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Releases: PoisotLab/SpeciesDistributionToolkit.jl

v1.0.0

27 Oct 21:31
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v1.0.0
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SpeciesDistributionToolkit v1.0.0

Diff since v0.1.3

Merged pull requests:

Closed issues:

  • DuckDB (#205)
  • Move test to @testitem (#211)
  • SDeMo chokes on some decision trees when a single node is involved (#287)
  • Add maxdepth to decision trees (#288)
  • add a dispatch to the ConfusionMatrix functions (#290)
  • cannot cross-validate when using the consensus argument (#293)
  • data providers are flaky (#295)
  • Update gameplan (#296)
  • Update the PR comment issue (#298)
  • Tag GBIF v1.0.0 (#301)
  • Tag Fauxcurrences v1.0.0 (#302)
  • Tag SpeciesDistributionToolkit v1.0.0 (#303)

Contributors

tpoisot
Assets 2
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SDeMo-v1.0.0

26 Oct 18:57
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SDeMo-v1.0.0
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SDeMo-v1.0.0

SDeMo SDeMo-v1.0.0

Diff since SDeMo-v0.0.7

Merged pull requests:

Closed issues:

  • data providers are flaky (#295)
  • Tag GBIF v1.0.0 (#301)
  • Tag Fauxcurrences v1.0.0 (#302)

Contributors

tpoisot
Assets 2
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GBIF-v1.0.0

25 Oct 16:06
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GBIF-v1.0.0
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GBIF-v1.0.0

GBIF GBIF-v1.0.0

Diff since GBIF-v0.4.5

Merged pull requests:

Closed issues:

  • ecoClimate - Climatic layers from PMIP3 CMIP5 (#33)
  • Logo (#27)
  • Generate release notes that list what changes in all the packages (#189)
  • DuckDB (#205)
  • Move test to @testitem (#211)
  • Move vignettes out of the documentation? (#213)
  • LUH² (#217)
  • PaleoClim (#228)
  • Masking/segmentating layer based on vector (#231)
  • Move documentation to VitePress (#245)
  • Restore the Fauxcurrences tutorial (#252)
  • Update the tutorial for future climate data (#254)
  • Additional method to interpolate when we already have the destination layer (#258)
  • Add fields to the SimpleSDMDatasets interface (#259)
  • interpolate layer to same CRS/size as target layer (#267)
  • zeros/ones for layers is buggy - is it maintaining everything??? (#269)
  • The bounding box should be converted from WGS84 to the layer CRS (#270)
  • The fscore formula is wrong (#278)
  • Dispatch for Ensemble prediction is ambiguous (#279)
  • Define abstract types for Bagging and Ensemble (#280)
  • Add pop!, push!, etc to Ensemble (#281)
  • New versions (note to self) (#285)
  • SDeMo chokes on some decision trees when a single node is involved (#287)
  • Add maxdepth to decision trees (#288)
  • add a dispatch to the ConfusionMatrix functions (#290)
  • cannot cross-validate when using the consensus argument (#293)
  • data providers are flaky (#295)
  • Update the PR comment issue (#298)
  • Tag GBIF v1.0.0 (#301)
  • Tag Fauxcurrences v1.0.0 (#302)

Contributors

tpoisot and gottacatchenall
Assets 2
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Fauxcurrences-v1.0.0

24 Oct 00:41
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Fauxcurrences-v1.0.0
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Fauxcurrences-v1.0.0

Fauxcurrences Fauxcurrences-v1.0.0

Diff since Fauxcurrences-v0.2.0

Merged pull requests:

Closed issues:

  • DuckDB (#205)
  • Move test to @testitem (#211)
  • LUH² (#217)
  • Masking/segmentating layer based on vector (#231)
  • Move documentation to VitePress (#245)
  • Restore the Fauxcurrences tutorial (#252)
  • Update the tutorial for future climate data (#254)
  • Additional method to interpolate when we already have the destination layer (#258)
  • Add fields to the SimpleSDMDatasets interface (#259)
  • interpolate layer to same CRS/size as target layer (#267)
  • zeros/ones for layers is buggy - is it maintaining everything??? (#269)
  • The bounding box should be converted from WGS84 to the layer CRS (#270)
  • The fscore formula is wrong (#278)
  • Dispatch for Ensemble prediction is ambiguous (#279)
  • Define abstract types for Bagging and Ensemble (#280)
  • Add pop!, push!, etc to Ensemble (#281)
  • New versions (note to self) (#285)
  • SDeMo chokes on some decision trees when a single node is involved (#287)
  • Add maxdepth to decision trees (#288)
  • add a dispatch to the ConfusionMatrix functions (#290)
  • cannot cross-validate when using the consensus argument (#293)
  • data providers are flaky (#295)
  • Update the PR comment issue (#298)
  • Tag Fauxcurrences v1.0.0 (#302)

