Consistently use gfm rather than markdown_github

content/articles/communicating/index.Rmd

@@ -6,8 +6,9 @@ bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 This page lists **selected** literature and online resources. Some are related to existing tutorial pages, while others are not. They are supposed to be of high interest to this site's users.

content/articles/communicating/index.md

@@ -6,8 +6,9 @@ bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 This page lists **selected** literature and online resources. Some are
@@ -18,8 +19,7 @@ Several of the resources were added based on an inspiring
 [talk](https://docs.google.com/presentation/d/10KkXEv4r3wWtdKvB6RFOPe809eMNldODaRqQxn-jeME/edit?usp=sharing)
 by Julia Lowndes at the SAFRED conference, Brussels, 27 Feb 2018.
 
-Sharing data
-------------
+## Sharing data
 
 -   Ellis & Leek (2017): guidelines for **providing data** to a
     scientist / statistician: provide raw data, format consistently,
@@ -30,14 +30,12 @@ Sharing data
     and considerations to be made
 -   Perkel (2016): **data repository sites** like github and others
 
-Communicating
--------------
+## Communicating
 
 -   Smith *et al.* (2016): recommendations of the FORCE11 Software
     Citation Working Group
 
-Bibliography
-------------
+## Bibliography
 
 Culina A., Baglioni M., Crowther T.W., Visser M.E., Woutersen-Windhouwer
 S. & Manghi P. (2018). Navigating the unfolding open data landscape in

content/articles/computing/index.Rmd

@@ -6,9 +6,9 @@ bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
-        variant: gfm
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 This page lists **selected** literature and online resources. Some are related to existing tutorial pages, while others are not. They are supposed to be of high interest to this site's users.

content/articles/computing/index.md

@@ -6,9 +6,9 @@ bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
-        variant: gfm
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 This page lists **selected** literature and online resources. Some are
@@ -21,34 +21,34 @@ by Julia Lowndes at the SAFRED conference, Brussels, 27 Feb 2018.
 
 ## Overviews
 
-  - Wilson *et al.* (2017): set of **good computing practices** that
+-   Wilson *et al.* (2017): set of **good computing practices** that
     every researcher can adopt
-  - British Ecological Society (2014): planning the **data life cycle**;
+-   British Ecological Society (2014): planning the **data life cycle**;
     creating, processing, documenting, preserving, sharing & reusing
     data
-  - Goudeseune *et al.* (2019): **open data management**, data
+-   Goudeseune *et al.* (2019): **open data management**, data
     management plan, repositories, standards and licenses
-  - Cooper & Hsing (2017): file organisation, workflow documentation,
+-   Cooper & Hsing (2017): file organisation, workflow documentation,
     **code** reproducibility and readability, writing reproducible
     reports, version control and code archiving
-  - Marwick *et al.* (2018): the **research compendium** as a solution
+-   Marwick *et al.* (2018): the **research compendium** as a solution
     to share research in a reproducible way
-  - Ibanez *et al.* (2014): vision on reproducible science, routine
+-   Ibanez *et al.* (2014): vision on reproducible science, routine
     **practices**, collaboration, literate computing
 
 See also some resources related to [learning and education](../skills)
 and the [discipline of open and reproducible science](../open_science).
 
 ## Specific tools
 
-  - Ross *et al.* (2017): about **tidyverse** workflow and tools
-  - <https://www.tidyverse.org>: website of the tidyverse **packages**
+-   Ross *et al.* (2017): about **tidyverse** workflow and tools
+-   <https://www.tidyverse.org>: website of the tidyverse **packages**
 
 ## Focus on version control workflows
 
-  - Bryan (2017): rationale, workflows and tools regarding version
+-   Bryan (2017): rationale, workflows and tools regarding version
     control for project organization
-  - Bryan *et al.* (2019): getting started with git and github workflows
+-   Bryan *et al.* (2019): getting started with git and github workflows
     in RStudio
 
 ## Bibliography

content/articles/geospatial_standards/index.Rmd

@@ -8,9 +8,9 @@ bibliography: ../reproducible_research.bib
 categories: ["r", "gis"]
 tags: ["gis", "r", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
-        variant: gfm
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 Some inspiration for this post came from the beautiful books of @lovelace_geocomputation_2020, @pebesma_edzer_spatial_2019 and @heijmans_spatial_2019, and from various websites.

content/articles/geospatial_standards/index.md

@@ -8,9 +8,9 @@ bibliography: ../reproducible_research.bib
 categories: ["r", "gis"]
 tags: ["gis", "r", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
-        variant: gfm
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 Some inspiration for this post came from the beautiful books of Lovelace
@@ -19,25 +19,25 @@ various websites.
 
