- possibility to add external richness data
- add evaluation for MEMs
- add ensemble method for MEMs
- implement trait range stacking method
- implement checkerboard stacking method
- add finer tests
- document all S4 class and methods
- Occurrences.csv and TRAVIS gdal
- Vignettes 2, misspelling, and TRAVIS
- SSDM and GUI vignettes
- AppVeyor integration
mapDiversity
S4 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.R
with MEM bug fixedstacking.R
with 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
spThin
package responsible for the doc issue, not fixed but currently just commenting the pacakge to unactivate it in waiting. thread open onRoxygen2
development repository: r-lib/roxygen2#597.
- 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
rgdal
issue on travis due totest_load_occ
rgdal
issue on travis due toload_var
rgdal
in DEPENDENCIES for testthat in Travis- cran-comment.md
- NEWS link in README
- .Rbuildignore
- Travis test
- formal testing with
testthat
(39%) quit
button in guistack_modelling
example fix- warning messages corrected or removed
- T/F replace by
TRUE
andFALSE
goodpractice
package checklength(x)
replaced byseq_len(x)
<-
instead of=
in examples- Package startup message
shinyFiles
in DEPENDENCIES- Spelling checked in
plot(SSDM)
- Raw
Env
andOccurrences
data - 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!