @@
+name: Env var on PR
+
+on:
+ pull_request:
+ branches:
+ - main
+
+jobs:
+ build-website:
+ runs-on: ubuntu-latest
+ name: "test env var in PR"
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_PAT }}
+ steps:
+ - name: Checkout repo
+ uses: actions/checkout@v2
+ - name: test
+ run: |
+ echo 'GitHub actions:' $GITHUB_ACTIONS
+ echo 'Event name:' $GITHUB_EVENT_NAME
+ echo 'ref:' $GITHUB_REF
+ echo 'ref name:' $GITHUB_REF_NAME
+ echo 'base ref:' $GITHUB_BASE_REF
+ echo 'head ref:' $GITHUB_HEAD_REF
+ echo 'repo:' $GITHUB_REPOSITORY
diff --git a/.github/workflows/update-website-test.yml b/.github/workflows/update-website-test.yml
new file mode 100644
index 00000000..c7ac762f
--- /dev/null
+++ b/.github/workflows/update-website-test.yml
@@ -0,0 +1,23 @@
+name: On merge to main, build the protocol and add it to the website "Log RECENT_MERGED_BRANCH_NAME"
+
+on:
+ push:
+ branches:
+ - main
+
+jobs:
+ build-website:
+ runs-on: ubuntu-latest
+ name: "add protocol to website"
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_PAT }}
+ steps:
+ - name: Checkout repo
+ uses: actions/checkout@v2
+ - uses: tonynguyenit18/github-action-custom-vars@v1
+ - name: test
+ run: |
+ echo 'GitHub actions:' $GITHUB_ACTIONS
+ echo 'Event name:' $GITHUB_EVENT_NAME
+ echo 'ref:' $GITHUB_REF
+ echo 'recent merged branch:' $RECENT_MERGED_BRANCH_NAME
diff --git a/.zenodo.json b/.zenodo.json
index fe70320d..2e3d4299 100644
--- a/.zenodo.json
+++ b/.zenodo.json
@@ -1,40 +1,40 @@
{
- "title": "Source code of protocols of the Research Institute for Nature and Forest (INBO)",
- "description": "This archive provides the source code of protocols used at the Research Institute for Nature and Forest (INBO), Brussels, Belgium (www.inbo.be). The protocols are written in R markdown and are compiled as html using the bookdown package. The website with the compiled protocols (including older versions) is at https://protocols.inbo.be.",
- "license": "cc-by",
- "upload_type": "other",
- "access_right": "open",
- "creators": [
- {
- "name": "Van Calster, Hans",
- "affiliation": "Research Institute for Nature and Forest",
- "orcid": "0000-0001-8595-8426"
- },
- {
- "name": "De Bie, Els",
- "affiliation": "Research Institute for Nature and Forest",
- "orcid": "0000-0001-7679-743X"
- },
- {
- "name": "Onkelinx, Thierry",
- "affiliation": "Research Institute for Nature and Forest",
- "orcid": "0000-0001-8804-4216"
- },
- {
- "name": "Vanderhaeghe, Floris",
- "affiliation": "Research Institute for Nature and Forest",
- "orcid": "0000-0002-6378-6229"
- }
- ],
- "keywords": [
- "open protocol",
- "open science",
- "research institute",
- "nature",
- "forest",
- "environment",
- "markdown",
- "Flanders",
- "Belgium"
- ]
+ "title": "Source code of protocols of the Research Institute for Nature and Forest (INBO)",
+ "description": "This archive provides the source code of protocols used at the Research Institute for Nature and Forest (INBO), Brussels, Belgium (www.inbo.be<\/a>). The protocols are written in R markdown and are compiled as html using the bookdown package. The website with the compiled protocols (including older versions) is at https://protocols.inbo.be<\/a>.",
+ "license": "cc-by",
+ "upload_type": "other",
+ "access_right": "open",
+ "creators": [
+ {
+ "name": "Van Calster, Hans",
+ "affiliation": "Research Institute for Nature and Forest",
+ "orcid": "0000-0001-8595-8426"
+ },
+ {
+ "name": "De Bie, Els",
+ "affiliation": "Research Institute for Nature and Forest",
+ "orcid": "0000-0001-7679-743X"
+ },
+ {
+ "name": "Onkelinx, Thierry",
+ "affiliation": "Research Institute for Nature and Forest",
+ "orcid": "0000-0001-8804-4216"
+ },
+ {
