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NEWS

SSDM 0.2.9

bug fixes: - totally removing rgdal following r-spatial evolution - moving from sp to sf and leaflet following r-spatial evolution

SSDM 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

SSDM 0.2.7.9001

• stringsAsFactors = TRUE in read.csv2 from load_occ.R folowwing the new defaulot in R 4.0.0

SSDM 0.2.6.9003

• gplots::heatmap.2 replaced by ggplot2 heatmap

SSDM 0.2.6.9002

• #74 fixed

SSDM 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

SSDM 0.2.6

• CRAN v0.2.6 submission

SSDM 0.2.5.9001

• #36 and #49 fixed

SSDM 0.2.5.9000

• #46 fixed
• Fixed division by zero bug (NA propagation) in project

SSDM 0.2.5

• CRAN v0.2.5 submission

SSDM 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

SSDM 0.2.3.9010

• solved compatibility issue with new raster version

SSDM 0.2.3.9009

• evaluation unactivation with eval=F in stacking function for Robin issue

SSDM 0.2.3.9008

• issue #32 fixed related to shinyFiles version 0.7.0

SSDM 0.2.3.9007

• fixed GBM and removed MAXENT for MEM issue #24 from @BoiMau

SSDM 0.2.3.9006

• fixed second issue #24 from @BoiMau

SSDM 0.2.3.9005

• fixed issue #24 from @BoiMau

SSDM 0.2.3.9004

• fixed issue #20 from @Rekyt

SSDM 0.2.3.9003

• fixed issue #22 from @Rekyt

SSDM 0.2.3.9002

• rmarkdown added to VignetteBuilder field in DESCRIPTION
• CTATION file added following article publication

SSDM 0.2.3.9001

• axes contribution evaluation when only one variable

SSDM 0.2.3

• CRAN submission following article submission in MEE

SSDM 0.2.2.9002

• Occurrences.csv and TRAVIS gdal
• Vignettes 2, misspelling, and TRAVIS
• Flo & Dim check

SSDM 0.2.2.9001

• SSDM and GUI vignettes

SSDM 0.2.9000

• AppVeyor integration

SSDM 0.1.9040

• mapDiversity S4 methods for SSDM with pSSDM, bSSDM, Bernoulli, MaximumLikelyhood, PRR.MEM, PRR.pSSDM

SSDM 0.1.9039

• stylistic rules correction with formatR and goodpractice

SSDM 0.1.9038

• Travis-CI 0.1.9037 fixed
• Pre formatR test

SSDM 0.1.9037

• community evaluations for SSDM (see Pottier et al) in evaluate.Stack.SDM
• SSDM evaluation in doc, plot and gui

SSDM 0.1.9036

• doc about new stacking methods (including literature)
• include new stacking method in GUI

SSDM 0.1.9036

• 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

SSDM 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

SSDM 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.

SSDM 0.1.9033

• Algortihm.SDM.R file splitted in multiple files (searching for doc issue)

SSDM 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

SSDM 0.1.9031

• rgdalissue on travis due to test_load_occ

SSDM 0.1.9030

• rgdalissue on travis due to load_var

SSDM 0.1.9029

• rgdal in DEPENDENCIES for testthat in Travis
• cran-comment.md
• NEWS link in README
• .Rbuildignore

SSDM 0.1.9028

• Travis test

SSDM 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

SSDM 0.1.9026

• checkargs
• stack_modelling cores
• NEWS & README

SSDM 0.1.9025

Dimitri Justeau: endemism parameter bug in the gui fixed

SSDM 0.1.9024

• Enable host and port option when launching the gui Dimitri Justeau
• README

SSDM 0.1.9023

• tmmpath in stack_modelling()
• split with ‘.Ensemble.SDM’ instead of ‘.’ in save, plot, and gui

SSDM 0.1.9022

• ESDM list in plot.model bug fixed

SSDM 0.1.9021

• CRAN second submit changes

SSDM 0.1.9020

• CRAN first submit changes

SSDM 0.1.9019

• Occurrences man url corrected
• Check -as–cran
• Check on CRAN win-build

SSDM 0.1.9018

• save tab in gui debug for ESDM (Jay)

SSDM 0.1.9017

• tmppath in ensemble_modelling dir creation (Jay)
• tmp doc in ensemble_ and stack_modelling Florian de Boissieu

SSDM 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

SSDM 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

SSDM 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

SSDM 0.1.9013

• Parallel computing: for loop correctly removed
• load_var tested

SSDM 0.1.9012

• Parallel computing for stack_modelling with parallel::mclapply

SSDM 0.1.9011

• load_var format and reso + extent bugged fixed Dimitri Justeau

SSDM 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)

SSDM 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

SSDM 0.1.9008

• Windows gui data input fix (default switch)

SSDM 0.1.9007

• load_occ porr data load improvement (occ not in spatial extent + less than 3 occ)

SSDM 0.1.9006

• ShinyApp structure in inst and shinyFiles working

SSDM 0.1.9005

• All inputs changed with shinyFiles package + Pcol text + Description (gui and pkg doc)

SSDM 0.1.9004

• Previous model input change (windows comptibilty)

SSDM 0.1.0

• Initial private beta release!

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They may not be fully stable and should be used with caution. We make no claims about them.