Articles open science: update with some extra resources

content/articles/communicating/index.Rmd

@@ -1,7 +1,7 @@
 ---
 title: "Sharing and communicating"
 date: 2018-03-21
-csl: ../inbo.csl
+csl: '`r cslfile <- file.path(tempdir(), "research-institute-for-nature-and-forest.csl"); download.file("https://github.com/inbo/styles/raw/inbocsl-0.1.0/research-institute-for-nature-and-forest.csl", cslfile); cslfile`'
 bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]

content/articles/communicating/index.md

@@ -1,7 +1,7 @@
 ---
 title: "Sharing and communicating"
 date: 2018-03-21
-csl: ../inbo.csl
+csl: '/tmp/RtmpnGa7xS/research-institute-for-nature-and-forest.csl'
 bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
@@ -13,7 +13,7 @@ weight: 4
 
 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.
+supposed to be of high interest to this site’s users.
 
 Several of the resources were added based on an inspiring
 [talk](https://docs.google.com/presentation/d/10KkXEv4r3wWtdKvB6RFOPe809eMNldODaRqQxn-jeME/edit?usp=sharing)
@@ -42,27 +42,29 @@ Bibliography
 
 Culina A., Baglioni M., Crowther T.W., Visser M.E., Woutersen-Windhouwer
 S. & Manghi P. (2018). Navigating the unfolding open data landscape in
-ecology and evolution. Nature Ecology & Evolution 2 (3): 420–426. URL:
-<https://www.nature.com/articles/s41559-017-0458-2>. DOI:
-[10.1038/s41559-017-0458-2](https://doi.org/10.1038/s41559-017-0458-2).
+ecology and evolution. Nature Ecology & Evolution 2 (3): 420–426.
+<https://doi.org/10.1038/s41559-017-0458-2>.
 
 Ellis S.E. & Leek J.T. (2017). How to share data for collaboration.
-PeerJ Preprints 5: e3139v5. URL: <https://peerj.com/preprints/3139>.
-DOI:
-[10.7287/peerj.preprints.3139v5](https://doi.org/10.7287/peerj.preprints.3139v5).
+PeerJ Preprints 5: e3139v5.
+<https://doi.org/10.7287/peerj.preprints.3139v5>.
 
 Perkel J. (2016). Democratic databases: Science on GitHub. Nature News
-538 (7623): 127. URL:
-<http://www.nature.com/news/democratic-databases-science-on-github-1.20719>.
-DOI: [10.1038/538127a](https://doi.org/10.1038/538127a).
+538 (7623): 127. <https://doi.org/10.1038/538127a>.
 
 Smith A.M., Katz D.S. & Niemeyer K.E. (2016). Software citation
-principles. PeerJ Computer Science 2: e86. URL:
-<https://peerj.com/articles/cs-86>. DOI:
-[10.7717/peerj-cs.86](https://doi.org/10.7717/peerj-cs.86).
+principles. PeerJ Computer Science 2: e86.
+<https://doi.org/10.7717/peerj-cs.86>.
 
 Wilkinson M.D., Dumontier M., Aalbersberg I.J., Appleton G., Axton M.,
 Baak A., Blomberg N., Boiten J.-W., Silva Santos L.B. da, Bourne P.E.,
-et al. (2016). The FAIR Guiding Principles for scientific data
-management and stewardship. Scientific Data 3: 160018. URL:
-<http://dx.doi.org/10.1038/sdata.2016.18>.
+Bouwman J., Brookes A.J., Clark T., Crosas M., Dillo I., Dumon O.,
+Edmunds S., Evelo C.T., Finkers R., Gonzalez-Beltran A., Gray A.J.G.,
+Groth P., Goble C., Grethe J.S., Heringa J., Hoen P.A.C. ’t, Hooft R.,
+Kuhn T., Kok R., Kok J., Lusher S.J., Martone M.E., Mons A., Packer
+A.L., Persson B., Rocca-Serra P., Roos M., Schaik R. van, Sansone S.-A.,
+Schultes E., Sengstag T., Slater T., Strawn G., Swertz M.A., Thompson
+M., Lei J. van der, Mulligen E. van, Velterop J., Waagmeester A.,
+Wittenburg P., Wolstencroft K., Zhao J. & Mons B. (2016). The FAIR
+Guiding Principles for scientific data management and stewardship.
+Scientific Data 3: 160018. <http://dx.doi.org/10.1038/sdata.2016.18>.

content/articles/computing/index.Rmd

@@ -1,13 +1,14 @@
 ---
 title: "Scientific computing and data handling workflows"
-date: 2018-03-21
-csl: ../inbo.csl
+date: 2020-09-23
+csl: '`r cslfile <- file.path(tempdir(), "research-institute-for-nature-and-forest.csl"); download.file("https://github.com/inbo/styles/raw/inbocsl-0.1.0/research-institute-for-nature-and-forest.csl", cslfile); cslfile`'
 bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
     md_document:
         preserve_yaml: true
+        variant: gfm
 weight: 2
 ---
 
@@ -21,14 +22,17 @@ by Julia Lowndes at the SAFRED conference, Brussels, 27 Feb 2018.
 