+ "name": "Vanderhaeghe, Floris",
+ "affiliation": "Research Institute for Nature and Forest",
+ "orcid": "0000-0002-6378-6229"
+ }
+ ],
+ "keywords": [
+ "open protocol",
+ "open science",
+ "research institute",
+ "nature",
+ "forest",
+ "environment",
+ "markdown",
+ "Flanders",
+ "Belgium"
+ ]
}
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..347286c7
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,97 @@
+FROM rocker/verse
+
+ARG BUILD_DATE
+ARG VCS_REF
+LABEL org.label-schema.build-date=$BUILD_DATE \
+org.label-schema.name="RStable" \
+org.label-schema.description="A docker image with stable versions of R and a bunch of packages used to check and publish protocols." \
+org.label-schema.license="MIT" \
+org.label-schema.url="e.g. https://www.inbo.be/" \
+org.label-schema.vcs-ref=$VCS_REF \
+org.label-schema.vcs-url="https://github.com/inbo/protocolsource" \
+org.label-schema.vendor="Research Institute for Nature and Forest" \
+maintainer="Hans Van Calster "
+
+## for apt to be noninteractive
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBCONF_NONINTERACTIVE_SEEN true
+
+## Install nano
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+ nano
+
+COPY docker/Rprofile.site $R_HOME/etc/Rprofile.site
+
+## Install wget
+#RUN apt-get update \
+# && apt-get install -y --no-install-recommends \
+# wget
+
+## Install pandoc
+RUN wget https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-1-amd64.deb \
+ && dpkg -i pandoc-2.7.3-1-amd64.deb \
+ && rm pandoc-2.7.3-1-amd64.deb
+
+## Install git depencencies
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+# git \
+ openssh-client
+
+## Install curl dependencies
+#RUN apt-get update \
+# && apt-get install -y --no-install-recommends \
+# libcurl4-openssl-dev
+
+## Install ggplot2 dependencies
+#RUN apt-get update \
+# && apt-get install -y --no-install-recommends \
+# libfreetype6-dev
+
+## Install rgdal dependencies
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+ gdal-bin \
+ libgdal-dev \
+ libproj-dev \
+ proj-bin
+
+## Install openssl dependencies
+#RUN apt-get update \
+# && apt-get install -y --no-install-recommends \
+# libssl-dev
+
+## Install systemfonts dependencies
+#RUN apt-get update \
+# && apt-get install -y --no-install-recommends \
+# libfontconfig1-dev
+
+## Install textshaping dependencies
+#RUN apt-get update \
+# && apt-get install -y --no-install-recommends \
+# libharfbuzz-dev libfribidi-dev
+
+## Install V8 dependencies
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+ libv8-dev
+
+## Install xml2 dependencies
+#RUN apt-get update \
+# && apt-get install -y --no-install-recommends \
+# libxml2-dev
+
+WORKDIR /github/workspace
+
+RUN R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"
+RUN R -e "renv::consent(provided = TRUE)"
+COPY renv.lock renv.lock
+RUN R -e "renv::restore()"
+RUN R -e "renv::isolate()"
+
+COPY docker/entrypoint_website.sh /entrypoint_website.sh
+COPY docker/entrypoint_update.sh /entrypoint_update.sh
+COPY docker/entrypoint_check.sh /entrypoint_check.sh
+
+ENTRYPOINT ["/entrypoint_check.sh"]
diff --git a/NEWS.md b/NEWS.md
index 39b76bfb..db99893a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+## Version 2022.01
+
+- Protocol code: sfp-401-nl
+- Title: Klassieke vegetatieopname in een proefvlak aan de hand van visuele inschattingen van bedekking van soorten in (semi-)terrestrische vegetatie
+
\ No newline at end of file
+-->
diff --git a/build_push.sh b/build_push.sh
new file mode 100644
index 00000000..1e639415
--- /dev/null
+++ b/build_push.sh
@@ -0,0 +1,47 @@
+#to be used on protocolsource (change entrypoint below in Dockerfile to run other parts)
+
+docker build --tag=inbo/protocols .
