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jaatha (version 3.0.0)

Simulation-Based Maximum Likelihood Parameter Estimation

Description

An estimation method that can use computer simulations to approximate maximum-likelihood estimates even when the likelihood function can not be evaluated directly. It can be applied whenever it is feasible to conduct many simulations, but works best when the data is approximately Poisson distributed. It was originally designed for demographic inference in evolutionary biology. It has optional support for conducting coalescent simulation using the 'coala' package.

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Install

install.packages('jaatha')

Monthly Downloads

321

Version

3.0.0

License

GPL (>= 3)

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Maintainer

Paul Staab

Last Published

December 3rd, 2015

Functions in jaatha (3.0.0)

create_jaatha_data

Prepare the observed data for Jaatha
estimate_llh

Estimate the Log-Likelihood for a given parameter combination
create_jaatha_model.function

Specify a jaatha model using a simulation function
create_jaatha_model.coalmodel

Use a coala model in Jaatha
create_jaatha_stat

Create a summary statistic for Jaatha
jaatha

Simulation based maximum likelihood estimation
coarsen_jsfs

Divides the joint site frequency spectrum (jsfs) into blocks and returns the sum of the jsfs entries for each block.
create_jaatha_model

Specify a Model for a Jaatha Analysis
boot_jaatha

Parametric Bootstrapping of Jaatha Estimates
jaatha-package

Jaatha: Simulation-based maximum likelihood parameter estimation