gatoRs Submission

[mgaynor1]

Submission of gatoRs which streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).

[sylvainschmitt]

@mgaynor1 , thanks for the submission. Please can you further describe the reason to answer yes for the field you did linking to your package's functionalities? See for instance #35 .

[mgaynor1]

Please add these instructions to your contribution guide.

You can see out functions here: https://nataliepatten.github.io/gatoRs/reference/index.html

I would also suggest referring to Table 1 in our publication.

flag	Response	Comment
occ_acquisition	yes	See function gator_download().
occ_cleaning	yes	The package contains some helper functions for preparing biodiversity data including functions for identifying missing information, removing missing or redacted records, merging datasets, removing duplicate records, taxonomic harmonization, locality-based cleaning, basis cleaning, spatial thinning, and more. See functions under "Clean Data"
data_integration	no	Not included.
env_collinearity	no	Not included.
env_process	no	Not included.
bias	yes	Spatially thinning of occurrences included. See thin_points() and one_point_per_pixel()
study_region	no	Not included.
backg_sample	no	Not included.
data_partitioning	no	Not included.
mod_fit	no	Not included.
mod_tuning	no	Not included.
mod_ensemble	no	Not included.
mod_stack	no	Not included.
mod_evaluate	no	Not included.
mod_multispecies	no	Not included.
mod_mechanistic	no	Not included.
pred_general	no	Not included.
pred_extrapolation	no	Not included.
limitingpred_inspect	no	Not included.
post_processing	no	Not included.
gui	yes	See process_flagged()
metadata	no	Not included.

[sylvainschmitt]

Great. I'm looking for two reviewers: @jamiemkass, @hannahlowens, @luismurao, @MayaGueguen, @AMBarbosa, @gepinillab, @azizka, @marlonecobos, @babaknaimi, @ecospat, @danlwarren, @sgvignali, @sjevelazco, @damariszurell, @mlammens, @IanOndo, @rvalavi, @AndreaSanchezTapia, @codelab3 are you available? Please have a look at the reviewing guidelines

[hannahlowens]

Great to see this submission, @mgaynor1! I flagged two inconsistencies with your submission details, and based on an admittedly quick reading of your paper, suggest one "yes" that is currently a "no".

[hannahlowens]

I think this might actually be a yes, unless I misunderstand citation_bellow()--I'd call citations metadata.

[mgaynor1]

Correct! Thanks for catching this!

[hannahlowens]

Inconsistent with submission table. Please change to "no".

[mgaynor1]

Corrected!

[hannahlowens]

Inconsistent with submission table. Please change to "no".

[mgaynor1]

Corrected, thanks for catching this too!

[sylvainschmitt]

@hannahlowens thanks. @mgaynor1 please fix or answer comments for acceptance.

[mgaynor1]

@sylvainschmitt corrected based on @hannahlowens comments.

[jamiemkass]

Thanks for your submission. Everything looks fine in the latest version except "gui". This typically refers to a separate GUI with buttons, forms, etc. that can be used to implement some of the functionality of your package. It seems that process_flagged() runs a leaflet map, which I would not call a "GUI". It is certainly interactive though.

[mgaynor1]

updated!