Extracts the most important results from the output of the forward, backward, or both phases of a SURFACE analysis
Usage
surfaceSummary(fwd = NULL, bwd = NULL)
Value
A list with the following components:
n_steps
number of iterations in the stepwise analysis
lnls
matrix of traits-by-iterations, giving the log-likelihood for each trait at each iteration of the analysis
n_regimes_seq
matrix of the summaries of regime structure at each iteration of the model
aics
vector giving the AICc value at each step
shifts
shifts present in the final fitted Hansen model
n_regimes
summary of regime structure of the final fitted Hansen model (see note below)
alpha
estimate of alpha for each trait in the final model
sigma_squared
estimate of sigma_squared for each trait in the final model
theta
matrix of estimated optima (one per regime per trait) in the final model
Arguments
fwd
A list returned by surfaceForward (which may be stored as the $fwd component of the list returned by runSurface)
bwd
A list returned by surfaceBackward (which may be stored as the $bwd component of the list returned by runSurface)
Author
Travis Ingram
Details
If both fwd and bwd are provided, both phases of the analysis will be summarized together
References
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.