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bayou (version 2.1.1)

bayou.checkModel: Function for checking parameter lists, prior and models are consistent and error-free

Description

Function for checking parameter lists, prior and models are consistent and error-free

Usage

bayou.checkModel(pars = NULL, tree, dat, pred = NULL, SE = 0, prior,
  model = "OU", autofix = TRUE)

Arguments

pars

A list of parameters that will be specified as starting parameter

tree

An object of class ``phylo''

dat

A named data vector that matches the tip lables in the provided tree

pred

A matrix or data frame with named columns with predictor data represented in the specified formula

SE

The standard error of the data. Either a single value applied to all the data, or a vector of length(dat).

prior

A prior function made using make.prior

model

Either one of c("OU", "QG" or "OUrepar") or a list specifying the model to be used.

autofix

A logical that indicates whether certain errors should be automatically fixed.

Value

A list of results of the checks and if 'autofix==TRUE', then ..$autofixed returns a list of all the input elements, with corrections.

Details

A series of checks are performed, run internally within bayou.makeMCMC, but can also be run on provided inputs prior to this. Errors are reported.

If autofix == TRUE, then the following errors will be automatically corrected:

Branch lengths == 0; any branches of length 0 will be given length .Machine$double.eps is.binary(tree) == FALSE; runs multi2di pars do not match prior$fixed; parameters are resimulated from prior