use development version of nat package when doing install_github of nat.nblast
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nat.nblast 1.6.3 Unreleased
fixes/examples for show_similarity
allow score matrices to be passed as first param to nhclust (but issue a warning)
change vignette engine to rmarkdown
nat.nblast 1.6.2 2016-04-26
minor fixes for 3.3
add vignette
simplify travis setup
nat.nblast 1.6.1 Unreleased
dev: fix test for different normalisation types
nat.nblast 1.6 Unreleased
fix handling of non-square matrices in sub_score_mat
minor doc fixes
nat.nblast 1.5 2014-09-19
switch from importing nat to depending on it
nat.nblast 1.4 Unreleased
use nabor package, not RANN, for finding nearest neighbours
add functions for creating sparse score matrices, using spam package
speed up extraction of diagonal elements for on-disk score matrices
nblast now handles all combinations of neuron and dotprops objects
nat.nblast 1.3 Unreleased
functions to create scoring matrices; see create_scoringmatrix for details.
fix: really use nhclust’s distfun argument
new nblast_allbyall function
add plyr support (gives parallelisation and progress bar options)
nat.nblast 1.2 Unreleased
add nhclust, plot3d.hclust, subset.hclust to help cluster/plot based on nblast scores (all ported from flycircuit package).
rename showSimilarity -> show_similarity
dev: make sure tests run during check()
test: update baselines given score matrix changes in 1.1
nat.nblast 1.1 Unreleased
fix: make smat.fcwb the default scoring matrix (rather than smat_alpha) when nblast’s UseAlpha parameter is FALSE (the default) and smat_alpha.fcwb the default when UseAlpha=TRUE.
rename smat->smat.fcwb and smat_alpha->smat_alpha.fcwb to make it clear that these are defined in the FCWB template space (though they should work OK for other fly template brains that have an absolute physical scale)
don’t set options(“nat.nblast.defaultsmat”"), just query it.