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The Emcee sampler

Ensemble walker sampling

Name: Emcee

Version: 2.1.0

Author(s): Dan Foreman-Mackey and contributors

URL: http://dan.iel.fm/emcee/

Cite: PASP, 125, 925, 306-312

Parallel: parallel

The emcee sampler is a form of Monte-Carlo Markov Chain that uses an ensemble of 'walkers' that explore the parameter space. Each walker chooses another walker at random and proposes along the line connecting the two of them using the Metropolis acceptance rule. The proposal scale is given by the separation of the two walkers.

It is parallel, so multiple processes can be used to speed up the running. It is also affine invariant, so that no covariance matrix or other tuning is required for the proposal.

The burn-in behavior of emcee can sometimes be poor; it is much better to start the chain as near to the maximum posterior as possible. The maxlike or similar samplers can help you find this.

The total number of samples taken is walkers*samples.

Installation

emcee is included in the cosmosis bootstrap, but if you are installing manually you can get emcee using one of the following commands:

pip install emcee        # to install centrally, may require sudo
                         # or ...
pip install emcee --user # to install just for you

Parameters

These parameters can be set in the sampler's section in the ini parameter file.
If no default is specified then the parameter is required. A listing of "(empty)" means a blank string is the default.

Parameter Type Meaning Default
walkers integer number of walkers in the space
samples integer number of jumps to attempt per walker
nsteps integer number of sample steps taken in between writing output
random_start bool whether to start the walkers at random points in the prior instead of near the start. Usually a bad idea N
start_points string a file containing starting points for the walkers. If not specified walkers are initialized randomly from the prior distribution. (empty)
covmat string a file containing a covariance matrix for initializing the walkers. (empty)

Updated