 ## Why use open standards?
 
-  - Open file standards ease collaboration, portability and
+-   Open file standards ease collaboration, portability and
     compatibility between users, machines and applications.
-  - Their (file) structure is fully documented.
-      - Consequently, scientists and programmers can build new software
+-   Their (file) structure is fully documented.
+    -   Consequently, scientists and programmers can build new software
         / packages and make innovations that use these standards, while
         maintaining interoperability with existing applications.
-      - And, there is a much higher chance that your data will still be
+    -   And, there is a much higher chance that your data will still be
         readable in a hundred years from now. The standard’s open
         documentation makes it relatively easy to build tools that can
-        read an ancient open-standard file\!
+        read an ancient open-standard file!
 
-Luckily, quite a list of open standards is available\! Below, some
+Luckily, quite a list of open standards is available! Below, some
 powerful and widely-used single-file formats are introduced. Single-file
 data sources are readily amenable to exchange and publication.
 
 I see you can’t wait to start practicing, so you can also head straight
 over to the [tutorial on vector
 formats](../../tutorials/spatial_standards_vector/) and the [tutorial on
-raster formats](../../tutorials/spatial_standards_raster/)\! In these
+raster formats](../../tutorials/spatial_standards_raster/)! In these
 tutorials, a comparison table of vector/raster file formats is also
 presented.
 
@@ -46,9 +46,9 @@ presented.
 **[GDAL](https://gdal.org)** (Geospatial Data Abstraction Library) is by
 far the most used collection of open-source drivers for:
 
-  - a lot of [raster](https://gdal.org/drivers/raster/index.html)
+-   a lot of [raster](https://gdal.org/drivers/raster/index.html)
     formats;
-  - a lot of [vector](https://gdal.org/drivers/vector/index.html)
+-   a lot of [vector](https://gdal.org/drivers/vector/index.html)
     formats.
 
 In other words, it is the preferred workhorse for reading and writing
@@ -62,27 +62,27 @@ So, in R we use packages that use GDAL in the background, such as
 
 ## The GeoPackage file format
 
-  - Its website is <https://www.geopackage.org>.
-  - It is a standardized implementation of an SQLite database for
+-   Its website is <https://www.geopackage.org>.
+-   It is a standardized implementation of an SQLite database for
     geospatial data. Hence, a GeoPackage is a **binary** file
     (`filename.gpkg`). It shares this property with shapefiles, which
-    however pose multiple limitations,\[1\] so the GeoPackage is a more
+    however pose multiple limitations,[^1] so the GeoPackage is a more
     than suitable replacement.
-  - The GeoPackage can store one or *multiple* **vector** layers
+-   The GeoPackage can store one or *multiple* **vector** layers
     (points, lines, polygons and related feature types). Besides vector
     data, it can also store **raster** data or extra standalone
     **tables**. These properties make it somehow comparable to the
     ‘personal geodatabase’ of ArcGIS – ESRI’s closed, Windows-only
-    format.\[2\]
-  - The GeoPackage standard is
+    format.[^2]
+-   The GeoPackage standard is
     [maintained](https://www.opengeospatial.org/standards/geopackage) by
     the [Open Geospatial Consortium](https://www.opengeospatial.org/)
     (OGC), which stands out as a reference when it comes to open
     geospatial standards.
 
