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BSL (version 3.0.0)

Bayesian Synthetic Likelihood

Description

Bayesian synthetic likelihood (BSL, Price et al. (2018) ) is an alternative to standard, non-parametric approximate Bayesian computation (ABC). BSL assumes a multivariate normal distribution for the summary statistic likelihood and it is suitable when the distribution of the model summary statistics is sufficiently regular. This package provides a Metropolis Hastings Markov chain Monte Carlo implementation of three methods (BSL, uBSL and semiBSL) and two shrinkage estimations (graphical lasso and Warton's estimation). uBSL (Price et al. (2018) ) uses an unbiased estimator to the normal density. A semi-parametric version of BSL (semiBSL, An et al. (2018) ) is more robust to non-normal summary statistics. Shrinkage estimations can help to bring down the number of simulations when the dimension of the summary statistic is high (e.g., BSLasso, An et al. (2019) ). Extensions to this package are planned.

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Version

Install

install.packages('BSL')

Monthly Downloads

338

Version

3.0.0

License

GPL (>= 2)

Maintainer

Ziwen An

Last Published

July 10th, 2019

Functions in BSL (3.0.0)

gaussianSynLike

Estimating the Gaussian synthetic likelihood
BSLMODEL-class

S4 class ``BSLMODEL''
bsl

Performing BSL, BSLasso and semiBSL
BSL-package

Bayesian synthetic likelihood
fn

Functions to be used in bsl (for internal use)
bsl-class

S4 class ``bsl''.
gaussianRankCorr

Gaussian rank correlation
cell

Cell biology example
cor2cov

Convert a correlation matrix to a covariance matrix
combinePlotsBSL

Plot the densities of multiple ``bsl'' class objects.
show.bsl

Show method for class ``bsl''. Display the basic information of a bsl object.
summary.bsl

Summary method for class ``bsl''
selectPenalty

Selecting BSLasso Penalty
plot.bsl

Plot method for class ``bsl''
semiparaKernelEstimate

Estimating the semi-parametric joint likelihood
setns

Find the length of summary statistics (for internal use)
ma2

An MA(2) model
gaussianSynLikeGhuryeOlkin

Estimating the Gaussian synthetic likelihood with an unbiased estimator
mgnk

The multivariate G&K example
penbsl

S3 reference class of the result from tuning to select the optimal penalty for BSLasso