+
+#entrypoint_check
+docker run --rm --env GITHUB_REPOSITORY="ElsLommelen/protocolsource" --env BRANCH_SOURCE="dockertests" --env PROTOCOL_CODE="sfp-401-nl" --env INPUT_TOKEN inbo/protocols
+#INPUT_TOKEN is als omgevingsvariabele toegevoegd op laptop
+
+#entrypoint_update
+docker run --rm --env GITHUB_REPOSITORY="ElsLommelen/protocolsource" --env BRANCH_SOURCE="dockertests" --env PROTOCOL_CODE="sfp-401-nl" --env INPUT_TOKEN inbo/protocols
+
+#entrypoint_website
+docker run --rm --env GITHUB_REPOSITORY_SOURCE="ElsLommelen/protocolsource" --env BRANCH_SOURCE="dockertests" --env GITHUB_REPOSITORY_DEST="ElsLommelen/protocols" --env INPUT_TOKEN --env GITHUB_ACTIONS=true --env GITHUB_EVENT_NAME=push --env GITHUB_REF=refs/heads/main --env PROTOCOL_CODE="sfp-401-nl" inbo/protocols
+
+
+
+#examples
+docker build --no-cache --tag=inbobmk/checklist .
+
+docker build --tag=inbobmk/checklist .
+
+docker push inbobmk/checklist
+
+# run on branch
+docker run --rm --env GITHUB_REPOSITORY="inbo/checklist" --env GITHUB_SHA=$(git rev-parse HEAD) --env INPUT_TOKEN=$GITHUB_PAT --env INPUT_PATH="." --env ORCID_TOKEN=$ORCID_TOKEN --env CODECOV_TOKEN=$CODECOV_TOKEN inbobmk/checklist
+docker run --rm -it --entrypoint=/bin/bash --env GITHUB_REPOSITORY="inbo/checklist" --env GITHUB_SHA=$(git rev-parse HEAD) --env INPUT_TOKEN=$GITHUB_PAT --env INPUT_PATH="." --env ORCID_TOKEN=$ORCID_TOKEN --env CODECOV_TOKEN=$CODECOV_TOKEN inbobmk/checklist
+
+# run on main
+docker run --rm --env GITHUB_REPOSITORY="inbo/checklist" --env GITHUB_SHA=$(git rev-parse HEAD) --env GITHUB_PAT=$GITHUB_PAT --env INPUT_PATH="." --env ORCID_TOKEN=$ORCID_TOKEN --env CODECOV_TOKEN=$CODECOV_TOKEN --env GITHUB_ACTIONS=true --env GITHUB_EVENT_NAME=push --env GITHUB_REF=refs/heads/main inbobmk/checklist
+
+
+
+#zinvolle env uit github
+GITHUB_BASE_REF: name of target branch of the PR
+GITHUB_EVENT_NAME: name of the event that triggered the workflow run
+GITHUB_HEAD_REF: source branch of the PR
+GITHUB_REF: full ref of branch or tag that triggered the workflow run (best niet gebruiken bij PR)
+GITHUB_REF_NAME: short ref name of branch or tag that triggered the workflow run
+GITHUB_REPOSITORY: owner and repository name, bv. inbo/protocolsource
+
+#aan te passen env
+BRANCH_SOURCE (on PR) -> GITHUB_HEAD_REF
+BRANCH_SOURCE (on push) -> GITHUB_REF_NAME
+PROTOCOL_CODE -> BRANCH_SOURCE (zie hierboven)
+INPUT_TOKEN???
