Dear Freesurfer users,
I am pleased to announce the 2nd major release of my R package for graph
theory analysis of brain MRI data, "brainGraph".
The main page on CRAN is at: https://cran.r-project.org/
web/packages/brainGraph/index.html
The GitHub repository is at: https://github.com/cwatson/brainGraph
*Installation*
The latest version is already on CRAN for Linux distributions, and should
be for Windows and Mac OS X soon (but there may be issues on non-Linux
systems; see Chapter 1 of the User Guide).
To install directly from CRAN:
> install.packages('brainGraph')
In the meantime (and for development versions), you may install from GitHub
using the R package "devtools":
> devtools::install_github('cwatson/brainGraph')
*Getting help*
The new User Guide has been completely overhauled, and now has a permanent
link at: my GitHub Pages site (PDF warning)
<https://cwatson.github.io/files/brainGraph_UserGuide.pdf>. Please start at
the "Preface".
You may also get help by opening an Issue
<https://github.com/cwatson/brainGraph/issues> on the GitHub
repository, or join
the Google Group
<https://groups.google.com/forum/?hl=en#%21forum/brainGraph-help>.
*New features*
You can find the release notes/changelog in NEWS.md, at:
https://github.com/cwatson/brainGraph/blob/master/NEWS.md
Major additions (since v1.0.0) that should be of interest include:
- Vertex- and graph-level *mediation analysis* (chapter 11 of the Guide)
- Multi-threshold permutation correction (MTPC) for GLM analyses
(chapter 9)
- Extension of GLM-based functions (including the *network-based
statistic [NBS]* and MTPC) to allow for multiple contrasts in a single
function call, and to allow for both T- and F-contrasts
- Permutation/randomization is now done using the *Freedman-Lane
algorithm* (as in *randomise* and *PALM*), although models are limited
to simple GLM's
- Introduction of R's *S3 classes* to simplify plotting and summarizing
results
- Calculation of a network's *s-core* membership
- Calculation of network *communicability* and vertex *communicability
betweenness centrality*
Please let me know if you have any issues, bug reports, feature requests,
etc.
Chris Watson
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