NEWS

July 9, 2026 ยท View on GitHub

SSDM 0.2.12

bug fixes: #142 fixing deprecated xfun::attr with a more robust approach following @billy34

SSDM 0.2.11

bug fixes: #142 fixing deprecated xfun::attr

SSDM 0.2.10

bug fixes: noLD fails on test_modelling

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

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!