bug fixes:
- totally removing rgdal following r-spatial evolution
- moving from sp to sf and leaflet following r-spatial evolution
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
- stringsAsFactors = TRUE in read.csv2 from load_occ.R folowwing the new defaulot in R 4.0.0
- gplots::heatmap.2 replaced by ggplot2 heatmap
- #74 fixed
- 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
- CRAN v0.2.6 submission
- #36 and #49 fixed
- #46 fixed
- Fixed division by zero bug (NA propagation) in
project
- CRAN v0.2.5 submission
- Fixed dependency compatibility with raster 2.9-5
- Changed maintainter mail adress (permanent adress)
- Removed rgdal from vignette builder as asked by mail
- solved compatibility issue with new raster version
- evaluation unactivation with
eval=Fin stacking function for Robin issue
- issue #32 fixed related to
shinyFilesversion 0.7.0
- fixed GBM and removed MAXENT for MEM issue #24 from @BoiMau
- fixed second issue #24 from @BoiMau
- fixed issue #24 from @BoiMau
- fixed issue #20 from @Rekyt
- fixed issue #22 from @Rekyt
rmarkdownadded to VignetteBuilder field in DESCRIPTION- CTATION file added following article publication
- axes contribution evaluation when only one variable
- CRAN submission following article submission in MEE
- Occurrences.csv and TRAVIS gdal
- Vignettes 2, misspelling, and TRAVIS
- Flo & Dim check
- SSDM and GUI vignettes
- AppVeyor integration
mapDiversityS4 methods for SSDM with pSSDM, bSSDM, Bernoulli, MaximumLikelyhood, PRR.MEM, PRR.pSSDM
- stylistic rules correction with formatR and goodpractice
- Travis-CI 0.1.9037 fixed
- Pre formatR test
- community evaluations for SSDM (see Pottier et al) in
evaluate.Stack.SDM - SSDM evaluation in doc, plot and gui
- doc about new stacking methods (including literature)
- include new stacking method in GUI
- further testing of probability ranking stacking method with real data
project.Rwith MEM bug fixedstacking.Rwith MEM bug fixed- Travis-CI note removed with .Rbuildignore
- 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
spThinpackage responsible for the doc issue, not fixed but currently just commenting the pacakge to unactivate it in waiting. thread open onRoxygen2development repository.
- Algortihm.SDM.R file splitted in multiple files (searching for doc issue)
- 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
rgdalissue on travis due totest_load_occ
rgdalissue on travis due toload_var
rgdalin DEPENDENCIES for testthat in Travis- cran-comment.md
- NEWS link in README
- .Rbuildignore
- Travis test
- formal testing with
testthat(39%) quitbutton in guistack_modellingexample fix- warning messages corrected or removed
- T/F replace by
TRUEandFALSE goodpracticepackage checklength(x)replaced byseq_len(x)<-instead of=in examples- Package startup message
shinyFilesin DEPENDENCIES- Spelling checked in
plot(SSDM) - Raw
EnvandOccurrencesdata - Example data in
gui - Fixed working directory in
gui - Repository and bug report in DESCRIPTION
- Travis support
- checkargs
- stack_modelling cores
- NEWS & README
Dimitri Justeau: endemism parameter bug in the gui fixed
- Enable host and port option when launching the gui Dimitri Justeau
- README
- tmmpath in stack_modelling()
- split with '.Ensemble.SDM' instead of '.' in save, plot, and gui
- ESDM list in plot.model bug fixed
- CRAN second submit changes
- CRAN first submit changes
- Occurrences man url corrected
- Check -as--cran
- Check on CRAN win-build
- save tab in gui debug for ESDM (Jay)
- tmppath in ensemble_modelling dir creation (Jay)
- tmp doc in ensemble_ and stack_modelling Florian de Boissieu
- 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
- 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
- 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
- Parallel computing: for loop correctly removed
- load_var tested
- Parallel computing for stack_modelling with parallel::mclapply
- load_var format and reso + extent bugged fixed Dimitri Justeau
- 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)
-Stacking Algo. Corr. row names duplicate (strsplit) - Duplicated '.tif' in load_occ docDimitri Justeau - Null supported by Spcol (default) in .checkargs Dimitri Justeau
- Windows gui data input fix (default switch)
- load_occ porr data load improvement (occ not in spatial extent + less than 3 occ)
- ShinyApp structure in inst and shinyFiles working
- All inputs changed with shinyFiles package + Pcol text + Description (gui and pkg doc)
- Previous model input change (windows comptibilty)
- Initial private beta release!