Changes in version 6.18.0 new features / enhancements / changes - new function plotMarkers to visualise the selected features in block analyses (see #134) - auroc title now fixed (#135) - cimDiablo takes trim argument to customise outlier filtering (#136) - plotIndiv.pca default shape set to 16 - circosPlot & network now support blocks with similar feature names - circosPlot now has methods for block.spls objects - circosPlot now takes new formal and advanced args for customisation. See ?circosPlot. bug fixes - plotVar legend colour mismatch bug fixed - plotDiablo error undefined variable (Y) fixed - nipals initialisation bug with high-variance high-NA rate column fixed - cim bug with high NA rate data fixed using imputation by the column mean Changes in version 6.16.0 new features / enhancements / changes - biplot default colours now match plotIndiv - biplot now takes cex argument - nipals now takes center and scale arguments - nipals now only outputs p, t and eig - new function impute.nipals to impute missing values using NIPALS algorithm - nipals function checks for orthogonality of components when NA present - plot.tune legends improved - plot.tune now uses colour-blind friendly colours - new tune.spls function to perform variable selection on both X and Y - tune.spls now chooses optimal keepX even if nrepeat < 3 - tune.spls now takes validation arg - tune.spca is now much faster - circosPlot links can now have adjustable width (#118) - plotDiablo now takes col.per.group (#119) - terminology change: consensus renamed to average in Diablo context bug fixes - plotVar bug fixed Changes in 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 Changes in 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 Changes in 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 Changes in version 6.8.0 - NOW HOSTED ON BIOCONDUCTOR - Refer to ./inst/legacy/NEWS-old on GitHub repo