Statisticalrethinking.jlJulia version of selected functions in the R package `rethinking`. Used in the StatisticalRethinkingStan and StatisticalRethinkingTuring projects.
McmcCollection of Monte Carlo (MC) and Markov Chain Monte Carlo (MCMC) algorithms applied on simple examples.
Shinystanshinystan R package and ShinyStan GUI
MiciManifold Markov chain Monte Carlo methods in Python
Stan.jlStan.jl illustrates the usage of the 'single method' packages, e.g. StanSample, StanOptimize, etc.
Beast2Bayesian Evolutionary Analysis by Sampling Trees
Data science blogsA repository to keep track of all the code that I end up writing for my blog posts.
ExoplanetFast & scalable MCMC for all your exoplanet needs!
Mcmcchains.jlTypes and utility functions for summarizing Markov chain Monte Carlo simulations
Beast McmcBayesian Evolutionary Analysis Sampling Trees
GpstuffGPstuff - Gaussian process models for Bayesian analysis
Advancedhmc.jlRobust, modular and efficient implementation of advanced Hamiltonian Monte Carlo algorithms
GgmcmcGraphical tools for analyzing Markov Chain Monte Carlo simulations from Bayesian inference
NimbleThe base NIMBLE package for R
Machine Learning NumpyGathers Machine learning models using pure Numpy to cover feed-forward, RNN, CNN, clustering, MCMC, timeseries, tree-based, and so much more!
ParamonteParaMonte: Plain Powerful Parallel Monte Carlo and MCMC Library for Python, MATLAB, Fortran, C++, C.
Bat.jlA Bayesian Analysis Toolkit in Julia
GetdistMCMC sample analysis, kernel densities, plotting, and GUI
GerrychainUse MCMC to analyze districting plans and gerrymanders
Turing.jlBayesian inference with probabilistic programming.
BayesiantoolsGeneral-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics
EmceeThe Python ensemble sampling toolkit for affine-invariant MCMC
DblinkDistributed Bayesian Entity Resolution in Apache Spark
Cmdstan.jlCmdStan.jl v6 provides an alternative, older Julia wrapper to Stan's `cmdstan` executable.
PsgldAAAI & CVPR 2016: Preconditioned Stochastic Gradient Langevin Dynamics (pSGLD)
DeepbayesBayesian methods in deep learning Summer School
PygtcMake a sweet giant triangle confusogram (GTC) plot
OwlOwl - OCaml Scientific and Engineering Computing @ http://ocaml.xyz
Bayesian Neural NetworksPytorch implementations of Bayes By Backprop, MC Dropout, SGLD, the Local Reparametrization Trick, KF-Laplace, SG-HMC and more
RstanRStan, the R interface to Stan
Pymc3Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Aesara
ConvchainBitmap generation from a single example with convolutions and MCMC
Dbda PythonDoing Bayesian Data Analysis, 2nd Edition (Kruschke, 2015): Python/PyMC3 code
BayaderaHigh-performance Bayesian Data Analysis on the GPU in Clojure
Bayesplotbayesplot R package for plotting Bayesian models
smfsbDocumentation, models and code relating to the 3rd edition of the textbook Stochastic Modelling for Systems Biology
autoreparamAutomatic Reparameterisation of Probabilistic Programs
BayesianTutorialsImplementing MCMC sampling from scratch in R for various Bayesian models
Torstenlibrary of C++ functions that support applications of Stan in Pharmacometrics
BayesHMMFull Bayesian Inference for Hidden Markov Models
pyanetiA multi-planet Radial Velocity and Transit modelling software
cmdstanrCmdStanR: the R interface to CmdStan
SMC.jlSequential Monte Carlo algorithm for approximation of posterior distributions.
ChempyStart with the Chempy tutorial
phymlPhyML -- Phylogenetic estimation using (Maximum) Likelihood
mcmcA C++ library of Markov Chain Monte Carlo (MCMC) methods
l2hmc-qcdApplication of the L2HMC algorithm to simulations in lattice QCD.
postsPieces of code that have appeared on my blog with a focus on stochastic simulations.
BASBAS R package https://merliseclyde.github.io/BAS/
CorBinianCorBinian: A toolbox for modelling and simulating high-dimensional binary and count-data with correlations