Menghan Zhang's repositories
PANDA
Phylogenetic ANalyses of DiversificAtion
DataViz
Data visualization tools for Matlab
gramm
Gramm is a complete data visualization toolbox for Matlab. It provides an easy to use and high-level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.
Inferring-language-dispersal-patterns-with-velocity-field-estimation
R package and tutorial of the language velocity field estimation (LVF) for reconstructing langauge dispersal pattern.
pyslim
Tools for dealing with tree sequences coming to and from SLiM.
LDBlockShow
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
concepticon-data
The curation repository for the data behind Concepticon.
admixr
An R package for reproducible and automated ADMIXTOOLS analyses
rethinking
Statistical Rethinking course and book package
geographiclib-octave
Octave/MATLAB implementation
sBayes
MCMC algorithms to identify linguistic contact zones
treetime
Maximum likelihood inference of time stamped phylogenies and ancestral reconstruction
comap
A package for detecting coevolving positions in a sequence alignment, using COsubstitution MAPping.
fitspphylo
function to fit a model using GLS and account for spatial and phylogenetic autocorrelation
turboMEDUSA
Fitting of piecewise diversification models to time-calibrated phylogenetic trees.
fallpaddy
R codes for simulating and detecting punctuated evolution in any clades, from dinosaurs to viruses
rr2
R2 for correlated data; see https://academic.oup.com/sysbio/advance-article/doi/10.1093/sysbio/syy060/5098616
burstclock
Models, Paper and Data on the Semi-Strict Clock
CourseComparativeMethods
Examples of application of comparative methods in R
QuIBL
Quantifying Introgression via Branch Lengths
bayroot
Bayesian root-to-tip regression for dating reservoir sequences
transnewguineaorg
CLDF dataset derived from Greenhill's "TransNewGuinea.org" from 2015
dispersal-simulation
Model the settlement of the Americas using an agent-based model on a hex grid with resource depletion, migration, and culture-dependent cooperation.
Rbeast
Bayesian Change-Point Detection and Time Series Decomposition
SimRA
SimRA (Simulation based on Random-graphs Algorithms) is a framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture. The algorithm generates a network structure, called Ancestral Recombination Graph (ARG), that models coalescence and genetic exchange events (recombinations) with SNP as well as STR polymorphisms.
packages
Released BEAST 2 packages
Babel
BEAST analysis backing effective linguistics
chinese-poetry
The most comprehensive database of Chinese poetry 🧶最全中华古诗词数据库, 唐宋两朝近一万四千古诗人, 接近5.5万首唐诗加26万宋诗. 两宋时期1564位词人，21050首词。