SpectralInference - v0.1.0 Preprint

Version of library used for preprint analysis of Doran et al. 2023

- Julia
Published by BenjaminDoran almost 2 years ago

SpectralInference - v0.4.1

SpectralInference v0.4.1

Diff since v0.4.0

- Julia
Published by github-actions[bot] over 2 years ago

SpectralInference - v0.4.0

v0.4.0

Large update changing name of the package to SpectralInference

Change Log:

Updated docs and added some additional ("rough draft") example scripts for calculating bootstrap support values on the spectral tree and calculating MI across the spectral tree.

API changes:

calcspimtx => spectraldistances calcspitrace => spectraldisancestrace calcspcorrmtx => spectralcorrelations nwstr => newickstring minspaceneeded => distancetracespaceneeded spimtxspaceneeded => distancematrixspaceneeded

Other changes:

Used new feature of Julia 1.9 to add package extension for NewickTree, to negate the need for loading NewickTreeTools when working with trees. using SpectralInference, NewickTree automatically loads these functions for working with trees:

julia function getleafnames end function network_distance end function network_distances end function patristic_distance end function patristic_distances end function fscore_precision_recall end function cuttree end function mapinternalnodes end function maplocalnodes end function collectiveLCA end function as_polytomy! end function as_polytomy end function pairedMI_across_treedepth end function clusters_per_cutlevel end function ladderize! end function spectral_lineage_encoding end

Added precompile workloads. So the first time installing the package may be a little slower, but the first time using the functions should generally be faster.

- Julia
Published by BenjaminDoran almost 3 years ago