NEWS.md

In R.SamBada: Processing Pipeline for 'SamBada' from Pre- To Post-Processing

R.SamBada 0.1.3

Bug fixes

• 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.

Updates in the test dataset

• Update of the file 'uganda-subset-mol-Out-2.csv'

R.SamBada documentation built on Jan. 5, 2022, 1:08 a.m.