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Maxent pipeline: some docs, bug fix, defaults and simplified create background function #110

Merged
merged 12 commits into from
Nov 14, 2023
Merged

Maxent pipeline: some docs, bug fix, defaults and simplified create background function #110

merged 12 commits into from
Nov 14, 2023

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frousseu
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@frousseu frousseu commented Oct 4, 2023

Described a bit more some arguments and functions, simplified the create background function and added the thickening and inclusion_buffer method which were not working/available, now accepts the - in soilgrids variable names, reduced the resolution for faster runs

François Rousseu and others added 11 commits September 8, 2023 15:28
be explicit about the possible methods and exact since there is some …
77ffa30 
…fuzzy matching for the method names
check argument value to make sure it goes to a specific place
6814b92
slightly better documentation for create_background
73c134f
as.data.frame does not check names which avoids the conversion of - i…
c49b39a 
…n . in col names coming from io and do not convert col names when reading data
some transition to terra (started because raster also converts - to .…
494e57e 
… in variable names)
changed some defaults for faster pipeline runs and more predictors
a829f19
default back to block
fc87e2b
replaced with a simplified version and added some options that were u…
d282d20 
…navailable/not working
added background thickening as an option
165ceef
update description with what was on remote
2a5953b 
Merge branch 'sdm' of github.com:GEO-BON/biab-2.0 into sdm

# Conflicts:
#	scripts/SDM/selectBackgroundFunc.R
@frousseu
added some metada to pipeline
d076032
jmlord
jmlord reviewed Oct 5, 2023
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Someone needs to review the R code

pipelines/SDM/SDM_maxEnt.json Show resolved Hide resolved
@tpoisot
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tpoisot commented Oct 12, 2023

Any thoughts about using maxnet instead of maxent.jar? The differences are covered in the paper (https://onlinelibrary.wiley.com/doi/10.1111/ecog.03049), and the results are about the same, with no need for an extra java (closed-source) dependency?

@frousseu
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From my limited experience, maxent.jar seems faster and less buggy than maxnet, but I agree maxnet is more open-source and has fewer dpendencies. I changed the algorithm to maxent.jar, because it scales variables behing the scene, while maxnet does not and I was running into numerical problems resulting from non-scaled variables. We could easily scale variables ourselves, but it can be a bit of a pain when exploring results and I wanted to avoid that. Another option could be to wait for maxnet to scale variables mrmaxent/maxnet#24 (or to submit a pull request to maxnet to allow for scaling in glmnet).

glaroc
glaroc approved these changes Nov 14, 2023
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scripts/SDM/selectBackgroundFunc.R
#' @param obs data.frame, containing the observations. Used with method == "thickening" or "inclusion_buffer"
#' @param width_buffer int, buffer width around observations. Used with method == "inclusion_buffer"
#' @param species string, species name.
#' @param predictors SpatRasterr, containing the predictor variables
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SpatRaster

@glaroc glaroc merged commit 30fc263 into main Nov 14, 2023
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@jmlord jmlord deleted the sdm branch November 14, 2023 21:37
biorey pushed a commit to PEM-Humboldt/biab-2.0 that referenced this pull request Jul 15, 2024
@glaroc
Merge pull request GEO-BON#110 from GEO-BON/sdm
70ba4bd 
Maxent pipeline: some docs, bug fix, defaults and simplified create background function
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@frousseu @tpoisot @glaroc @jmlord