Finish functions - Githubissues

b-cubed-eu / pdindicatoR

Repository for the phylogenetic indicator calculation workflow as part of the Bcubed project.

MIT License

0 stars 1 forks source link

Finish functions #24

Closed LBreugelmans closed 5 days ago

LBreugelmans commented 1 week ago

Extended functionality for using timegroups and plotting multiple plots (rshiny)
Renamed functions to comply with good practices
All functions now have documentation
All functions are confirmed to be working (as confirmed by readme example)
Updated readme

wlangera commented 1 week ago

If the dataset is not too large, it might be nice to have it in the package as an example dataset. In that case you only have to remove it from the .gitignore file.

LBreugelmans commented 1 week ago

Hi Ward, I can provide the datasets used in the readme as example datasets and put them in the .buildignore file. Do they need t go in the inst folder then?

I will take care of the imports now.

wlangera commented 1 week ago

You can put the datasets in the data folder.

If you want them as an example dataset in the package, you can just remove them from the .gitignore file.
If you do not want them as an example dataset in the package, you remove them from the .gitignore file and also add it to .Rbuildignore

With example dataset I mean that users can also access the dataset and use it to test out the functions for example.

I am just thinking it might be nice to have them in the package, because the user might not be familiar with the datatypes. But this might not be good if they are too large. What do you think is preferable in your case?

https://r-pkgs.org/data.html

LBreugelmans commented 1 week ago

testdata folder added
R CMD check errors partly resolved

Only remaining errors are of form 'no visible binding for global variable 'pa''.

LBreugelmans commented 6 days ago

Hi @wlangera ,

I have ran R CMD checks and solved most notes and errors, but there remains one error which is related to the rendering of the examples. I am unable to locate the issue, as the error doesn't give clear indication of where the problem is generated (the printed code lines do not correspond to the quoted function name). Could you please have a look to see if you can resolve it?

wlangera commented 5 days ago

Hi @LBreugelmans

Please check out the branch fix-technical-issues. I got an error in generate_map_and_indicator.R. Currently, I resolved it by putting rnaturalearthdata in DESCRIPTION. This still results in a note, but at least it is not an error anymore.

There is a mistake in your function get_pd(). You have a variable mcube. This should be species I think?
I still cannot run the readme because I do not have the shapefiles, can you send them to me via mail?

Can you check this and run the checks again in the branch fix-technical-issues?

wlangera commented 5 days ago

Hi @LBreugelmans

I have merged your code with my branch. You can find the new PR here: #27.

We can work further together in this branch.