changes_in_version0.54.txt

#Changes in version 0.54

1) The package now works when only one variable is provided in Y, Z, or W matrices
2) Fixed the legend labels for 4-way analysis in network graphs
3) Changed all.missing.thresh to a user-defined option. Missing value filtering is performed after RSD filtering in pairwise analyses.
4) Fixed max_var settings for 3-way and 4-way analysis in X by Z pairwise comparison. No changes to 2-way analysis.
5) Removed redundant calls to network function, which first generated network at corthresh=0 and then at the defined threshold. Only one network at the user-defined (or minimum based on p-value) threshold is generated now.
6) Added degree.count, degree.weight, and closeness centrality options for centrality analysis (see Manual)
7) Community detection: the software now compares walktrap and multilevel community and selects the option that gives higher modularity measure
8) Fixed the "row.name" length error for the repeated measures analysis
9) Removed the restriction for only using the nodes selected in all samples analysis for class-wise comparisons. Some nodes are only signficantly associated in sub-class analysis.
10) Changed the default settings for max_connections to NA; can be changed to any numeric value (e.g. 100000)
11) The package now also report network statistics such as graph clustering coefficient (how well nodes cluster globally; ranges between 0 (no clustering) to 1 (high)) and modularity measure (how well the communities are defined; higher is better)