v1.1.0

• R/modulePreservation.R: 'nPerm' argument may now be set to 0 to calculate
  the module preservation statistics across two datasets while skipping
  the permutation test procedure.

• src/permutations.cpp: reorganised code to return the observed test
  statistics without performing the permutation test procedure when the
  'nPerm' argument in modulePreservation() is set to 0.

• src/permutationsNoData.cpp: reorganised code to return the observed test
  statistics without performing the permutation test procedure when the
  'nPerm' argument in modulePreservation() is set to 0.

• man/modulePreservation.Rd: added description detailing the use case for
  'nPerm=0'.

• man/*: minor changes in all man files due to generation with roxygen 6.0.1
  instead of roxygen 5.0.1.

Version 1.0.3

• DESCRIPTION: Release 1.0.3
• README: updated to reflect publication in Cell Systems and package
  publication on CRAN (as of version 1.0.2).
• R/NetRep.R: fixed spelling mistake in package documentation.
• man/NetRep.Rd: compilation of R/NetRep.R spelling fix.
• R/check-user-input.R: in processInput() improved handling of user input
  arugments 'modules', 'moduleAssignments', 'backgroundLabel' and 'test'
  to handle cases where user code has overwritten a necessary list element
  with 'NULL'.
• R/check-user-input.R: numeric labels in 'modules' are now returned as
  "character", fixing a bug where the incorrect modules would be reported
  in the 'contigency' table list element returned by contigencyTable() in
  R/contingency.R
• R/contingency.R: fixed bug where ratios returned in the 'propVarsExplained'
  list element by contingencyTable() were greater than 1 due to mismatch in
  in module order of the vectors when calculating the ratios (one ordered
  as text, one numerically).
• R/contingency.R: improved the 'contingency' table list element returned by
  contigencyTable() so that it now reports module sizes in their discovery
  datasets, the number of nodes present in the other dataset in the
  contigency table comparison, and includes modules with no nodes present in
  the other dataset.
• R/networkProperties.R: in netPropsInternal() improved progress reporting
  messages so that the module discovery dataset is listed as well as the
  dataset in which the module properties are being calculated.

Version 1.0.2

First release to CRAN

Software review

This version was sent to reviewers as part of Cell Systems' Software Certification process for the paper "A scalable permutation approach reveals replication and preservation patterns of network modules"

The Biomarker GlycA Is Associated with Chronic Inflammation and Predicts Long-Term Risk of Severe Infection

This package version was used to assess the replication of GlycA-associated modules in "The Biomarker GlycA Is Associated with Chronic Inflammation and Predicts Long-Term Risk of Severe Infection".

Installation can be performed by downloading the gzipped tarball below and using install.packages("NetRep-0.10.4.tar.gz", type="source") from within R. Common installation problems, such as missing software dependencies, are described on the main repository page.

A scalable permutation approach reveals replication and preservation patterns of network modules

Version used in "A scalable permutation approach reveals replication and preservation patterns of network modules" to assess module preservation.

Installation can be performed by downloading the gzipped tarball below and using install.packages("NetRep-0.23.0.tar.gz", type="source") from within R. Common installation problems, such as missing software dependencies, are described on the main repository page.