# reconstruct

##### Continuous Ancestral Character Estimation

This function estimates ancestral character states, and the associated
uncertainty, for continuous characters. It mainly works as the
`ace`

function, from which it differs in the fact that
optimisations are not performed by numerical algorithms but through
matrix computations.

- Keywords
- models

##### Usage

`reconstruct(x, phyInit, method = "ML", CI = TRUE)`

##### Arguments

- x
- a vector or a factor.
- phyInit
- an object of class
`"phylo"`

. - method
- a character specifying the method used for
estimation. Three choices are possible:
`"ML"`

,`"REML"`

or`"GLS"`

. - CI
- a logical specifying whether to return the 95% confidence intervals of the ancestral state estimates.

##### Details

The default model is Brownian motion where characters evolve randomly
following a random walk. This model can be fitted by maximum
likelihood (Felsenstein 1973, Schluter et al. 1997 - the default),
residual maximum likelihood, or generalized least squares
(`method = "GLS"`

, Martins and Hansen 1997, Cunningham et
al. 1998).

##### Value

- a list with the following elements:
ace the estimates of the ancestral character values. CI95 the estimated 95% confidence intervals. sigma2 if `method = "ML"`

, the maximum likelihood estimate of the Brownian parameter.loglik if `method = "ML"`

, the maximum log-likelihood.

##### References

Cunningham, C. W., Omland, K. E. and Oakley, T. H. (1998)
Reconstructing ancestral character states: a critical
reappraisal. *Trends in Ecology & Evolution*, **13**,
361--366.

Felsenstein, J. (1973) Maximum likelihood estimation of evolutionary
trees from continuous characters. *American Journal of Human
Genetics*, **25**, 471--492.

Martins, E. P. and Hansen, T. F. (1997) Phylogenies and the
comparative method: a general approach to incorporating phylogenetic
information into the analysis of interspecific data. *American
Naturalist*, **149**, 646--667.

Schluter, D., Price, T., Mooers, A. O. and Ludwig, D. (1997)
Likelihood of ancestor states in adaptive radiation. *Evolution*,
**51**, 1699--1711.

Yang, Z. (2006) *Computational Molecular Evolution*. Oxford:
Oxford University Press.

Royer-Carenzi, M. and Didier, G. (2014) Comparison of ancestral state reconstruction methods for continuous characters under directional evolution. Submitted.

##### See Also

Reconstruction of ancestral sequences can be done with the package
`?ancestral.pml`

).

##### Examples

```
### Some random data...
data(bird.orders)
x <- rnorm(23)
### Compare the three methods for continuous characters:
reconstruct(x, bird.orders)
reconstruct(x, bird.orders, method = "REML")
```

*Documentation reproduced from package ape, version 3.2, License: GPL (>= 2)*