Description Usage Arguments Value Author(s) References
View source: R/optim.likRatePhylo.R
Function for the maximum likelihood estimation of rate parameters on a trait and phylogeny.
1 | optim.likRatePhylo(rateData, rate = NULL, fixed = NULL, rateMIN = 0.001, rateMAX = 50, common.mean = FALSE, lambda.est=TRUE, meserr)
|
rateData |
an object of class "rateData" |
rate |
a vector of relative rate parameters. The length of the vector is equal to the number of rates being estimated. If |
fixed |
A vector stating whether each parameter should be allowed to vary (either |
rateMIN |
Minimum value for the rate parameters |
rateMAX |
Maximum value for the rate parameters |
common.mean |
a logical specififying whether each rate category should have its own mean ( |
lambda.est |
Logical. Fit Pagel's lambda. |
meserr |
Logical. Include measurement error. |
MLRate |
Maximum likelihood estimates of the rate parameters |
Max.lik |
Maximum (log) likeihood |
AIC |
AIC for maximum likelihood model |
AICc |
AICc for maximum likelihood model |
convergence |
convergence value from |
n.parameters |
Number of parameters in the model (how many means and rate categories) |
Gavin Thomas
Thomas GH, Freckleton RP, & Szekely T. 2006. Comparative analyses of the influence of developmental mode on phenotypic diversification rates in shorebirds. Proceedings of the Royal Society B 273, 1619-1624.
Thomas GH, Meiri S, & Phillimore AB. 2009. Body size diversification in Anolis: novel environments and island effects. Evolution 63, 2017-2030.
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