 - @wilson_good_2017: set of **good computing practices** that every researcher can adopt
 - @british_ecological_society_guide_2014: planning the **data life cycle**; creating, processing, documenting, preserving, sharing & reusing data
+- @goudeseune_guidance_2019: **open data management**, data management plan, repositories, standards and licenses
 - @cooper_guide_2017: file organisation, workflow documentation, **code** reproducibility and readability, writing reproducible reports, version control and code archiving
+- @marwick_packaging_2018: the **research compendium** as a solution to share research in a reproducible way
 - @ibanez_practicing_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_declutter_2017: about **tidyverse** workflow and tools
+- <https://www.tidyverse.org>: website of the tidyverse **packages**
 
 ## Focus on version control workflows
 

content/articles/computing/index.md

@@ -1,85 +1,134 @@
 ---
 title: "Scientific computing and data handling workflows"
-date: 2018-03-21
-csl: ../inbo.csl
+date: 2020-09-23
+csl: '/tmp/RtmpJcw7yp/research-institute-for-nature-and-forest.csl'
 bibliography: ../reproducible_research.bib
 categories: ["literature"]
 tags: ["literature", "open science"]
 output: 
     md_document:
         preserve_yaml: true
+        variant: gfm
 weight: 2
 ---
 
 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.
+supposed to be of high interest to this site’s users.
 
 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.
 
-Overviews
----------
+## 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
--   Cooper & Hsing (2017): file organisation, workflow documentation,
+  - Goudeseune *et al.* (2019): **open data management**, data
+    management plan, repositories, standards and licenses
+  - Cooper & Hsing (2017): file organisation, workflow documentation,
     **code** reproducibility and readability, writing reproducible
     reports, version control and code archiving
--   Ibanez *et al.* (2014): vision on reproducible science, routine
+  - 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
     **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
---------------
+## Specific tools
 
--   Ross *et al.* (2017): about **tidyverse** workflow and tools
+  - Ross *et al.* (2017): about **tidyverse** workflow and tools
+  - <https://www.tidyverse.org>: website of the tidyverse **packages**
 
-Focus on version control workflows
-----------------------------------
+## 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
-------------
+## Bibliography
 
-British Ecological Society (Ed.) (2014). A guide to data management in
+<div id="refs" class="references">
+
+<div id="ref-british_ecological_society_guide_2014">
+
+British Ecological Society (ed.) (2014). A guide to data management in
 ecology and evolution. BES Guides to Better Science. British Ecological
 Society, London.
 
+</div>
+
+<div id="ref-bryan_excuse_2017">
+
 Bryan J. (2017). Excuse me, do you have a moment to talk about version
-control? PeerJ Preprints 5: e3159v2. URL:
-<https://peerj.com/preprints/3159>. DOI:
-[10.7287/peerj.preprints.3159v2](https://doi.org/10.7287/peerj.preprints.3159v2).
+control? PeerJ Preprints 5: e3159v2.
+<https://doi.org/10.7287/peerj.preprints.3159v2>.
+
+</div>
+
+<div id="ref-bryan_happy_2019">
 
 Bryan J., the STAT 545 TAs & Hester J. (2019). Happy Git and GitHub for
-the useR. URL: <https://happygitwithr.com/>.
+the useR. <https://happygitwithr.com/>.
 
-Cooper N. & Hsing P.-Y. (Eds.) (2017). A guide to reproducible code in
+</div>
+
+<div id="ref-cooper_guide_2017">
+
+Cooper N. & Hsing P.-Y. (eds.) (2017). A guide to reproducible code in
 ecology and evolution. BES Guides to Better Science. British Ecological
 Society, London.
 
+</div>
+
+<div id="ref-goudeseune_guidance_2019">
+
+Goudeseune L., Le Roux X., Eggermont H., Bishop B., Bléry C., Brosens
+D., Coupremanne M., Davis R., Hautala H., Heughebaert A., Jacques C.,
+Lee T., Rerig G. & Ungvári J. (2019). Guidance document for scientists
+on data management, open data, and the production of Data Management
+Plans.  BiodivERsA report. Zenodo.
+<https://doi.org/10.5281/zenodo.3448251>.
+
+</div>
+
+<div id="ref-ibanez_practicing_2014">
+
 Ibanez L., Schroeder W.J. & Hanwell M.D. (2014). Practicing open
-science. In: Stodden V., Leisch F., Peng R.D. (editors). Implementing
+science. In: Stodden V., Leisch F. & Peng R.D. (eds.). Implementing
 reproducible research. CRC Press, Boca Raton, FL.
 
