Add script for point selection and csv update to repo

[fjasteen]

Margot & Bieke are selecting points through Mymaps. This maps is exported as kml and attributes are updated through an R-script before saving as the localities.csv Damiano needs for the map visualizing distribution.

This is now a seperate Rproj in a different repo (craywatcht_selection) and should be added here for version control of the localities.csv.

@damianooldoni could you guide this noob on where to put this in the folder structure?

[peterdesmet]

@fjasteen Is this issue meant for the craywatch repo?

[fjasteen]

oops :-)

[peterdesmet]

No worries, I have moved it now.

[damianooldoni]

@peterdesmet , where do you suggest to put one or two R files and a Rproj file? The goal of this R code is to produce an output which is very important for the website, i.e. the localities.csv in ./assets. So, they should be placed in this repo. Thanks

[peterdesmet]

I would create a separate R or src directory

[peterdesmet]

Add it to the exclude files: https://github.com/inbo/craywatch/blob/7de47d4336c310b4af4ac55d851d9f1b60734bef/_config.yml#L31-L35

[damianooldoni]

Thanks, @peterdesmet. I prefect the R directory. @fjasteen: can you create a new branch with a correspondent Pull Request?

• Create the /R folder in craywatch repo root.
• Add code and Rstudio project in /R.
• Add map with extension .kml to /assets. In this way the code should be fully reproducible by everyone, me included. Probably you will need to slightly modify the path to read the kml file.
• Add the entire folder to the exclude: in _config.yaml as shown by @peterdesmet here above.

Assign me as reviewer, please. I will give a look too. Thanks.

[fjasteen]

Yes, thanks @damianooldoni . What about the './R/data/input/shapefiles/', I used it as a dump for all static shapefiles. Should I add the folder to the .gitignore file in the root? As in "# Negeer shapefiles en R-specifieke bestanden uit ./R/" /R/data/input/shapefiles/ /R/.Rproj.user /R/.Rhistory /R/.RData /R/.Ruserdata

[damianooldoni]

If such files are needed I would not put them in the .gitignore unless they contain sensitive data. By adding a line with - R to the exclude: section in the _config.yml file, you will tell to jekyll that all files and subdirectories in R have to be excluded while generating the website.

[fjasteen]

Yes but the folder is quite giant, because of all the shapefiles, is there need to store them in the repo?

[damianooldoni]

The folder is not really big, no worries. The size of the files is also not an issue for GitHub. The biggest one is 45 MB: everything below 50MB is fine. Having everything in this repository will help the future-you to reproduce everything in the future and to maintain everything up to date. You could then also consider to remove the same files from the GDrive.

[fjasteen]

oké perfect. What happens with the git files etc related to the current repo? Sorry for the stupid question, but I'm trying to find out how all stuff is related.

[damianooldoni]

Some standard files are indeed ignored by default in a .gitignore. A typical example is the .Rhistory. What you could do is then add all files contained in the gitignore in your repository to the .gitignore of this repository, prepending the folder R/ as your R project will not stay in the root folder, but in /R.

[peterdesmet]

In this case I would suggest to have a separate .gitignore in the R directory. Use the R template for gitignore, like here: https://github.com/inbo/camtrapdp/blob/main/.gitignore

[damianooldoni]

@fjasteen, @margotvermeylen: I think this has been solved last week. If you agree, please close this issue. Otherwise, let us know what has still to be done, thanks.