Temporarily added jasenfinch/missForest as a remote until stekhoven/missForest pull request #25 is resolved.

The limit of the number of plotted features in plotExplanatoryHeatmap() can now be specified using the featureLimit argument.

plotExplanatoryHeatmap() now returns NULL and displays a message when no explanatory features are found.

Fixed the alignment of the dendrogram branches with heat map rows in plotExplanatoryHeatmap().

Fixed ggplot2::guides() warning in plotFeature() and plotTIC().

Fixed bug in explanatoryFeatures() methods for Analysis class and lists where the threshold was not able to be customised.

Fixed the error in plotRSD() method for the Analysis class.

Corrected the text in the modelling vignette concerning the results of using unsupervised random forest for outlier detection.

Package version, creation date and verbose argument added to prototype of Analysis class.

All generics are now defined as standard generics.

Added metrics method for Analysis class.

metrics method for lists now ignores list elements that are not of class RandomForest.

Added a NEWS.md file to track changes to the package.

pkgdown site now available at https://jasenfinch.github.io/metabolyseR/.

Bug reports and issues URL at https://github.com/jasenfinch/metabolyseR/issues added to package DESCRIPTION.

Dedicated vignettes now available for a quick start example analysis, data pre-treatment and data modelling.

Function examples added to all documentation pages.

Unit test coverage increased to > 95%.

Parallel processing is now implemented using the future package.

plan() from the future package is re-exported.

RandomForest and Univariate classes now inherit from class the AnalysisData class.

Improvements to plot theme aesthetics.

type argument added to plotPCA(), plotLDA(), plotUnsupervisedRF() and plotSupervisedRF() methods for the Analysis class.

"pre-treated" for specifying type argument in Analysis class methods now used over "preTreated"

Added clsRename() method for renaming class information columns.

plotMeasures() method renamed to plotMetrics().

Added plotMDS(), plotImportance() and plotMetrics() methods for lists of RandomForest class objects.

Added plotExplanatoryHeatmap() method for lists of RandomForest or Univariate class objects.

Renamed keepVariables() and removeVariables() methods to keepFeatures() and removeFeatures().

Added the helper functions preTreatmentElements(), preTreatmentMethods() and preTreatParameters() for declaring pre-treatment parameters for the AnalysisParameters class.

Added the helper functions modellingMethods() and modellingParameters() for declaring modelling parameters for the AnalysisParameters class.

Added helper function correlationsParameters() for declaring correlations parameters for the AnalysisParameters class.

Added binaryComparisons() method for retrieving all possible binary class comparisons from an AnalysisData class object.

changeParameter() now assigns parameter values through direct assignment.

Added analysisResults() method from extracting analysis elements results from the Analysis class.

Added exportParameters() method for exporting analysis parameters to YAML file format.

Added dat() and sinfo() accessor methods for the Analysis class.

Relative standard deviation (RSD) values are now specified and returned as percentages.