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Notes:
Beta version 0.30 - 06/10/14
Major feature and bugfix update:
1) small bugfixes in all stages
2) all properties previously calculated/tested (in stages 3 & 4)
for all weights simultaneously are now calculated/tested for each
sign separately (modularity still calculated on entire matrix)
3) clustering coefficient, local efficiency, matching index, rich
club, & transitivity added to full network calculations/testing
4) participation coefficient & within-module z added to thresholded
matrix calculations/testing
5) calculation/testing of properties for negative weights in the
thresholded matrices is now automatic (to be consistent with fully
connected matrices)
6) option added to calculate/test properties for absolute value of
weights
7) 'handles' structure now used (in all stages) to pass information
between functions (rather than using a globalized variable),
allowing users to launch processes from the same GUI with less
chance of info from the previous process interfering
8) important change to the way in which matrices are thresholded in
Stage 3; the previous version sometimes allowed the threshold to be
negative, which was most common for higher densities for negative
weight networks (unlikely to have had much of an impact for for
positive weights); thus, when calculating properties for negative
weights, positive weights were sometime allowed in at higher
densities, making it more likely for properties for positive and
negative weights to be negatively correlated; now, only weights of
the appropriate sign are allowed in; as a consequence, it is
possible that the requested maximum density cannot be reached (more
problematic for 'sparser' matrices); therefore, the maximum
possible density is now calculated and, if smaller than the
requested density, this new value is used (so be sure to check the
actual maximum density used)
Changes:
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