nmatzke

BioGeoBEARS

BioGeography with Bayesian (and likelihood) Evolutionary Analysis with R Scripts

3diphy

Maximum likelihood structural phylogenetics by including Foldseek 3Di characters. Supporting Information for Puente-Lelievre et al. 2023n for

BEASTmasteR

R code for writing Beast2 XML (especially morphology/tip-dating)

biopython

Nick Matzke's git mirror of the Biopython CVS repository, for GSoC 2009 project: BioGeography module for biopython

PhyBEARS.jl

Phylogenetic biogeography SSE models for large state spaces

bgbwk

Phylogenetic biogeography workshop files

phyloENM

Phylogenetic Environmental Niche Modeling

bioinfRhints

Bioinformatics hints in R

rexpokit

rexpokit: R Wrappers for EXPOKIT; Other Matrix Functions

Ashman_etal_Gehyra

Supplementary data and code for Ashman et al. study of Australian Gehyra

cladoRcpp

cladoRcpp: C++ implementations of phylogenetic cladogenesis calculations

CPs

Masafumi CPs project

DarwinsBulldogs

Rediscovering the anti-racist legacies of Darwin, Huxley, and other great evolutionists.

ENMTools

ENMTools R Package

Klaus_traits

Supplemental Data for Klaus & Matzke paper on trait-dependent dispersal

M21

Supplemental Files for Matzke (2021), rebutting Ree & Sanmartin (2018)

Matzke_Irmis_2018_PeerJ_autapomorphies_SuppData

Supplemental Data for Matzke & Irmis (2018), "Including autapomorphies is important for paleontological tip-dating with clocklike data, but not with non-clock data." PeerJ 6:e4553. https://doi.org/10.7717/peerj.4553 Permanent Zenodo archive of Supplemental Data: https://zenodo.org/badge/latestdoi/128717052

Matzke_R_binaries

Archiving CRAN binaries of R packages (as CRAN does not)

minbaru

Replicating the "baraminic distance correlation" calculations that creationists use on cladistic morphology datasets. Should be entertaining.

modiscdata

This package contains data files for use in the examples in the "modiscloud" package. The files are MODIS Level 2 Cloud Product files, downloaded from the NASA MODIS archive, or TIFs derived from them.

modiscloud

Package for processing downloaded MODIS Cloud Product HDF files and derived files. Specifically, MOD35_L2 cloud product files, and the associated MOD03 geolocation files (for MODIS-TERRA); and MYD35_L2 cloud product files, and the associated MYD03 geolocation files (for MODIS-AQUA). The package will be most effective if the user installs MRTSwath (MODIS Reprojection Tool for swath products; https://lpdaac.usgs.gov/tools/modis_reprojection_tool_swath), and adds the directory with the MRTSwath executable to the default R PATH by editing ~/.Rprofile.

njmtools

Nifty Jeneric Methods for R by Nicholas Joseph Matzke (practicing GitHub)

nmatzke.github.io

Dr. Nicholas J. Matzke: Integrating Ecological and Historical Biogeography with Statistical Phylogenetics

Ordovician_dispersal

Supplementary Material for Lam, Stigall, and Matzke (2017), "Dispersal in the Ordovician"

pandasthumb.github.io

PhyloBits.jl

Phylogenetic tree tables and other phylogenetic utilities. (Functions include: prt(tr) and other utilities. Also includes the PhyloNetworks tree object/reader/writer, with minimal dependencies.)

practice1

Practicing registering C routine etc. for R packages

reviews

Writing reviews of academic papers

test

treeflaws

Collection of tree files with parsing problems in various programs; for tests, debugging. Feel free to join/contribute!