Full function for maximum likelihood estimation of rate parameters and comparison to a single rate model.
ML.RatePhylo(rateData, rate = NULL, fixed = NULL, pretty = TRUE,
rateMIN = 0.001, rateMAX = 50, common.mean = FALSE, lambda.est = TRUE,
est.CI = FALSE, meserr = FALSE, file = NULL)an object of class "rateData"
a vector of relative rate parameters. The length of the vector is equal to the number of rates being estimated. If rate=NULL then rates are equal.
A vector stating whether each parameter should be allowed to vary (either FALSE which results in a start value of 1, or a numeric start value) or should be fixed (TRUE).
Display the output nicely (pretty=TRUE) or as a list (pretty=FALSE)
Minimum value for the rate parameters.
Maximum value for the rate parameters
a logical specififying whether each rate category should have its own mean (common.mean=FALSE) or all categories should have the same mean (common.mean=FALSE). See Thomas et al. (2009) for a discussion on the impact of assumptions about mean on rate estimates.
Logical. Estimate Pagel's lambda.
Logical. Estimate approximate confidence intervals for rate parameters.
Logical. Incorporate measurement error.
File string for output. Only used if pretty=TRUE.
If pretty=FALSE, returns a list containing:
MLRate Maximum likelihood estimates of the rate parameters
Lambda Maximum likelihood estimate of lambda
LCI Approximate lower confidence intervals for rate
UCI Approximate upper confidence intervals for rate parameters
means Means for each category
nParam Number of parameters in the model (how many means and rate categories)
Max.lik Maximum (log) likeihood
AIC for maximum likelihood model
AICc for maximum likelihood model
LambdaSingle Maximum likelihood estimate of lambda for the single rate model
Lik1 Likelihood of the equivalent single rate model
Likelihood ratio statistic of "Max.lik" vs "Lik1"
P P values for the LR statistic
df Degrees of freedom for the LR statistic
AIC.rate1 AIC for single rate model
AICc.rate1 AICc for single rate model
If pretty=TRUE, prints a nice version of the list to screen. If file is specified the pretty output will be sent to file, not the console.
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.