Description Usage Arguments Value Author(s) References Examples

`pGLS`

An Generalized Least Square model for Comparative Phylogenetics

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`formula` |
a formula describing the model to be fit. Note, that an intercept is included at default. |

`data` |
the data frame including the predictors (X's) and the response (Y) |

`covarmatrix` |
the var-covariance matrix that is derived from phylogeny or other sources |

`na.action` |
a dummy term for data cleaning. |

`intercept` |
TRUE (default) if the specified model is with a intercept. It is rare to fit a such model without intercepts. |

A list object of class `"z"`

containing the results of GLS fitting.
The components are:

`pred` |
fitted values and standard errors of the fitted values. |

`coefficients` |
estimated coefficients. |

`cov.coeff` |
estimated covariance matrix of the coefficients |

`"sigma^2"` |
estimated variance |

`pred.cond.` |
(for unknown species only)predicted y-values conditioning on the known species. Note if there are no unknown species present in the data, conditional prediction is not calculated. |

`R-Sq` |
fraction of total variance explained by the GLS model |

Xianyun Mao xianyunmao at gmai1.com replace 1 by l.

Garland, T., Jr., and A. R. Ives. (2000)

Using the past to predict the present: Confidence intervals
for regression equations in phylogenetic comparative methods. *American Naturalist 155:346-364.*

Martins, E. P., and T. F. Hansen. (1996)

The statistical analysis
of interspecific data: a review and evaluation of
comparative methods. * Pages 22-75 in E. P. Martins, ed.
Phylogenies and the comparative method in animal behavior.
Oxford University Press, Oxford.*

Box, G. E. P., G. M. Jenkins, and G. C. Reinsel. (1994)

*Pages 282-285 Time series analysis: forecasting and control. Prentice Hall,
Englewood Cliffs, N.J.*

Anderson, T.W. (2003).

* An Introduction to Multivariate Statistical Analysis. Wiley-Interscience; 3rd edition*

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