prepareOutput: Ensure compatibility with new version of as.vector
R.SamBada 0.1.2
Improvements
createEnv: possibility to enter the resolution of the worldclim dataset
plotResultInteractive: possibility to enter the ensembl host version
Bug fixes
prepareGeno: suppressed warnings "arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only"
cpp function for MGF filtering only compiled when mgfThresh is not null
use system2() instead of system() to invoke recode-plink, to avoid the program to get stucked unexpectedly
createEnv: checks that the csv file has x and y column inside + a third column
prepareEnv: suppress variables correlated above a threshold IN ABSOLUTE VALUE
checks if idName present in envFile
sambadaParallel: - bug fix when keepAllFiles=TRUE (files previously saved in temporary directory)
bug fix when wordDelim=,
bug fix when cores=1 to save storey file
removes SamBada error log that is created when SamBada's installation is tested
improved parameter checks
suppressed warnings "arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only"
use system2() instead of system() to invoke sambada, to avoid the program to get stucked unexpectedly
prepareOutput: bug fix when reading the file when popStr=FALSE
bug fix when opening storey file when wordDelim was different from space in sambadaParallel
plotResultInteractive: added axis-label to the boxplot
bug fix when gds created from a .bed (error snp.rs.id: no such GDS node!)
plotMap: - bug fix when rasterName was not null (open raster and draw legend)
bug fix when environmental variable was not a bioclimatic variable
bug fix when gds created from a .bed
crop raster to dataset to avoid memory issue
prepareGeno and sambadaParallel: - bug fix when directory given in relative path
Update in the documentation
better explanation on plots shown with interactiveChecks=TRUE or if file given in relative path in prepareOutput
better indication on which species can be handled and of the details of plots shown in plotResultInteractive
indication on how to install sambada in sambadaParallel and prepareGeno
indication of which variable is deleted when two variables are too highly correlated
R.SamBada 0.1.1
Bug fixes
downloadSambada: bug fix for MacOS
prepareGeno, sambadaParallel: error message when sambada is not installed
plotResultInteractive: bug fix when click on Manhattan plot
Update of the vignette and documentation
Simplification of the vignette. Some details have been moved from the vignette to the documentation. Reference to files used in the vignette is simplified.