+</div>
+
+<div id="ref-marwick_packaging_2018">
+
+Marwick B., Boettiger C. & Mullen L. (2018). Packaging Data Analytical
+Work Reproducibly Using R (and Friends). The American Statistician 72
+(1): 80–88. <https://doi.org/10.1080/00031305.2017.1375986>.
+
+</div>
+
+<div id="ref-ross_declutter_2017">
+
 Ross Z., Wickham H. & Robinson D. (2017). Declutter your R workflow with
-tidy tools. PeerJ Preprints 5: e3180v1. URL:
-<https://peerj.com/preprints/3180>. DOI:
-[10.7287/peerj.preprints.3180v1](https://doi.org/10.7287/peerj.preprints.3180v1).
+tidy tools. PeerJ Preprints 5: e3180v1.
+<https://doi.org/10.7287/peerj.preprints.3180v1>.
+
+</div>
+
+<div id="ref-wilson_good_2017">
 
 Wilson G., Bryan J., Cranston K., Kitzes J., Nederbragt L. & Teal T.K.
 (2017). Good enough practices in scientific computing. PLOS
-Computational Biology 13 (6): e1005510. URL:
-<http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510>.
-DOI:
-[10.1371/journal.pcbi.1005510](https://doi.org/10.1371/journal.pcbi.1005510).
+Computational Biology 13 (6): e1005510.
+<https://doi.org/10.1371/journal.pcbi.1005510>.
+
+</div>
+
+</div>

content/articles/geospatial_standards/index.Rmd

@@ -3,12 +3,11 @@ title: "Meet some popular open geospatial standards!"
 description: "A short introduction to the powerful GeoPackage, GeoJSON and GeoTIFF standards"
 author: "Floris Vanderhaeghe"
 date: 2020-02-03
-csl: ../inbo.csl
+csl: '`r cslfile <- file.path(tempdir(), "research-institute-for-nature-and-forest.csl"); download.file("https://github.com/inbo/styles/raw/inbocsl-0.1.0/research-institute-for-nature-and-forest.csl", cslfile); cslfile`'
 bibliography: ../reproducible_research.bib
 categories: ["r", "gis"]
 tags: ["gis", "r", "open science"]
 output: 
-    html_document: default
     md_document:
         preserve_yaml: true
         variant: gfm

content/articles/geospatial_standards/index.md

@@ -3,15 +3,14 @@ title: "Meet some popular open geospatial standards!"
 description: "A short introduction to the powerful GeoPackage, GeoJSON and GeoTIFF standards"
 author: "Floris Vanderhaeghe"
 date: 2020-02-03
-csl: ../inbo.csl
+csl: '/tmp/RtmpsgOF7D/research-institute-for-nature-and-forest.csl'
 bibliography: ../reproducible_research.bib
 categories: ["r", "gis"]
 tags: ["gis", "r", "open science"]
 output: 
     md_document:
         preserve_yaml: true
         variant: gfm
-    html_document: default
 ---
 
 Some inspiration for this post came from the beautiful books of Lovelace
@@ -113,7 +112,7 @@ So, in R we use packages that use GDAL in the background, such as
         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
+        declaration). This resulted in inconveniences (cf. [this
         post](https://github.com/r-spatial/sf/issues/344#issue-229118527)
         in the `sf`-repository).
       - A [specific
@@ -156,21 +155,20 @@ So, in R we use packages that use GDAL in the background, such as
 
 <div id="ref-heijmans_spatial_2019">
 
-Hijmans R. (2019). Spatial Data Science with R. URL:
-<https://rspatial.org/>.
+Hijmans R. (2019). Spatial Data Science with R. <https://rspatial.org/>.
 
 </div>
 
 <div id="ref-lovelace_geocomputation_2020">
 
 Lovelace R., Nowosad J. & Muenchow J. (2020). Geocomputation with R.
-URL: <https://geocompr.robinlovelace.net>.
+<https://geocompr.robinlovelace.net>.
 
 </div>
 
 <div id="ref-pebesma_edzer_spatial_2019">
 
-Pebesma E. & Bivand R. (2019). Spatial Data Science. URL:
+Pebesma E. & Bivand R. (2019). Spatial Data Science.
 <https://www.r-spatial.org/book>.
 
 </div>