+GITHUB_REPOSITORY_SOURCE -> GITHUB_REPOSITORY
+GITHUB_REPOSITORY_DEST: meegeven als env!
diff --git a/docker/Rprofile.site b/docker/Rprofile.site
new file mode 100644
index 00000000..69f17930
--- /dev/null
+++ b/docker/Rprofile.site
@@ -0,0 +1,48 @@
+options(
+ papersize = "a4",
+ tab.width = 2,
+ width = 80,
+ help_type = "html",
+ keep.source.pkgs = TRUE,
+ xpinch = 300,
+ ypinch = 300,
+ yaml.eval.expr = TRUE,
+ repos = c(
+ CRAN = "https://cloud.r-project.org/",
+ INLA = "https://inla.r-inla-download.org/R/stable",
+ inbo = "https://inbo.r-universe.dev"
+ ),
+ install.packages.check.source = "yes",
+ install.packages.compile.from.source = "always",
+ inbo_required = c("checklist", "fortunes", "remotes", "INBOmd", "INBOtheme")
+)
+
+if ("checklist" %in% rownames(utils::installed.packages())) {
+ options(
+ lintr.linter_file = system.file("lintr", package = "checklist")
+ )
+}
+
+if (
+ interactive() &&
+ !all(getOption("inbo_required") %in% rownames(utils::installed.packages()))
+) {
+ warning(
+ c(
+ "\n",
+ rep("^", getOption("width")),
+ "\nThis R installation lacks some required INBO packages.",
+ "\nPlease install them using the code below:\n",
+ "\ninstall.packages(c(",
+ paste0(
+ "\"",
+ getOption("inbo_required")[
+ !getOption("inbo_required") %in% rownames(utils::installed.packages())
+ ],
+ "\"", collapse = ", "
+ ),
+ "))\n\n",
+ rep("^", getOption("width"))
+ )
+ )
+}
diff --git a/docker/check_all.R b/docker/check_all.R
new file mode 100644
index 00000000..49861050
--- /dev/null
+++ b/docker/check_all.R
@@ -0,0 +1,20 @@
+# bundled checks for protocols
+library(protocolhelper)
+check_all <- function(protocol_code) {
+ #protocol_code <- Sys.getenv("PROTOCOL_CODE")
+ fail <- FALSE
+ tryCatch(
+ protocolhelper::check_frontmatter(protocol_code),
+ error = function(e) e,
+ finally = fail <- TRUE
+ )
+ tryCatch(
+ protocolhelper::check_structure(protocol_code),
+ error = function(e) e,
+ finally = fail <- TRUE
+ )
+ if (fail) {
+ stop("\nThe source code failed some checks. Please check the error message above.\n")
+ }
+}
+check_all(Sys.getenv("PROTOCOL_CODE"))
diff --git a/docker/entrypoint_check.sh b/docker/entrypoint_check.sh
new file mode 100755
index 00000000..7d4bf2a4
--- /dev/null
+++ b/docker/entrypoint_check.sh
@@ -0,0 +1,62 @@
+#!/bin/sh -l
+
+echo '\nGetting the code...\n'
+git clone --quiet https://$INPUT_TOKEN@github.com/$GITHUB_REPOSITORY check
+cd check
+git checkout $BRANCH_SOURCE
+#ls -a
+rm .Rprofile
+
+echo '\nSession info\n'
+Rscript -e 'sessioninfo::session_info()'
+
+#echo '\nChecking if branch is up to date with main...\n'
+#main_in_branch=$(git merge-base $BRANCH_SOURCE main)
+#echo $main_in_branch
+#git checkout main
+#git pull
+#head_main=$(git rev-parse HEAD)
+#echo $head_main
+#if [ $main_in_branch != $head_main ]; then
+# echo '\nThis branch does not contain the latest version of the main branch. Please merge the main branch into this branch first\n';
+# exit 1
+#fi
+
+echo '\nUpdate version number...\n'
+git config --global user.email "info@inbo.be"
+git config --global user.name "INBO"
+UPDATED=$(Rscript -e 'protocolhelper::update_version_number("'$PROTOCOL_CODE'")')
+echo 'output updated:' $UPDATED
+if [ "$UPDATED" = "[1] TRUE" ]; then
+ # remake the last commit without deletion of .Rprofile
+# MESSAGE=$(git log -1 --pretty=%B)
+# git reset --soft HEAD^
+# git reset HEAD .Rprofile
+# git commit --message="$MESSAGE"
+
+ git push -f
+ echo '\ncommit with new version pushed\n'
+fi
+
+echo '\nChecking protocols specific tests...\n'
+#git checkout $BRANCH_SOURCE
+#rm .Rprofile
+ls -a
+
+Rscript "docker/check_all.R"
+#Rscript --no-save --no-restore -e 'check_all("'$PROTOCOL_CODE'")'
+if [ $? -ne 0 ]; then
+ echo '\nThe source code failed some checks. Please check the error message above.\n';
+ exit 1
+fi
+
+# Rscript 'protocolhelper::check_frontmatter("'$PROTOCOL_CODE'")'
+# test1=$?
