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NEWS.md

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version 6.14.0

new features / enhancements / changes

  • circosPlot: The radial location of feature names can now be cutomised using var.adj
  • added plot and print methods for nipals ouput (#87)
  • all Discriminat Analyses now run solely on mode=regression (#79)
  • cim argument change: threshold replaced by cutoff
  • nipals and pca with missing values allow skipping reconstitution of the input matrix
  • tune.block.splsda now allows random number seed also for parallel processing (#72)
  • New biplot methods for the pca family (#90)

bug fixes

  • plotIndiv: Legend bug which misspecified the groups resolved
  • plotIndiv: Legends now ordered as inputted, and not alphabetically
  • plot method issue for spca resolved
  • plotLoadings.spca bug with var.names now fixed (#81)
  • ipca deprecation warning fixed

version 6.12.0

new features / enhancements

  • plotLoadings's infamous figure margins too large error now handled and informative condition thrown
  • circosPlot's lines argument default to FALSE now
  • circosPlot's inconsistentcy of blocks with identical X names fixed
  • consensus and weighted consensus plots now supported for plotIndiv with relevant block analyses
  • plotLoadings's feature name trimming can be customised
  • block.splsda bug which could drop some Y factors with near.zero.variance=TRUE fixed
  • perf.block.splsda now supports calculation of combined and per-block AUC
  • model improvement significance can be custmoised in all perf and tune functions
  • perf.block.splsda is now much faster and supports FORK clusters
  • tune.(s)pls(da), perf.(s)plsda now support FORK clusters

bug fixes

  • circosPlot's faded lines bug when many NAs present fixed
  • tune.block.splsda() bug when using fixed test.keepX over two or more blocks fixed
  • circosPlot and plotLoadings bug caused by features with NAs fixed
  • plotIndiv(..., ind.names = FALSE) warning/bug fixed
  • tune.block.splsda bug on Windows parallelisation fixed
  • perf and tune functions' issue when choosing the optimum component resolved
  • added option to suppress auroc from printing all the AUCs

version 6.10.0

new features / enhancements

  • parallel processing on tune.block.splsda improved
  • tune.block.splsda now supports more distances
  • You can now customise auroc plots. Refer to documentation for more info

bug fixes

  • single factor multilevel error in pls fixed
  • fixed over-estimated correlation of cim for mixo_(s)pls objects with single component
  • margin error in cim now handled properly
  • fixed plotLoadings error for very long variable names
  • predict function bug for single sample prediction fixed
  • plotLoadings bug for long variable names fixed
  • Fixed tune.spls and pef.plsda bugs when using cpus argument for parallel processing
  • perf.plot bug in extracting names fixed
  • Few fixes for tune.splsda with AUC

minor improvements

  • missing values in plotIndiv's group argument no more throws error
  • mixOmics::predict function documentation now more accessible
  • names of linnerud datasets fixed
  • plot.perf now respects ylim arguments for custom y range
  • package startup message with direct liks to useful resources
  • mixOmics function documentation disambiguated with instruction on how to get package help
  • Updated onLoad message with discussion forum info, bug reports, and more
  • Dropped legacy comp.tol argument from pca
  • plot.perf now respects ylim arguments for custom y range
  • Added Code of Conduct

version 6.8.0

  • NOW HOSTED ON BIOCONDUCTOR

version < 6.8.0

  • Refer to ./inst/legacy/NEWS-old on GitHub repo