v0.1.0 Preprint

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

v0.4.1

SpectralInference v0.4.1

Diff since v0.4.0

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:

calc_spi_mtx => spectraldistances
calc_spi_trace => spectraldisances_trace
calc_spcorr_mtx => spectralcorrelations
nwstr => newickstring
minspaceneeded => distancetrace_spaceneeded
spimtx_spaceneeded => distancematrix_spaceneeded

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:

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.