+# Rscript -e 'protocolhelper::check_structure("'$PROTOCOL_CODE'")'
+# test2=$?
+#
+# if [ $test1 -ne 0 ] || [ $test2 -ne 0 ]; then
+# #echo $error1
+# echo '\nThe source code failed some checks. Please check the error message above.\n';
+# exit 1
+# fi
diff --git a/docker/entrypoint_update.sh b/docker/entrypoint_update.sh
new file mode 100644
index 00000000..229cebbd
--- /dev/null
+++ b/docker/entrypoint_update.sh
@@ -0,0 +1,25 @@
+#!/bin/sh -l
+
+echo '\nGetting the code...\n'
+git clone --branch=$BRANCH_SOURCE https://$INPUT_TOKEN@github.com/$GITHUB_REPOSITORY /update
+git config --global user.email "info@inbo.be"
+git config --global user.name "INBO"
+cd /update
+
+rm .Rprofile
+
+echo '\nSession info\n'
+Rscript -e 'sessioninfo::session_info()'
+
+echo '\nUpdating zenodo...\n'
+Rscript --no-save --no-restore -e 'protocolhelper:::update_zenodo()'
+git add .zenodo.json
+git commit --message="update .zenodo.json"
+
+echo '\nUpdating general NEWS.md...\n'
+Rscript --no-save --no-restore -e 'protocolhelper:::update_news_release("'$PROTOCOL_CODE'")'
+git add NEWS.md
+git commit --message="update general NEWS.md"
+
+echo 'git push'
+git push -f
diff --git a/docker/entrypoint_website.sh b/docker/entrypoint_website.sh
new file mode 100755
index 00000000..3acbf70b
--- /dev/null
+++ b/docker/entrypoint_website.sh
@@ -0,0 +1,66 @@
+#!/bin/sh -l
+
+echo '\nGetting the code...\n'
+git clone --quiet https://$INPUT_TOKEN@github.com/$GITHUB_REPOSITORY_SOURCE /render
+cd /render
+git checkout $BRANCH_SOURCE
+git config --global user.email "info@inbo.be"
+git config --global user.name "INBO"
+
+rm .Rprofile
+
+echo '\nSession info\n'
+#Rscript -e "renv::restore()"
+Rscript -e 'sessioninfo::session_info()'
+
+echo '\nAdd tag to merge commit protocolsource...\n'
+echo 'GitHub actions:' $GITHUB_ACTIONS
+echo 'Event name:' $GITHUB_EVENT_NAME
+echo 'ref:' $GITHUB_REF
+git rev-parse --abbrev-ref origin/HEAD | sed 's/origin\///' | xargs git checkout
+Rscript --no-save --no-restore -e 'protocolhelper:::set_tags("'$PROTOCOL_CODE'")'
+git push --follow-tags
+
+# look up tag names and tag messages to push to repo protocols later
+# (not possible to run set_tags() when not in protocolsource anymore)
+TAGNAME_GENERAL=$(git tag -l protocols-* --points-at)
+TAGNAME_SPECIFIC=$(git tag -l s*p* --points-at)
+TAGMESSAGE_GENERAL=$(git for-each-ref refs/tags/$TAGNAME_GENERAL --format='%(contents)')
+TAGMESSAGE_SPECIFIC=$(git for-each-ref refs/tags/$TAGNAME_SPECIFIC --format='%(contents)')
+
+echo 'tagname general:' $TAGNAME_GENERAL
+echo 'tag message general:' $TAGMESSAGE_GENERAL
+echo 'tagname specific:' $TAGNAME_SPECIFIC
+echo 'tag message specific:' $TAGMESSAGE_SPECIFIC
+
+echo 'Rendering the Rmarkdown files...\n'
+#rm .Rprofile
+Rscript -e "protocolhelper:::render_release()"
+if [ $? -ne 0 ]; then
+ echo '\nRendering failed. Please check the error message above.\n';
+ exit 1
+else
+ echo '\nAll Rmarkdown files rendered successfully\n'
+fi
+
+echo 'Publishing the rendered files...\n'
+git clone --quiet --depth=1 --single-branch --branch=main https://$INPUT_TOKEN@github.com/$GITHUB_REPOSITORY_DEST /destiny
+#git config --global user.email "info@inbo.be"
+#git config --global user.name "INBO"
+
+cp -R /render/publish/. /destiny/.
