# Bayesian Synthetic Likelihood

## Documentation for package ‘BSL’ version 3.2.4

- DESCRIPTION file.

## Help Pages

BSL-package | Bayesian synthetic likelihood
BSL | Bayesian synthetic likelihood
bsl | Performing BSL, uBSL, semiBSL and BSLmisspec
BSL-class | S4 class "BSL".
BSLclass | S4 class "BSL".
cell | Cell biology example
cell_prior | Cell biology example
cell_sim | Cell biology example
cell_sum | Cell biology example
combinePlotsBSL | Plot the densities of multiple "bsl" class objects.
cor2cov | Convert a correlation matrix to a covariance matrix
estimateLoglike | Estimate the synthetic likelihood
estimateWhiteningMatrix | Estimate the Whitening matrix to be used in the "wBSL" method of Priddle et al. (2021)
gaussianRankCorr | Gaussian rank correlation
gaussianSynLike | Estimate the Gaussian synthetic (log) likelihood
gaussianSynLikeGhuryeOlkin | Estimate the Gaussian synthetic (log) likelihood with an unbiased estimator
getGamma | Obtain the gamma samples (the latent parameters for BSLmisspec method) from a "BSL" object
getGamma-method | S4 class "BSL".
getLoglike | Obtain the log-likelihoods from a "BSL" object
getLoglike-method | S4 class "BSL".
getPenalty | Obtain the selected penalty values from a "PENALTY" object
getPenalty-method | S4 class "PENALTY"
getTheta | Obtain the samples from a "BSL" object
getTheta-method | S4 class "BSL".
ma2 | An MA(2) model
ma2_prior | An MA(2) model
ma2_sim | An MA(2) model
ma2_sim_vec | An MA(2) model
ma2_sum | An MA(2) model
mgnk | The multivariate G&K example
mgnk_sim | The multivariate G&K example
mgnk_sum | The multivariate G&K example
MODEL | S4 class "MODEL"
MODEL-class | S4 class "MODEL"
newModel | S4 class "MODEL"
obsMat2deltax | Convert an observation matrix to a vector of n-day displacements
PENALTY | S4 class "PENALTY"
PENALTY-class | S4 class "PENALTY"
PENALTYclass | S4 class "PENALTY"
plot-method | S4 class "BSL".
plot-method | S4 class "PENALTY"
selectPenalty | Selecting the Penalty Parameter
semiparaKernelEstimate | Estimate the semi-parametric synthetic (log) likelihood
show-method | S4 class "BSL".
show-method | S4 class "PENALTY"
simulate_cell | Simulation function of the cell biology example
simulation | Run simulations with a give "MODEL" object
simulation-method | S4 class "MODEL"
sim_toad | The simulation function for the toad example
summary-method | S4 class "BSL".
summStat | Compute the summary statistics with the given data
summStat-method | S4 class "MODEL"
synLikeMisspec | Estimate the Gaussian synthetic (log) likelihood whilst acknowledging model incompatibility
toad | Toad example
toad_prior | Toad example
toad_sim | Toad example
toad_sum | Toad example