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,
  verbose = TRUE
)

Value

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

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.
verbose: Determines whether information is outputted to the console for the user to view

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