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Upgrade to SimpleSDMLayers.jl v0.3.0 #18

Merged
merged 58 commits into from
Oct 22, 2020
Merged

Upgrade to SimpleSDMLayers.jl v0.3.0 #18

merged 58 commits into from
Oct 22, 2020

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gabrieldansereau
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@gabrieldansereau gabrieldansereau commented Jul 24, 2020 •
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Upgrading to SimpleSDMLayers.jl v0.3.0. Requires a lot of rewriting to move from NaN to nothing for missing values. Also a lot of functionalities were added to the package directly, so many overloads are not needed anymore.

  • Sliding window & mask?
  • Switch to EarthEnv land cover data instead of Copernicus?

Scripts checklist

  • 00b_preparation_ebd-preparation.jl
  • 00c_preparation_landcover.jl
    • Fix coordinates different between worldclim() and landcover()
  • 01_distributions.jl
    • Workaround undef error caused by groupIdentifier column
    • Fix the undef error!!
    • Fix parallelization of presence_absence()
    • Workaround map not iterating correctly on GroupedDataFrames
    • Fix calculate_Y() to allow nothing
    • Figure out why observed sites are different from before
    • Figure out why new ebd_warblers_prep is bigger than before
    • Update species glossary (or include() somewhere else in workflow)
  • 02_training_*.R :
    • Re-run with new WorldClim 2.1 data
    • Fix velox loading error
    • Update Random Forests scripts? Later 😉
    • Fix model loading workflow
  • 03_predictions_*.jl
    • Update for nothing instead of NaN
    • Re-run with new WorldClim 2.1 data
    • Investigate if single species models are similar to previous ones
  • 04_analysis.jl
    • Update calculate_richness() and calculate_lcbd() to allow type Nothing
    • Update figures & results with WorldClim 2.1 data
    • Figure out if colorbar scale in LCBD figures should be 0 to 1 or min to 1
    • Downscale figures to 200 dpi?
  • 05_subareas.jl
  • 06_moving-windows.jl
  • Update scripts in the others/ folder
  • Delete backup files with NaNs

gabrieldansereau and others added 30 commits July 22, 2020 17:28
@gabrieldansereau
📦 switch to dev version of SimpleSDMLayers
6bbcc14
@gabrieldansereau
⬆️ update packages
78c9199
@gabrieldansereau
🚧 hope that VS Code will work without module
d0b316d
@gabrieldansereau
🔥 remove worldclim 2.0 files from version control
f0a19e3
@gabrieldansereau
🙈 ignore worldclim files
3a1d61c
@gabrieldansereau
🚧 something is broken with DataFrames subsets
7456f4f
@gabrieldansereau
🚧 something is broken with presence_absence
72ac9d6
@gabrieldansereau
🚧 something is broken with worldclim
be69035
@gabrieldansereau
🚧 something is broken with filter
174e01a
@gabrieldansereau
🚧 something is broken with plot
aeda66e
@gabrieldansereau
🔧 update path to SimpleSDMLayers dev version
bc18f14
@gabrieldansereau
🐛 fix missing parenthesis
54037d7
@gabrieldansereau
⬆️ update packages
ce57deb
@gabrieldansereau
⬆️ re-update packages :face_with_rolling_eyes:
7fddb0a
@gabrieldansereau
😆 remove 'print(LOL XD)'
f9a74d1
@gabrieldansereau
⬆️ upgrade to julia 1.5 & upgrade packages
b58976d
@gabrieldansereau
➕ add compat entry for Julia version
9c6effa
@gabrieldansereau
⬆️ update packages
a1aad53
@gabrieldansereau
🚧 remove deprecated copycols argument in CSV.file
3c46572
@gabrieldansereau
🚧 use nothing instead of NaN in landcover function
c5733a9
@gabrieldansereau
✨ use integer for resolution in landcover function
7c6e315
@gabrieldansereau
🔧 workaround undef error with groupIdentifier column
d0e2ec5
@gabrieldansereau
🔧 workaround map not working with groupedDataFrames
4e942f4
@gabrieldansereau
✨ raw distribution data with nothing instead of NaN
3c9c06a
@gabrieldansereau
📦 temporarily use dev version of SimpleSDMLayers
84e9c70
@gabrieldansereau
🐛 fix default resolution in landcover()
aa6c9cd
@gabrieldansereau
✨ update environmental figures with WorldClim 2.1 & nothing values
260ea1f
@gabrieldansereau
✨ update env csv file with WorldClim 2.1 data
195ece3
@gabrieldansereau
✨ allow nothing values in Y matrix functions
1f9e073
@gabrieldansereau
🐛 remove type Nothing in Ytransf for RCall
ad58304
@gabrieldansereau
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gabrieldansereau commented Oct 21, 2020 •
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BART models & predictions updated with WorldClim 2.1 data! 🎉

Updating 02c_training_bart.R ✔️

@gabrieldansereau
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BART prediction layers updated with WorldClim 2.1 data & nothing values! 🎉

Updating 03c_predictions_bart.jl ✔️

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Analysis figures updated with WorldClim 2.1 data & nothing values! 🎉 🚀

Updating 04_analysis.jl ✔️

@gabrieldansereau gabrieldansereau changed the title Update to SimpleSDMLayers.jl v0.3.0 Upgrade to SimpleSDMLayers.jl v0.3.0 Oct 22, 2020
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Updating 05_subareas.jl ✔️

Updating 06_moving-windows.jl ✔️

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Updating important files in the others/ folder ✔️ (but not necessarily tested)

@gabrieldansereau gabrieldansereau mentioned this pull request Oct 22, 2020
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gabrieldansereau commented Oct 22, 2020 •
edited
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Upgrade completed! 🎉 ✨
Everything now works with SimpleSDMLayers v0.3.0! 🎉

I put the remaining checklist items in #19

@gabrieldansereau gabrieldansereau merged commit f0386fd into dev Oct 22, 2020
@gabrieldansereau gabrieldansereau deleted the feat/ssl-update branch October 22, 2020 17:17
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