+cd /destiny
+ls -a
+
+git config user.name
+git config user.email
+git add --all
+git commit --message="Add new protocol"
+git push -f https://$INPUT_TOKEN@github.com/$GITHUB_REPOSITORY_DEST
+
+git rev-parse --abbrev-ref origin/HEAD | sed 's/origin\///' | xargs git checkout
+git tag -a $TAGNAME_GENERAL -m "$TAGMESSAGE_GENERAL"
+git tag -a $TAGNAME_SPECIFIC -m "$TAGMESSAGE_SPECIFIC"
+git push --follow-tags
+
+echo '\nNew version published...'
diff --git a/docker/render.R b/docker/render.R
new file mode 100755
index 00000000..7577d710
--- /dev/null
+++ b/docker/render.R
@@ -0,0 +1 @@
+protocolhelper:::render_release()
diff --git a/src/thematic/4_vegetation/sfp-401-nl_vegopname-terrest/index.Rmd b/src/thematic/4_vegetation/sfp-401-nl_vegopname-terrest/index.Rmd
index 716649a5..56182068 100644
--- a/src/thematic/4_vegetation/sfp-401-nl_vegopname-terrest/index.Rmd
+++ b/src/thematic/4_vegetation/sfp-401-nl_vegopname-terrest/index.Rmd
@@ -1,14 +1,20 @@
---
-title: Klassieke vegetatieopname in een proefvlak aan de hand van visuele inschattingen van bedekking van soorten in (semi-)terrestrische vegetatie
-subtitle:
+title: Klassieke vegetatieopname in een proefvlak aan de hand van visuele inschattingen
+ van bedekking van soorten in (semi-)terrestrische vegetatie
+subtitle: null
author:
- - name: Els De Bie
- orcid: 0000-0001-7679-743X
-date: "`r Sys.Date()`"
-reviewers: [Hans Van Calster,Lieve Vriens,Jan Wouters,Wouter Van Gompel,Els Lommelen]
+- name: Els De Bie
+ orcid: 0000-0001-7679-743X
+date: '2022-07-18'
+reviewers:
+- Hans Van Calster
+- Lieve Vriens
+- Jan Wouters
+- Wouter Van Gompel
+- Els Lommelen
file_manager: Hans Van Calster
protocol_code: sfp-401-nl
-version_number: "2021.01"
+version_number: '2021.01'
language: nl
theme: vegetation
params:
@@ -16,28 +22,31 @@ params:
plot_length_openveg_m: 3
plot_width_forest_m: 16
plot_length_forest_m: 16
- plot_shape: "vierkant"
+ plot_shape: vierkant
height_herbshrublayer_openveg_m: 0.8
height_herbshrublayer_forest_m: 2
height_shrubtreelayer_openveg_m: 6
height_shrubtreelayer_forest_m: 8
- species_list: ["vaatplanten", "mossen", "lichenen"]
- phenology_values: "standaard inbo-fenologiecodes"
- coverscale_species: "Londo origineel"
- coverscale_structure: "inbo-structuur-schaal"
+ species_list:
+ - vaatplanten
+ - mossen
+ - lichenen
+ phenology_values: standaard inbo-fenologiecodes
+ coverscale_species: Londo origineel
+ coverscale_structure: inbo-structuur-schaal
site: bookdown::bookdown_site
-output:
+output:
bookdown::gitbook:
split_by: none
- split_bib: FALSE
- template: !expr protocolhelper::protocol_css()
+ split_bib: false
+ template: css/gitbook.html
css: css/inbo_rapport.css
config:
- toc:
- before: |
- 
- after: |
- 
+ toc:
+ before: |
+
+ after:
---
```{=html}