bayou.checkModel: Function for checking parameter lists, prior and models are...
In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description Usage Arguments Details Value

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

1 2	bayou.checkModel(pars = NULL, tree, dat, pred = NULL, SE = 0, prior, model = "OU", autofix = TRUE)

`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.

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

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

bayou documentation built on May 2, 2019, 2:46 a.m.