startingModel: Create an Initial Model for a SURFACE Analysis
In surface: Fitting Hansen Models to Investigate Convergent Evolution

Description Usage Arguments Details Value Author(s) References See Also Examples

Generate a model to start a SURFACE analysis, or fit specific Hansen or Brownian motion models that can be compared to the models returned by SURFACE

1	startingModel(otree, odata, shifts = NULL, brownian = FALSE)

`otree`	Phylogenetic tree in `ouchtree` format
`odata`	Data frame with rownames corresponding to `otree@labels`
`shifts`	A named character vector of regime shifts. Names should correspond to `otree@nodes`, and regime assignments can be any character other than `"a"` (see details). Defaults to `NULL`, in which case a single-regime OU model is returned.
`brownian`	A logical indicating whether to return the fitted Brownian motion model for the data set by calling the `ouch` function `brown` and obtaining AICs by adding log-likelihoods across traits. If TRUE, overrides any specified `shifts`

For most analysis, this function is not accessed by the user, but is called from within surfaceForward to initialize the run with a single-regime OU model. However, the user can optionally supply a starting model that imposes some regime shifts (e.g. if there is strong a priori reason to include them, or to evaluate how their inclusion changes the result of SURFACE analysis). If shifts are supplied, they are always modified so that the first element codes a basal regime 'shift' c("1"="a"). Thus, if any other element in shifts is specified as regime "a", or has name "1", an error will be returned. startingModel can also be used to obtain a fit (with AICc calculated after adding log-likelihoods across traits) for any hypothesized Hansen model or for Brownian motion (if brownian=TRUE) for comparison with models returned by SURFACE

A list of length 1 containing an object with the same structure as the lists returned by each iteration of surfaceForward and surfaceBackward (containing elements fit, all_aic, aic, savedshifts, and n_regimes). This allows it to be supplied as argument starting_list in a call to surfaceForward.

Travis Ingram

Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.

surfaceForward

data(surfaceDemo)
tree<-surfaceDemo$tree
dat<-surfaceDemo$sim$dat
olist<-convertTreeData(tree,dat)
otree<-olist[[1]]; odata<-olist[[2]]
startmod<-startingModel(otree, odata, shifts = c("6"="b"))