# corPagel

From ape v2.7-3
by Emmanuel Paradis

##### Pagel's ``lambda'' Correlation Structure

The correlation structure from the present model is derived from the Brownian motion model by multiplying the off-diagonal elements (i.e., the covariances) by $\lambda$. The variances are thus the same than for a Brownian motion model.

- Keywords
- models

##### Usage

```
corPagel(value, phy, form = ~1, fixed = FALSE)
## S3 method for class 'corPagel':
corMatrix(object, covariate = getCovariate(object),
corr = TRUE, ...)
## S3 method for class 'corPagel':
coef(object, unconstrained = TRUE, \dots)
```

##### Arguments

- value
- the (initial) value of the parameter $\lambda$.
- phy
- an object of class
`"phylo"`

. - form
- (ignored).
- fixed
- a logical specifying whether
`gls`

should estimate $\lambda$ (the default) or keep it fixed. - object
- an (initialized) object of class
`"corPagel"`

. - covariate
- (ignored).
- corr
- a logical value specifying whether to return the correlation matrix (the default) or the variance-covariance matrix.
- unconstrained
- a logical value. If
`TRUE`

(the default), the coefficients are returned in unconstrained form (the same used in the optimization algorithm). If`FALSE`

the coefficients are returned in ``natural'', possibly constrained, f - ...
- further arguments passed to or from other methods.

##### Value

- an object of class
`"corPagel"`

, the coefficients from an object of this class, or the correlation matrix of an initialized object of this class. In most situations, only`corPagel`

will be called by the user.

##### References

Freckleton, R. P., Harvey, P. H. and M. Pagel, M. (2002) Phylogenetic
analysis and comparative data: a test and review of evidence.
*American Naturalist*, **160**, 712--726.

Pagel, M. (1999) Inferring the historical patterns of biological
evolution. *Nature*, **401**,877--884.

*Documentation reproduced from package ape, version 2.7-3, License: GPL (>= 2)*

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