ape: reconstruct – R documentation

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reconstruct

Continuous Ancestral Character Estimation

Description

This function estimates ancestral character states, and the associated uncertainty, for continuous characters. It mainly works as the ace function, from which it differs, first, in the fact that computations are not performed by numerical optimisation but through matrix calculus. Second, besides classical Brownian-based reconstruction methods, it reconstructs ancestral states under Arithmetic Brownian Motion (ABM, i.e. Brownian with linear trend) and Ornstein-Uhlenbeck process (OU, i.e. Brownian with an attractive optimum).

Usage

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

Arguments

`x`	a numerical vector.
`phyInit`	an object of class `"phylo"`.
`method`	a character specifying the method used for estimation. Six choices are possible: `"ML"`, `"REML"`, `"GLS"`, `"GLS_ABM"`, `"GLS_OU"` or `"GLS_OUS"`.
`alpha`	a numerical value which accounts for the attractive strength parameter of `"GLS_OU"` or `"GLS_OUS"` (used only in these cases). If alpha = NULL (the default), then it is estimated by maximum likelihood using `optim` which may lead to convergence issue.
`CI`	a logical specifying whether to return the 95% confidence intervals of the ancestral state estimates.

Details

For "ML", "REML" and "GLS", the default model is Brownian motion. This model can be fitted by maximum likelihood (method = "ML", Felsenstein 1973, Schluter et al. 1997) - the default, residual maximum likelihood (method = "REML"), or generalized least squares (method = "GLS", Martins and Hansen 1997, Garland T and Ives AR 2000).

"GLS_ABM" is based on Brownian motion with trend model. Both "GLS_OU" and "GLS_OUS" are based on Ornstein-Uhlenbeck model.

"GLS_OU" and "GLS_OUS" differs in the fact that "GLS_OUS" assume that the process starts from the optimum, while the root state has to be estimated for "GLS_OU", which may rise some issues (see Royer-Carenzi and Didier, 2016). Users may provide the attractive strength parameter alpha, for these two models.

"GLS_ABM", "GLS_OU" and "GLS_OUS" are all fitted by generalized least squares (Royer-Carenzi and Didier, 2016).

Value

an object of class "ace" 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.

Note

GLS_ABM should not be used on ultrametric tree.

GLS_OU may lead to aberrant reconstructions.

Author(s)

Manuela Royer-Carenzi, Gilles Didier

References

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

Garland T. and Ives A.R. (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 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.

Royer-Carenzi, M. and Didier, G. (2016) A comparison of ancestral state reconstruction methods for quantitative characters. Journal of Theoretical Biology, 404, 126–142.

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.

Examples

### Some random data...
data(bird.orders)
x <- rnorm(23, m=100)
### Reconstruct ancestral quantitative characters:
reconstruct(x, bird.orders)
reconstruct(x, bird.orders, method = "GLS_OUS", alpha=NULL)

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24