plot2D function to improve visualisation. Please see below.bg has been added to plot2D to allow the use
of filled point characters see issue #153plot2D also has a new argument called palette to facilitate
the generation of nice colour schemes to work with filled
point characterssetStockbg, getStockbg, setUnknownbg and
getUnknownbg have been added for colour managementaddLegend when called with
argument where = "other". The call to dev.new() has been
removed so that instead of opening a new device and plotting
the legend it instead plots the legend on an empty plot in the
current window.grid in plot2D has been changed to FALSE.pRolocmarkers() has a new version argument, to allow for new
markers versions to be added.pRolocmarkers() under
version = 2 (new default).pRolocmarkers() has been updated to include a
description of version = 2 markers.SerialParam() (fix by
ococrook, see #142).mclust::mclustBICmvtnorm::dmvnorm <2019-06-21 Fri>mrkHClust now uses mrkConsProfiles and returns the hclust
object - see issue #130 for details and background <2018-12-19 Wed>fcol argument to plotDist to plot and colour all profiles
<2018-08-09 Thu>plotEllipse function to visualise and assess TAGM models
<2018-05-18 Fri>dplyr::left_join without attaching dplyr to avoid collision
between Biobase::exprs and dplyr::exprs <2018-04-04 Wed>.nipals method in dimensionality reduction for plot2D (closes
issue #103) <2018-01-16 Tue>Added keepNA argument to goTermToId so that if a GO term becomes obsolete and you cannot replace it with the ID name, you have the option to either replace it with a NA (previous and current default option) or now with keepNA = FALSE the term name will be replaced with the id name <2016-05-25 Wed>
Bump version of all packages that use knitr for vignettes. This is because of an issue (now fixed) in knitr which failed to create purl()'ed R files from vignette sources and include them in the package. This version bump will cause these packages to propagate with those R files included. d.tenenbaum
svmOpt sigma defaults changed from 10^(-2:3) to 10^(-3:2) [2014-08-15 Fri]
in xxxOptimisation, the best parameter(s) for the validation classification runs are now chosen at random instead of using the first best param (see change in pRoloc:::getBestParam that got a sample argument defaulted to TRUE) [2014-08-15 Fri]
When calculating macroF1 scores (xval and validation), NAs are set to 0 (via MLInterfaces:::.macroF1(..., naAs0 = TRUE)). The macro F1 will not be NA (when mean of F1s is calculated) but lowered. This avoids having an NA macro F1 when 1 (or more) classe(s) end(s) up with NA (also set to 0) precision(s) or recall(s) [2014-08-15 Fri]