NEWS

mixOmics 6.18.0

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.

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)

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

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

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

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