OUwieParSumm: Extract parameters from OUwie results
In willgearty/pcmtools: Tools for Phylogenetic Comparative Methods

Description Usage Arguments Details Value Examples

View source: R/OUwieAvg.R

Extract various parameter values from the results of (many) OUwie analyses and maps the parameter values to different regimes based on the inputted regime map. Returns the parameters in a 4-D array, where the first dimension is the models, the second dimension is the parameters (including AICc), the third dimension is the regimes, and the fourth dimension is the replicates.

1 2	OUwieParSumm(ou.results, regime.mat, params = c("Alpha", "Sigma.sq", "Theta", "Theta.se", "AICc"))

`ou.results`	A list of lists (or just a list) of unmodified results from an OUwie analysis
`regime.mat`	A data frame mapping regimes to total regime options for each model (see details)
`params`	A vector specifying which parameter should be calculated/returned (see details)

The regime.mat is the most important component, as it indicates which parameters should be mapped to which regime for each model. For example, in an OU1 model, the user would likely want the parameters mapped to all regimes, whereas in an OUM model, the user would likely want the parameters for each regime mapped exclusively to that regime. In more complex scenarios, the user may have multiple OUM models in which regimes are split or combined in different manners, such that the parameters for one regime in one OUM model may map to multiple regimes in the overall dataset. The rownames of this matrix should identify names for the regimes and the colnames should identify the models. It is assumed that the order of the models/colnames in regime.mat matches the order of the models in ou.results.

Valid options for params are "Alpha", "Sigma.sq", "Theta", "Theta.se", "Halflife" (phylogenetic half-life), "Stat.var" (stationary variance), "AIC", "AICc", and "BIC".

An ouwiepars object. Basically a 4-D array that can be passed to other functions for further analysis/visualization.

## Not run: 
library(OUwie)
data(tworegime)
ou.results <- list()
ou.results[[1]] <- OUwie(tree,trait,model=c("BM1"))
ou.results[[2]] <- OUwie(tree,trait,model=c("BMS"), root.station = FALSE)
ou.results[[3]] <- OUwie(tree,trait,model=c("OUM"))
ou.results[[4]] <- OUwie(tree,trait,model=c("OUMV"))

#Both regimes have same parameters for BM1 model. Both regimes have different parameters for other models.
regime.mat <- data.frame(BM1 = c(1, 1), BMS = c(1,2), OUM = c(1,2), OUMV = c(1,2), row.names = c(1,2))
## End(Not run)

OUwieParSumm(ou.results, regime.mat)