NetCoMi: Network Construction and Comparison for Microbiome Data

A minor release with bug fixes and some enhancements.

New features

• Objects of class microNetProps returned from netAnalyze() now have a summary method, which prints the computed network properties in a well-arranged format.

• gcoda() (originally written by Fang Huaying) now provides the possibility for parallel computing including a progress bar.

• cclasso() (originally written by Fang Huaying) is extended by a progress bar.

• The summary methods summary.microNetProps() and summary.microNetComp() are extended by an option for choosing the number of decimal places in the output.

• plot.microNetProps() has a new argument labelFile, which allows to store the original and renamed node labels in a .txt file.

Bug fixes

• Fixes an error caused by netConstruct() when passing an association or distance matrix to the data argument.

• The manipulation of node sizes in plot.micronetprops() now works satisfactorily. If node sizes vary (e.g. according to a centrality measure), the argument nodeSizeSpread controls their range so that node sizes differ more strongly the higher its value.

Further changes

• The argument numbTaxa of summary.microNetComp() has been changed into numbNodes.

• Several functions now have a progress bar instead of a progress message.

• Minor amendments in the documentation of netAnalyze() (hubPar argument) and netConstruct() (cores argument).