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metabolyseR 0.14.0

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@jasenfinch jasenfinch released this 16 Apr 16:41
· 227 commits to master since this release
v0.14.0
0a1aca3
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Learn about vigilant mode.

  • 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.

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