Changes in version 0.2.9000 - AppVeyor integration Changes in version 0.2.10 (2025-04-14) bug fixes: noLD fails on test_modelling Changes in version 0.2.9 (2023-10-24) bug fixes: - totally removing rgdal following r-spatial evolution - moving from sp to sf and leaflet following r-spatial evolution Changes in version 0.2.8.9000 new/edited: - make all algorithm parameters settable (#66) - implement parallelization everywhere possible (e.g. ensemble/stack modelling, projection, uncertainty, etc.) - replace parLapply with foreach (less memory use, #13/#30/#58) - add options to reduce memory use (minimal.memory, tmp="filepath", SDM.projections, #51) - add geographic buffering as new PA-sampling strategy (geobuffer) - added sdm::calibration as evaluation statistic - switch evaluation from SDMTools to dismo (#74/#78) - add final.fit.data to control test/train of final model (#77) - add information which data was used for final model training (obj@data$train) - restructure project function (Russian doll) - add option to return projections directly as rasters (output.format='rasters') - extend vignette bug fixes: - fix unequal fold sampling in cross-validation - fix Maxent projection (#70) - fix Maxent background sampling error (when area had less than 10,000 cells) - fix lost connection error when using tmp - stop stack_modelling immediately, if less than 1 species - add GBM default n.cores=1 to avoid parallelization conflicts Changes in version 0.2.7.9001 - stringsAsFactors = TRUE in read.csv2 from load_occ.R folowwing the new defaulot in R 4.0.0 Changes in version 0.2.6.9003 - gplots::heatmap.2 replaced by ggplot2 heatmap Changes in version 0.2.6.9002 - #74 fixed Changes in version 0.2.6.9001 - insertion of slot @sdms & @esdms in Ensemble.SDM & Stacked.SDM classes - renaming all enm references to esdm - addition of project methods for ESDMs and SSDMs (including description, test unit, and user input check for environmental data) - fix MaximumLikelihood stacking method (#28) - fix and extend GUI Changes in version 0.2.6 (2019-06-14) - CRAN v0.2.6 submission Changes in version 0.2.5.9001 - #36 and #49 fixed Changes in version 0.2.5.9000 - #46 fixed - Fixed division by zero bug (NA propagation) in project Changes in version 0.2.5 (2019-05-30) - CRAN v0.2.5 submission Changes in version 0.2.3.9011 - Fixed dependency compatibility with raster 2.9-5 - Changed maintainter mail adress (permanent adress) - Removed rgdal from vignette builder as asked by mail Changes in version 0.2.3.9010 - solved compatibility issue with new raster version Changes in version 0.2.3.9009 - evaluation unactivation with eval=F in stacking function for Robin issue Changes in version 0.2.3.9008 - issue #32 fixed related to shinyFiles version 0.7.0 Changes in version 0.2.3.9007 - fixed GBM and removed MAXENT for MEM issue #24 from @BoiMau Changes in version 0.2.3.9006 - fixed second issue #24 from @BoiMau Changes in version 0.2.3.9005 - fixed issue #24 from @BoiMau Changes in version 0.2.3.9004 - fixed issue #20 from @Rekyt Changes in version 0.2.3.9003 - fixed issue #22 from @Rekyt Changes in version 0.2.3.9002 - rmarkdown added to VignetteBuilder field in DESCRIPTION - CTATION file added following article publication Changes in version 0.2.3.9001 - axes contribution evaluation when only one variable Changes in version 0.2.3 (2017-05-09) - CRAN submission following article submission in MEE Changes in version 0.2.2.9002 - Occurrences.csv and TRAVIS gdal - Vignettes 2, misspelling, and TRAVIS - Flo & Dim check Changes in version 0.2.2.9001 - SSDM and GUI vignettes Changes in version 0.1.9040 - mapDiversity S4 methods for SSDM with pSSDM, bSSDM, Bernoulli, MaximumLikelyhood, PRR.MEM, PRR.pSSDM Changes in version 0.1.9039 - stylistic rules correction with formatR and goodpractice Changes in version 0.1.9038 - Travis-CI 0.1.9037 fixed - Pre formatR test Changes in version 0.1.9037 - community evaluations for SSDM (see Pottier et al) in evaluate.Stack.SDM - SSDM evaluation in doc, plot and gui Changes in version 0.1.9036 - doc about new stacking methods (including literature) - include new stacking method in GUI - further testing of probability ranking stacking method with real data - project.R with MEM bug fixed - stacking.R with MEM bug fixed - Travis-CI note removed with .Rbuildignore Changes in version 0.1.9035 - Adjusted binaries with probability ranking method - Add binary raster slot in SDM, ESDM and SSDM methods - Add binary computation in modelling, ensemble, stacking - Add binary tmp save in ensemble and stack modelling - Save binary in save function - Load binary in load function - Create binary if not in file with load function (for backward compatibility) - Adapt