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

View source: R/surfaceSummary.R

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 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 |

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`

(`k-kprime`

, 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 Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.

`surfaceForward`

, `surfaceBackward`

surface documentation built on May 30, 2017, 1:58 a.m.

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