 ## The GeoJSON file format
 
-  - One [GeoJSON](https://tools.ietf.org/html/rfc7946) file
+-   One [GeoJSON](https://tools.ietf.org/html/rfc7946) file
     (`filename.geojson`) contains *one* **vector** layer. Note that one
     vector layer can combine different [feature geometry
     types](https://r-spatial.github.io/sf/articles/sf1.html#simple-feature-geometry-types),
@@ -94,56 +94,56 @@ So, in R we use packages that use GDAL in the background, such as
     example). GeoJSON adds the necessary specification to JSON for
     standardized storage of geographic feature data, but it is still a
     plain JSON text file.
-  - The GeoJSON standard is maintained by the Internet Engineering Task
+-   The GeoJSON standard is maintained by the Internet Engineering Task
     Force ([IETF](https://www.ietf.org/)), a large open standards
     organization that develops Internet standards under the auspices of
     the Internet Society.
-  - Although the previous version of the GeoJSON standard – GeoJSON 2008
+-   Although the previous version of the GeoJSON standard – GeoJSON 2008
     – is still a lot in use, it is
     [obsoleted](http://geojson.org/geojson-spec.html) and a new version
     **[RFC7946](https://tools.ietf.org/html/rfc7946)** is establishing.
-      - This version is strict about the coordinate reference system
+    -   This version is strict about the coordinate reference system
         (CRS) – it is always [WGS84](https://epsg.io/4326) – and it also
         differs on a few other aspects (such as the recommendation for
         applications [not to
         inflate](https://tools.ietf.org/html/rfc7946#section-11.2)
         decimal coordinate precision).
-      - RFC7946 solves the problem that quite a few libraries –
+    -   RFC7946 solves the problem that quite a few libraries –
         including GDAL – simply assumed WGS84 in GeoJSON 2008 (without
         checking or transforming), even though WGS84 was not a
         requirement of GeoJSON 2008 (it did support an explicit *crs*
         declaration). This resulted in inconveniences (cf. [this
         post](https://github.com/r-spatial/sf/issues/344#issue-229118527)
         in the `sf`-repository).
-      - A [specific
+    -   A [specific
         section](https://gdal.org/drivers/vector/geojson.html#rfc-7946-write-support)
         in the documentation of GDAL’s GeoJSON driver gives a summary of
         the differences between both GeoJSON versions.
-  - While GDAL by default still follows the GeoJSON 2008 format,\[3\]
+-   While GDAL by default still follows the GeoJSON 2008 format,[^3]
     RFC7946 is supported by the option `RFC7946=YES`. Here, reprojection
     to WGS84 will happen automatically. It applies 7 decimal places for
     coordinates, i.e. approximately 1 cm. Given the advantages, ***we
     advise to explicitly use RFC7946***. Several functions in R allow
     the user to provide options that are passed to GDAL, so we can ask
     to deliver RFC7946 (see the
     [tutorial](../../tutorials/spatial_standards_vector/)).
-  - In order to keep it manageable (text file size, usage in versioning
-    systems\[4\] ) it can be wise to use GeoJSON for more simple cases
+-   In order to keep it manageable (text file size, usage in versioning
+    systems[^4] ) it can be wise to use GeoJSON for more simple cases
     (points and rather simple lines and polygons), and use the binary
     GeoPackage format for larger (more complex) cases.
 
 ## The GeoTIFF file format
 
-  - [GeoTIFF](https://en.wikipedia.org/wiki/GeoTIFF) is the preferred
+-   [GeoTIFF](https://en.wikipedia.org/wiki/GeoTIFF) is the preferred
     single-file open standard for **raster** data. It adheres to the
     open [TIFF](https://en.wikipedia.org/wiki/TIFF) specification; hence
     it is a TIFF image file (`filename.tif`). It
     [uses](http://docs.opengeospatial.org/is/19-008r4/19-008r4.html#_geotiff_file_structure_and_geotiff_crs_and_models_principles_informative)
     a small set of reserved TIFF tags to store information about CRS,
     extent and resolution of the raster.
-  - A GeoTIFF file can contain *one* or *multiple* rasters with the same
+-   A GeoTIFF file can contain *one* or *multiple* rasters with the same
     CRS, extent and resolution.
-  - The GeoTIFF standard is
+-   The GeoTIFF standard is
     [maintained](https://www.opengeospatial.org/standards/geotiff) by
     the [Open Geospatial Consortium](https://www.opengeospatial.org/)
     (OGC), which stands out as a reference when it comes to open
@@ -175,21 +175,21 @@ Pebesma E. & Bivand R. (2019). Spatial Data Science.
 
