load.bayou: Loads a bayou object

In uyedaj/bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Loads a bayou object

Description

load.bayou loads a bayouFit object that was created using bayou.mcmc()

Usage

load.bayou(bayouFit, saveRDS = TRUE, file = NULL, cleanup = FALSE, ref = FALSE)

Arguments

bayouFit	An object of class bayouFit produced by the function bayou.mcmc()
saveRDS	A logical indicating whether the resulting chains should be saved as an *.rds file
file	An optional filename (possibly including path) for the saved *.rds file
cleanup	A logical indicating whether the files produced by bayou.mcmc() should be removed.
ref	A logical indicating whether a reference function is also in the output

Details

If both save.Rdata is FALSE and cleanup is TRUE, then load.bayou will trigger a warning and ask for confirmation. In this case, if the results of load.bayou() are not stored in an object, the results of the MCMC run will be permanently deleted.

Examples

## Not run: 
data(chelonia)
tree <- chelonia$phy
dat <- chelonia$dat
prior <- make.prior(tree)
fit <- bayou.mcmc(tree, dat, model="OU", prior=prior, 
                                 new.dir=TRUE, ngen=5000)
chain <- load.bayou(fit, save.Rdata=FALSE, cleanup=TRUE)
plot(chain)

## End(Not run)

uyedaj/bayou documentation built on Jan. 28, 2024, 5:09 a.m.