Contributors

tpoisot and gottacatchenall
Assets 2
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OccurrencesInterface-v1.0.0

17 Oct 21:58
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OccurrencesInterface-v1.0.0
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OccurrencesInterface-v1.0.0

OccurrencesInterface OccurrencesInterface-v1.0.0

Merged pull requests:

  • CompatHelper: add new compat entry for Reexport at version 1, (keep existing compat) (#3) (@github-actions[bot])
  • Fix the issue with NODATA using the wrong encoding (#15) (@tpoisot)
  • Replace collect by values (#18) (@tpoisot)
  • Fix SimpleSDMLayers tests (#19) (@tpoisot)
  • CompatHelper: add new compat entry for ArchGDAL at version 0.9, (keep existing compat) (#22) (@github-actions[bot])
  • Convert to WGS84 using GDAL_WARP if needed (#34) (@tpoisot)
  • CompatHelper: add new compat entry for GDAL at version 1, (keep existing compat) (#41) (@github-actions[bot])
  • Allow additional drivers to the geotiff writer (#47) (@tpoisot)
  • [GBIF] add option to look for vector of taxa (#57) (@tpoisot)
  • Update the vignette on stats (#58) (@tpoisot)
  • Move the pseudo-absences to the top package and add additional methods (#59) (@tpoisot)
  • CompatHelper: add new compat entry for Distances at version 0.10, (keep existing compat) (#67) (@github-actions[bot])
  • CompatHelper: add new compat entry for StatsBase at version 0.33, (keep existing compat) (#69) (@github-actions[bot])
  • Add additional metadata to the providers (#72) (@tpoisot)
  • Add a Tables.jl interface for layers (#82) (@tpoisot)
  • CompatHelper: add new compat entry for Tables at version 1, (keep existing compat) (#85) (@github-actions[bot])
  • Aggregate code coverage analysis (#87) (@tpoisot)
  • Work on the dataset cards (#88) (@tpoisot)
  • Add some tests to SimpleSDMLayers (#89) (@tpoisot)
  • Merge git tags (#92) (@tpoisot)
  • [GBIF] Tables.jl (#96) (@tpoisot)
  • [SimpleSDMLayers] cell size (#98) (@tpoisot)
  • 📝 README (#100) (@tpoisot)
  • CompatHelper: add new compat entry for GBIF at version 0.4, (keep existing compat) (#102) (@github-actions[bot])
  • Make all layers broadcastable (#103) (@tpoisot)
  • 🗺️ Update plotting code to work with Makie as a default (#105) (@tpoisot)
  • CompatHelper: add new compat entry for SimpleSDMDatasets at version 0.1, (keep existing compat) (#108) (@github-actions[bot])
  • CompatHelper: bump compat for HTTP to 1 for package GBIF, (keep existing compat) (#109) (@github-actions[bot])
  • CompatHelper: add new compat entry for GBIF at version 0.4 for package Fauxcurrences, (keep existing compat) (#112) (@github-actions[bot])
  • CompatHelper: bump compat for ArchGDAL to 0.10, (keep existing compat) (#114) (@github-actions[bot])
  • CompatHelper: add new compat entry for MakieCore at version 0.6, (keep existing compat) (#132) (@github-actions[bot])
  • CompatHelper: add new compat entry for SimpleSDMLayers at version 0.9, (keep existing compat) (#133) (@github-actions[bot])
  • CompatHelper: add new compat entry for SimpleSDMLayers at version 0.9 for package Fauxcurrences, (keep existing compat) (#135) (@github-actions[bot])
  • Bring Fauxcurrences back in the main package (#137) (@tpoisot)
  • CompatHelper: add new compat entry for Fauxcurrences at version 0.1, (keep existing compat) (#141) (@github-actions[bot])
  • Fix clipping with exact coordinates (#144) (@gabrieldansereau)
  • 🐛 correct check on layer inner type (#146) (@tpoisot)
  • ✨ Split a layer into tiles (#148) (@tpoisot)
  • Test for clipping with natural coordinates (#152) (@gabrieldansereau)
  • 🩹 SimpleSDMLayers handling of clip with coordinates on cell boundaries (#153) (@tpoisot)
  • 🐛 Update the stitching code to get the right bounding box (#155) (@tpoisot)
  • GBIF throws 404 (not 410) for deleted resources (#156) (@tpoisot)
  • ✅ add edge case test for clip in SpeciesDistributionToolkit (#159) (@gabrieldansereau)
  • compression/format kwargs for geotiffs (#161) (@gottacatchenall)
  • fix typos (#162) (@spaette)
  • Update the documentation (#163) (@tpoisot)
  • Fix the GBIF issue for single argument queries (#166) (@tpoisot)
  • Fix the naming issue when imported from a submodule (#167) (@tpoisot)
  • Phylopic wrapper (#169) (@tpoisot)
