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NEWS.Rmd
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---
title: "NEWS"
output: github_document
---
# TO DO
- 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
# SSDM 0.2.2.9002
- Occurrences.csv and TRAVIS gdal
- Vignettes 2, misspelling, and TRAVIS
# 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: https://github.com/klutometis/roxygen/issues/597.
# 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
- `rgdal`issue on travis due to `test_load_occ`
# SSDM 0.1.9030
- `rgdal`issue 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_modelling`example 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 `Env`and `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](https://github.com/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](https://github.com/floriandeboissieu)
# 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](https://github.com/floriandeboissieu)
- raster::readAll to force loading Env in memory (load_var) [Florian de Boissieu](https://github.com/floriandeboissieu)
- Raster[Raster[]<=-900]=NA instead of reclassify [Florian de Boissieu](https://github.com/floriandeboissieu)
- Resample with more condition to avoid extra computing [Florian de Boissieu](https://github.com/floriandeboissieu)
- Add timestampt to ensemble_modelling [Florian de Boissieu](https://github.com/floriandeboissieu)
# 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](https://github.com/dimitri-justeau)
- Species in ./Species in save_stack [Dimitri Justeau](https://github.com/dimitri-justeau)
- Stack results in ./Stack in save_stack [Dimitri Justeau](https://github.com/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](https://github.com/dimitri-justeau)
# SSDM 0.1.9010
- uncertainties stack bug catch in try
- load_var with only folder path debug [Dimitri Justeau](https://github.com/dimitri-justeau)
- load_var parameter: factors -> categorical [Dimitri Justeau](https://github.com/dimitri-justeau)
- Presence / absence occurrences modelling (Robin Pouteau)
# SSDM 0.1.9009
-Stacking Algo. Corr. row names duplicate (strsplit)
- Duplicated '.tif' in load_occ doc[Dimitri Justeau](https://github.com/dimitri-justeau)
- Null supported by Spcol (default) in .checkargs [Dimitri Justeau](https://github.com/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!