Reviewing functions

[LuciaSegovia]

Functions were created to calculate some of the variables and to format the Fisheries Global NCT. Check:

• [x] All needed fuctions are included in the repository (no dependencies #1)
• [x] All functions are working and annotated
• [x] Documentation is provided for all functions (see #2)

[dzvoti]

Hi @LuciaSegovia, for reproducibility do you do :

library(dplyr)

or do you do :

dplyr::mutate( )

Also, what do you think of using a dependency management package like renv?

[dzvoti]

Also @LuciaSegovia , which repo am i annotating? This issue is in this FAO_Fisheries repo which I have not yet worked in.

[LuciaSegovia]

Hi @dzvoti, sorry I did not explain it well. This is meant to be a clean (for sharing) version of the fishereis script that is hosted in the UoN-FAO repo. So, ideally, if a person has access to the raw data by running the scripts in here should be able to reproduce the Fisheries Global NCT and the report. So the scripts to be annotated (and if possible documented in the markdown) would be the fuctions that you created in/ for the UoN-FAO. I hope that's ok :)

[LuciaSegovia]

Hi @LuciaSegovia, for reproducibility do you do :

library(dplyr)

or do you do :

dplyr::mutate( )

Also, what do you think of using a dependency management package like renv?

I was thinking of things like: file paths, data and packages dependecies. I haven't used renv before, but maybe that's a better option. I let you advise :)

[dzvoti]

Hi @dzvoti, sorry I did not explain it well. This is meant to be a clean (for sharing) version of the fishereis script that is hosted in the UoN-FAO repo. So, ideally, if a person has access to the raw data by running the scripts in here should be able to reproduce the Fisheries Global NCT and the report. So the scripts to be annotated (and if possible documented in the markdown) would be the fuctions that you created in/ for the UoN-FAO. I hope that's ok :)

Thank you, it is clearer now.

[dzvoti]

Hi @LuciaSegovia, for reproducibility do you do :

library(dplyr)

or do you do :

dplyr::mutate( )

Also, what do you think of using a dependency management package like renv?

I was thinking of things like: file paths, data and packages dependecies. I haven't used renv before, but maybe that's a better option. I let you advise :)

Yes, thank you. I will try renv on this repo and advise, but this should take care of dependencies. For data, I normally include a folder called data/ in the root folder but hide all other contents except a data/copy_data_to_this_folder.txt file.

I will try both and you review.

[LuciaSegovia]

Thanks @dzvoti !

For data, I normally include a folder called data/ in the root folder but hide all other contents except a data/copy_data_to_this_folder.txt file.

That's fine, I normally do the same thing, but the text document. what's in the data/copy_data_to_this_folder.txt file?

Thanks!

[dzvoti]

@LuciaSegovia , Mine usually contains nothing. It doubles up as an instruction and a placeholder because git doesn't track empty folders.

[dzvoti]

@LuciaSegovia , I have annotated the functions in summary_table_functions.R. It seems @TomCodd 's function were already well annotated.