Updated package to v2.3.0

[Chris Watson]

Hello, I have just updated the package to v2.3.0. As usual, you can find the NEWS.md file on the Github page: https://github.com/cwatson/brainGraph

This update consisted mostly of bugfixes:

* `mtpc`: fixed bug when calculating statistics for different values of "alternative"

* bootstrapping: fixed bug when calculating *weighted* global efficiency; new argument "xfm.type" to handle this; it is the same behavior as for `set_brainGraph_attr`

* `plot.brainGraph`: you now do not need to specify a value for "hemi" if you select "plane='sagittal'"; it will by default select "hemi='L'"

* `plot_rich_norm` had a few bugs, and now has a new argument "smooth". This only works with single-subject networks, and plots a smoother instead of a line for every subject's rich-club curve.

A new feature is that `set_brainGraph_attr` now calculates, at the graph-level, *weighted characteristic path length*; this is simply the mean of the vertex-level values.

Finally, if your *Study.ID* variable is integer/numeric, the functions in the package will convert to character to avoid any errors.

As usual, please let me know if there are issues. I will update the User Guide today or tomorrow (although there is not much to update).

Chris

[Chris Watson]

Hello, I have since updated the package 2 more times (bugfix updates).

2.3.1 fixed a minor bug in "brainGraph_permute" that was introduced by 2.3.0

2.3.2:
* fixed a regression bug in the GLM fitting functions for F contrasts

* fixed a minor bug (from earlier versions) in which "make_nbs_brainGraph" did not correctly assign the "p.nbs" vertex attribute for all vertices (only a subset of them were correct)

* I have also changed the output of NBS slightly. Specifically:

    - "T.mat" and "p.mat" are now 3-dimensional *arrays* (instead of lists of matrices). The extent of these arrays equals the number of contrasts tested. So if you are using the "dk.scgm" atlas (which has 82 vertices), and are testing 4 contrasts at once, these arrays will each have dimensions "82 x 82 x 4".

Please make sure you are using 2.3.2 instead of 2.3.0 or 2.3.1. I apologize for any issues these bugs have caused.

Chris