plot methods to new binary slot Changes in version 0.1.9034 - spThin package responsible for the doc issue, not fixed but currently just commenting the pacakge to unactivate it in waiting. thread open on Roxygen2 development repository. Changes in version 0.1.9033 - Algortihm.SDM.R file splitted in multiple files (searching for doc issue) Changes in version 0.1.9032 - richness input in function stacking - MEM computing in function stacking - backbone to implement all new stacking functions (warning implemented everywhere to alert not implemented parts) - update in doc - update in check args Changes in version 0.1.9031 - rgdalissue on travis due to test_load_occ Changes in version 0.1.9030 - rgdalissue on travis due to load_var Changes in version 0.1.9029 - rgdal in DEPENDENCIES for testthat in Travis - cran-comment.md - NEWS link in README - .Rbuildignore Changes in version 0.1.9028 - Travis test Changes in version 0.1.9027 - formal testing with testthat (39%) - quit button in gui - stack_modellingexample fix - warning messages corrected or removed - T/F replace by TRUE and FALSE - goodpractice package check - length(x)replaced by seq_len(x) - <- instead of = in examples - Package startup message - shinyFiles in DEPENDENCIES - Spelling checked in plot(SSDM) - Raw Envand Occurrences data - Example data in gui - Fixed working directory in gui - Repository and bug report in DESCRIPTION - Travis support Changes in version 0.1.9026 - checkargs - stack_modelling cores - NEWS & README Changes in version 0.1.9025 Dimitri Justeau: endemism parameter bug in the gui fixed Changes in version 0.1.9024 - Enable host and port option when launching the gui Dimitri Justeau - README Changes in version 0.1.9023 - tmmpath in stack_modelling() - split with '.Ensemble.SDM' instead of '.' in save, plot, and gui Changes in version 0.1.9022 - ESDM list in plot.model bug fixed Changes in version 0.1.9021 - CRAN second submit changes Changes in version 0.1.9020 - CRAN first submit changes Changes in version 0.1.9019 - Occurrences man url corrected - Check -as--cran - Check on CRAN win-build Changes in version 0.1.9018 - save tab in gui debug for ESDM (Jay) Changes in version 0.1.9017 - tmppath in ensemble_modelling dir creation (Jay) - tmp doc in ensemble_ and stack_modelling Florian de Boissieu Changes in version 0.1.9016 - Weighted endemism index major change : range definition - load_occ major beug fixed, wrong rows were removed - tmppath change in ensemble and stack_modelling (overwrite of path var issue) Florian de Boissieu - raster::readAll to force loading Env in memory (load_var) Florian de Boissieu - Raster[Raster[]<=-900]=NA instead of reclassify Florian de Boissieu - Resample with more condition to avoid extra computing Florian de Boissieu - Add timestampt to ensemble_modelling Florian de Boissieu Changes in version 0.1.9015 - n.cores parameter in GBM auto-adapted to parallel computing in stack_modelling - gc() added at the end of each modelling function to avoid memory loss - ensemble.AlgoSDM() weight corrected - .cran-comment in .Rbuildignore - shinyFiles in Suggests and checked when gui() is used - Check with 0 Notes 0 Warnings 0 Errors Changes in version 0.1.9014 - Parallel computing with parallel::parLapply - .csv in save_model Dimitri Justeau - Species in ./Species in save_stack Dimitri Justeau - Stack results in ./Stack in save_stack Dimitri Justeau - Pearson cor = NA or NULL in evaluate.axis Changes in version 0.1.9013 - Parallel computing: for loop correctly removed - load_var tested Changes in version 0.1.9012 - Parallel computing for stack_modelling with parallel::mclapply Changes in version 0.1.9011 - load_var format and reso + extent bugged fixed Dimitri Justeau Changes in version 0.1.9010 - uncertainties stack bug catch in try - load_var with only folder path debug Dimitri Justeau - load_var parameter: factors -> categorical Dimitri Justeau - Presence / absence occurrences modelling (Robin Pouteau) Changes in version 0.1.9009 -Stacking Algo. Corr. row names duplicate (strsplit) - Duplicated '.tif' in load_occ docDimitri Justeau - Null supported by Spcol (default) in .checkargs Dimitri Justeau Changes in version 0.1.9008 - Windows gui data input fix (default switch) Changes in version 0.1.9007 - load_occ porr data load improvement (occ not in spatial extent + less than 3 occ) Changes in version 0.1.9006 - ShinyApp structure in inst and shinyFiles working Changes in version 0.1.9005 - All inputs changed with shinyFiles package + Pcol text + Description (gui and pkg doc) Changes in version 0.1.9004 - Previous model input change (windows comptibilty) Changes in version 0.1.0 (2016-02-12) - Initial private beta release!