nodeEstimate {ppgm} | R Documentation |
nodeEstimate
Description
This function estimates the ancestral character states for continuous characters given a model of evolution or using the best fit model of evolution from the fitContinuous function in the geiger package. The ancestral states are estimated using GLS described in Martins and Hansen (1997).
Usage
nodeEstimate(treedata.obj, traitnum, model = "BM", bounds = list(),
control = list(), plot.est = FALSE)
Arguments
treedata.obj |
an object of the class "treedata". |
traitnum |
the column number of the trait within the treedata object to be reconstructed. |
model |
the model of evolution to use in the ancestral state reconstruction. Options are "estimate", "BM", "OU", "EB", "lambda", "kappa", "delta". |
bounds |
bounds used for the model, passes to |
control |
setting used for optimization of the model likelihood. Passes to |
plot.est |
logical. whether or not to plot the traitgram of the estimated ancestor states. |
Details
See the fitContinuous()
details for descriptions of the models of evolution and parameter estimation. nodeEstimate()
currently supports the following models of evolution: Brownian motion (Felsenstein, 1973), Ornstein-Uhlenbeck (Butler and King, 2004), early-burst (Harmon et al., 2010), lambda (Pagel, 1999), kappa (Pagel, 1999), and delta (Pagel, 1999).
Value
an object of the class "nodeEstimate".
model
if model = "estimate", the best fit model of evolution. If the model was specified, then model is the specified model.
est
the ancestral node estimates of the continuous character.
phy
the phylogeny used for the estimates, which might be transformed depending on the evolutionary model.
BM
if model = "BM", returned values from fitContinuous()
where the model is "BM"
OU
if model = "OU", returned values from fitContinuous()
where the model is "OU"
EB
if model = "EB", returned values from fitContinuous()
where the model is "EB"
lambda
if model = "lambda", returned values from fitContinuous()
where the model is "lambda"
kappa
if model = "kappa", returned values from fitContinuous()
where the model is "kappa"
delta
if model = "delta", returned values from fitContinuous()
where the model is "delta"
fitted
if model = "estimate", returned values from the best fit model of evolution.
Author(s)
A. Michelle Lawing, Alexandra F. C. Howard
References
Butler, M. A. and King, A. A. (2004) Phylogenetic comparative analysis: a modeling approach for adaptive evolution. American Naturalist, 164:683-695.
Felsenstein, J. (1973) Maximum likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics, 25:471-492
Harmon, L. J. et al. (2010) Early bursts of body size and shape evolution are rare in comparative data. Evolution, 64:2385-2396
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.
Pagel M. (1999) Inferring the historical patterns of biological evolution. Nature, 401:877-884
See Also
fitContinuous()
Examples
data(sampletrees)
data(occurrences)
occurrences <- getBioclimVars(occurrences, which.biovars=1)
sp_data_min<- tapply(occurrences[,4],occurrences$Species,min)
ex <- geiger::treedata(sampletrees[[1]], sp_data_min)
nodeEstimate(ex, 1, model = 'OU') #runs OU model