Extracts the most important results from the output of the forward, backward, or both phases of a SURFACE analysis
1  surfaceSummary(fwd = NULL, bwd = NULL)

fwd 
A list returned by 
bwd 
A list returned by 
If both fwd
and bwd
are provided, both phases of the analysis will be summarized together
A list with the following components:
n_steps 
number of iterations in the stepwise analysis 
lnls 
matrix of traitsbyiterations, giving the loglikelihood 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 
The elements n_regimes_seq
and n_regimes
contain measures of the regime structure in a SURFACE analysis (for each iteration, and in the final model, respectively). The measures returned are: k
(the number of regime shifts, counting the basal regime as 1), kprime
, (the number of regimes, some of which may be reached by multiple shifts), deltak
(kkprime
, a measure of convergence), c
(the number of shifts to convergent regimes, another measure of convergence), kprime_conv
(the number of convergent regimes shifted to multiple times), and kprime_nonconv
(the number of nonconvergent regimes only shifted to once)
Travis Ingram
Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting OrnsteinUhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416425.
surfaceForward
, surfaceBackward
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