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