 </div>
 
-1.   Some problems with shapefiles are: they’re not an open format, they
-    consist of multiple files and they have restrictions regarding file
-    size, column name length, number of columns and the feature types
-    that can be accommodated.
+[^1]:  Some problems with shapefiles are: they’re not an open format,
+    they consist of multiple files and they have restrictions regarding
+    file size, column name length, number of columns and the feature
+    types that can be accommodated.
 
-2.   Note that personal geodatabases have their size limited to 250-500
-    MB; a GeoPackage can have a size of about 140 TB if the filesystem
-    can handle it.
+[^2]:  Note that personal geodatabases have their size limited to
+    250-500 MB; a GeoPackage can have a size of about 140 TB if the
+    filesystem can handle it.
 
-3.   Though GeoJSON 2008 is obsoleted, the now recommended RFC7946
+[^3]:  Though GeoJSON 2008 is obsoleted, the now recommended RFC7946
     standard is still officially in a *proposal* stage. That is probably
     the reason why GDAL does not yet default to RFC7946. A somehow
     confusing stage, it seems.
 
-4.   When versioning GeoJSON files, mind the order of your data when
+[^4]:  When versioning GeoJSON files, mind the order of your data when
     rewriting them: reordering could produce large diffs. Interested in
     combining GeoJSON and GitHub? [Surprise
-    yourself](https://github.com/lyzidiamond/learn-geojson)\!
+    yourself](https://github.com/lyzidiamond/learn-geojson)!

content/articles/inbo_software/index.md

@@ -3,10 +3,6 @@ title: "Software by INBO: packages for environmentalists and ecologists!"
 date: 2020-12-03
 categories: ["development", "r", "statistics", "databases"]
 tags: ["open science", "packages", "r", "python"]
-output: 
-    md_document:
-        preserve_yaml: true
-        variant: gfm
 ---
 
 At the Research Institute for Nature and Forest (INBO), we are eager to sustain, promote and develop open-source software that is relevant to biodiversity researchers! This page lists **R and Python packages** which INBO developed or made a significant contribution to. Several of these packages continue being developed.

content/articles/inbo_stats_courses/index.md

@@ -5,10 +5,6 @@ authors: [hansvancalster]
 date: 2021-02-24
 categories: ["r", "statistics"]
 tags: ["r", "INLA", "mixed model", "uncertainty", "explorative data analysis", "analysis of variance", "generalized linear regression", "multivariate statistics"]
-output: 
-    md_document:
-        preserve_yaml: true
-        variant: gfm
 ---
 
 During the course of the years, we have taught many statistics courses at the Research Institute for Nature and Forest (INBO), both for scientists and technicians.

content/articles/open_science/index.Rmd

@@ -6,8 +6,9 @@ bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 This page lists **selected** literature and online resources. Some are related to existing tutorial pages, while others are not. They are supposed to be of high interest to this site's users.

content/articles/open_science/index.md

@@ -6,8 +6,9 @@ bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
-    md_document:
-        preserve_yaml: true
+  md_document:
+    preserve_yaml: true
+    variant: gfm+footnotes
 ---
 
 This page lists **selected** literature and online resources. Some are
@@ -29,8 +30,7 @@ computing workflows](../computing).
 -   Donati & Woolston (2017): how data science is becoming a large
     discipline
 
-Focus on reproducible research
-------------------------------
+## Focus on reproducible research
 
 -   Stodden *et al.* (2014): **book** on computational reproducibility
     and (experiment) replicability; the three parts are *Tools*,
@@ -42,8 +42,7 @@ Focus on reproducible research
 -   ROpenSci Contributors (2018): a comprehensive **overview** of
     aspects and R-oriented tools in reproducible research
 
-Bibliography
-------------
+## Bibliography
 
 Begley C.G., Buchan A.M. & Dirnagl U. (2015). Institutions must do their
 part for reproducibility. Nature 525 (7567): 25–27.