  • Read the GBIF enums from the API endpoints (#170) (@tpoisot)
  • compat(phylopic): add compat entries (#176) (@tpoisot)
  • Update the contributing guidelines (#177) (@tpoisot)
  • Add GBIF/Phylopic integration (#179) (@tpoisot)
  • Build website for tagged version (#180) (@tpoisot)
  • CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#183) (@github-actions[bot])
  • CompatHelper: bump compat for StatsBase to 0.34 for package Fauxcurrences, (keep existing compat) (#184) (@github-actions[bot])
  • CompatHelper: bump compat for StatsBase to 0.34 for package SimpleSDMLayers, (keep existing compat) (#185) (@github-actions[bot])
  • Add methods to invert a layer (#188) (@tpoisot)
  • Fixes the geotiff open (#191) (@tpoisot)
  • bug(datasets): keychecker fails to check some wrong arguments (#193) (@tpoisot)
  • Improving WithinRadius performance (#196) (@gottacatchenall)
  • Adding Offset Arrays back as a dependency (#197) (@gottacatchenall)
  • Build issue on phylopic (#199) (@tpoisot)
  • fix(GBIF): some records are missing a synonym field (#200) (@tpoisot)
  • CompatHelper: add new compat entry for OffsetArrays at version 1, (keep existing compat) (#201) (@github-actions[bot])
  • Change sample and add DistanceToEvent (#207) (@tpoisot)
  • semver(layers): fix (#209) (@tpoisot)
  • Bug/layers/method overwrite (#215) (@tpoisot)
  • CompatHelper: add new compat entry for Statistics at version 1 for package Fauxcurrences, (keep existing compat) (#218) (@github-actions[bot])
  • CompatHelper: add new compat entry for Downloads at version 1 for package SimpleSDMDatasets, (keep existing compat) (#219) (@github-actions[bot])
  • CompatHelper: add new compat entry for Statistics at version 1 for package SimpleSDMLayers, (keep existing compat) (#220) (@github-actions[bot])
  • CompatHelper: bump compat for MakieCore to 0.7, (keep existing compat) (#221) (@github-actions[bot])
  • Phylopic pre-compilation fix (#224) (@tpoisot)
  • SurfaceLike -> GridBased (#225) (@tpoisot)
  • Bug/sdt/surfacelike (#226) (@tpoisot)
  • Use CRS for SimpleSDMLayers (#227) (@tpoisot)
  • CompatHelper: bump compat for MakieCore to 0.8, (keep existing compat) (#229) (@github-actions[bot])
  • Fauxcurrences v0.2.0 (#232) (@tpoisot)
  • SimpleSDMDatasets v0.2.0 (#233) (@tpoisot)
  • SimpleSDMLayers v1.0.0 (#234) (@tpoisot)
  • Update TagBot.yml (#246) (@tpoisot)
  • Update README.md (#247) (@tpoisot)
  • CompatHelper: add new compat entry for TestItems at version 1, (keep existing compat) (#248) (@github-actions[bot])
  • Github actions for documentation (#249) (@tpoisot)
  • semver(datasets): v0.2.1 (#250) (@tpoisot)
  • VitePress for the top level doc site (#251) (@tpoisot)
  • Cleanup tutorial + howto (#253) (@tpoisot)
  • Future climate tutorial update (#255) (@tpoisot)
  • Restore fauxcurrence page (#256) (@tpoisot)
  • Simplify the navbar (#257) (@tpoisot)
  • Add interpolate! (#260) (@tpoisot)
  • Add a tutorial on building the BIOCLIM model (#261) (@tpoisot)
  • Bug fix: source argument missing from interpolate (#262) (@tpoisot)
  • Add support to mask/reveal/hide by polygons (#263) (@tpoisot)
  • CompatHelper: add new compat entry for Downloads at version 1, (keep existing compat) (#264) (@github-actions[bot])
  • Additional fields to the dataset interface (#265) (@tpoisot)
  • Mosaic with polygons (#266) (@tpoisot)
  • New interpolate method (#268) (@tpoisot)
  • Bounding box when reading is now in WGS84 (#271) (@tpoisot)
  • SDeMo (#272) (@tpoisot)
  • Prepare main package for SDeMo interop (#273) (@tpoisot)
  • chore: prep for tag (#274) (@tpoisot)
  • Update CompatHelper.yml (#275) (@tpoisot)
  • Create README.md (#276) (@tpoisot)
  • removing unnecessary(?) return in _write_geotiff (#277) (@gottacatchenall)
  • SDeMo update (#282) (@tpoisot)
  • CHELSA url changed? (#283) (@tpoisot)
  • SDeMo improvements: inflated response curves, better ensemble support, decision trees (#284) (@tpoisot)
  • semver(sdt): v0.1.3 (#286) (@tpoisot)
  • SDeMo QoL improvements (#289) (@tpoisot)
  • feat(demo): ensemble counterfactuals (#292) (@tpoisot)
  • OccurrencesInterface package (#294) (@tpoisot)
  • Links to all doc websites on PR (#299) (@tpoisot)
  • chore(occ): LICENSE (#304) (@tpoisot)

