- Keep scale factor when normalising (#38)
- Doc fixes
- pkgdown documentation
- use development version of nat package when doing install_github of nat.nblast
- spelling
- 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
- minor fixes for 3.3
- add vignette
- simplify travis setup
- dev: fix test for different normalisation types
- fix handling of non-square matrices in sub_score_mat
- minor doc fixes
- switch from importing nat to depending on it
- 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
- 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)
- 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
- 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.
- doc: basic package documentations