ibis.iSDM submission

[Martin-Jung]

Quick responses to submission flags in the yaml. For further explanation and details see the package website and in particular the vignettes.

flag	Response	Comment
occ_acquisition	no	Left to the user
occ_cleaning	yes	The package contains some helper functions for preparing biodiversity data including thinning (vignette).
data_integration	yes	Several approaches for integrating information are provided, including joint integration of different data types (vignette)
env_collinearity	yes	Range of options from collinear to Boruta application. See train
env_process	yes	The package contains some helper functions for preparing predictor data including the creation of derivates (vignette).
bias	yes	Options available via add_bias_control() or add_offset_bias()
study_region	yes	Key step for any model inference (vignette)
backg_sample	yes	Range of options available via pseudoabs_settings()
data_partitioning	no	Currently not implemented and has to be taken care by the user separately.
mod_fit	yes	Easily supported via train() (train).
mod_tuning	yes	Parameter option in train() and supported for most engines train.
mod_ensemble	yes	Call ensemble() on any number of fitted models
mod_stack	yes	Can easily be accomplished through summing outputs from a fitted model (mod$get_data()).
mod_evaluate	yes	Call validate() on any trained model with independent data.
mod_multispecies	no	Not yet supported, specific rank responses might be added in future versions for some engines.
mod_mechanistic	yes	Several wrappers for mechanistic species distribution models have been added.
pred_general	yes	Spatial and Spatial-temporal projections are fully supported through dedicated scenario() functions (vignette).
pred_extrapolation	yes	Functions for assessing similarity surfaces of covariates (similarity()) and limiting factors (limiting()) for future projections are supported.
limitingpred_inspect	yes	A range of different functions are supported to summarize model outputs and variable importance, including summary(), effects(), partial() and spartial() (reference)
post_processing	yes	Wide variety of options available to constrain projections (add_constraint()) smooth projections (see parameters in project()).
gui	no	Not planned
metadata	yes	A dedicated function that records model input and output parameters has been added (write_summary()).

[sylvainschmitt]

@Martin-Jung thanks for your submission. Your metadata check the one on CRAN. I will now seek reviewers for the other fields.

[sylvainschmitt]

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

[adamlilith]

Hey Sylvain, I’d be happy to do this. However, I recall I wasn’t sure how to use GitHub in the manner that you’d need for a review. Would you be able to meet with me online and show me how? I expect that there will be future reviews required once we get our paper published! Thanks, Adam From: Sylvain SCHMITT ***@***.***> Sent: Tuesday, October 3, 2023 2:56 AM To: sylvainschmitt/sdmverse ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [sylvainschmitt/sdmverse] ibis.iSDM submission (PR #35) I'm looking for two reviewers: @jamiemkass<https://github.com/jamiemkass>, @hannahlowens<https://github.com/hannahlowens>, @luismurao<https://github.com/luismurao>, @MayaGueguen<https://github.com/MayaGueguen>, @AMBarbosa<https://github.com/AMBarbosa>, @gepinillab<https://github.com/gepinillab>, @azizka<https://github.com/azizka>, @marlonecobos<https://github.com/marlonecobos>, @babaknaimi<https://github.com/babaknaimi>, @ecospat<https://github.com/ecospat>, @danlwarren<https://github.com/danlwarren>, @sgvignali<https://github.com/sgvignali>, @sjevelazco<https://github.com/sjevelazco>, @damariszurell<https://github.com/damariszurell>, @mlammens<https://github.com/mlammens>, @IanOndo<https://github.com/IanOndo>, @rvalavi<https://github.com/rvalavi>, @AndreaSanchezTapia<https://github.com/AndreaSanchezTapia>, @codelab3<https://github.com/codelab3> are you available? Please have a look at the reviewing guidelines<https://github.com/sylvainschmitt/sdmverse/blob/main/REVIEWING.md> — Reply to this email directly, view it on GitHub<#35 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABZZ3ZVGHX3BNBTDPXNTYNDX5PAHHAVCNFSM6AAAAAA5P7FTJSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBUGQYDGOJSHA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>>

[hannahlowens]

Looks great! Thanks for the careful work.

[sylvainschmitt]

Looks great! Thanks for the careful work.

Thanks for the review @hannahlowens

[sylvainschmitt]

Hey Sylvain, I’d be happy to do this. However, I recall I wasn’t sure how to use GitHub in the manner that you’d need for a review. Would you be able to meet with me online and show me how? I expect that there will be future reviews required once we get our paper published!

Hi @adamlilith , sorry I was not available last week but I am now. We can schedule a visio. However, I think I should note the information that helped you and start a collaborative wiki to help authors, reviewers, and editors.

[jamiemkass]

Hey folks, this PR was left hanging. Any updates?

[sylvainschmitt]

Hey folks, this PR was left hanging. Any updates?

Sorry @Martin-Jung , my bad I totally forgot. Maybe we should have several editors to avoid that. Based on @hannahlowens I will accept the submission.

[sylvainschmitt]

@Martin-Jung , thanks for the submission of ibis.iSDM. Your contribution can be integrated without further edits. After merging your pull request, you will be added to the repository contributors. Please expect to be contacted for a review request in the future.

[Martin-Jung]

Thanks a lot, happy to help :)