Closed issues:

  • Reading certain tiffs with geotiff is wrong if the CRS is not WGS84 (#32)
  • Allow options to ArchGDAL driver when saving Geotiff (#30)
  • ecoClimate - Climatic layers from PMIP3 CMIP5 (#33)
  • Add layer description to get human-readable description of layer names (#7)
  • Add a function to get the URL or reference for a data provider (#8)
  • Add a way to remove observations that are documented absences (#9)
  • CHELSA2 NODATA is incompatible with data type (#10)
  • Move pseudo-absence code to the top-level package (#11)
  • Unify distance generation in Fauxcurrences and pseudo-absence code (#12)
  • Update the GBIF docstrings (#13)
  • Update the model cards (#14)
  • Method to get the values in a layer should be values and not collect (#16)
  • Fix SimpleSDMLayers tests (#17)
  • Logo (#27)
  • Migrate issues about possible datasets to this repo (#28)
  • Clean the code handling the CRS transformation in geotiff (#35)
  • The order of arguments to read/save geotiffs make no sense (#38)
  • Vignette on scaling and quantiles (#48)
  • Add a method to get occurences for several taxa (#50)
  • The vignettes section is getting very large (#60)
  • The WorldClim tests are going to fail a lot (#61)
  • Find a way to aggregate the code coverage (#62)
  • Surface area of cells (#93)
  • Replace data frames function by a Tables.jl interface (#94)
  • Prepare repo for release of new versions (#95)
  • Add Boolean operations on Boolean layers (#99)
  • Link to documentation in the original repositories (#101)
  • Update plotting code to work with Makie as a default (#104)
  • TagBot trigger issue (#140)
  • Check the weight matrices in Fauxcurrences (#142)
  • Wrong coordinates returned when clipping with exact coordinates (#143)
  • IO not exported? (#145)
  • Split a layer into tiles (#147)
  • Add a test for clipping with exact coordinates (#149)
  • Avoid using stride when clipping (#150)
  • Add expand options to clip (#151)
  • Stitch returns the wrong bounding box in the end (#154)
  • Integrate w...
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Contributors

tpoisot, gottacatchenall, and 2 other contributors
Assets 2
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SDeMo-v0.0.7

16 Oct 03:12
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SDeMo-v0.0.7
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SDeMo SDeMo-v0.0.7

Diff since SDeMo-v0.0.6

Merged pull requests:

Contributors

tpoisot
Assets 2
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SDeMo-v0.0.6

15 Oct 14:15
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SDeMo-v0.0.6
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SDeMo-v0.0.6

SDeMo SDeMo-v0.0.6

Diff since SDeMo-v0.0.5

Merged pull requests:

Closed issues:

  • Move test to @testitem (#211)
  • add a dispatch to the ConfusionMatrix functions (#290)
  • cannot cross-validate when using the consensus argument (#293)
  • Update the PR comment issue (#298)

Contributors

tpoisot
Assets 2
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SDeMo-v0.0.5

02 Oct 16:27
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SDeMo-v0.0.5
b49f40e
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SDeMo-v0.0.5

SDeMo SDeMo-v0.0.5

Diff since SDeMo-v0.0.4

Merged pull requests:

Contributors

tpoisot
Assets 2
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SDeMo-v0.0.4

01 Oct 17:14
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SDeMo-v0.0.4
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SDeMo-v0.0.4

SDeMo SDeMo-v0.0.4

Diff since SDeMo-v0.0.3

Merged pull requests:

Closed issues:

  • New versions (note to self) (#285)
  • SDeMo chokes on some decision trees when a single node is involved (#287)
  • Add maxdepth to decision trees (#288)

Contributors

tpoisot
Assets 2
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v0.1.3

28 Sep 20:30
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v0.1.3
b6bf5ee
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v0.1.3

SpeciesDistributionToolkit v0.1.3

Diff since v0.1.2

Merged pull requests:

  • SDeMo improvements: inflated response curves, better ensemble support, decision trees (#284) (@tpoisot)
  • semver(sdt): v0.1.3 (#286) (@tpoisot)

Closed issues:

  • New versions (note to self) (#285)

Contributors

tpoisot
Assets 2
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