R: Test for Rate Variation Using delta-AICrc Test Statistic

fitdAICrc

R Documentation

Test for Rate Variation Using delta-AICrc Test Statistic

Description

Fits a specified set of rate-variable and rate-constant variants of the birth-death
model to branching times from phylogenetic data. The test statistic dAICrc is the difference
in AIC scores between the best rate-constant and rate-variable models.

the set of rate-constant and rate-variable candidate models to be fitted

ints

the number of intervals. See 'Details'

Details

fitdAICrc implements the dAICrc test statistic for temporal variation in diversification
rates as described in Rabosky (2006).

modelset is a list of the rate-constant and rate-variable models to consider. You should include
both rate-constant models (pureBirth and bd), as well as one or more candidate rate-variable
models. Available options are DDX, DDL, yule2rate, and yule3rate.
See full descriptions of each of these models this document.

'ints' is used in determining the number of shift points to consider. If 'ints = NULL' (the
default), the model will consider only observed branching times as possible shift points. See
yule-n-rate for additional discussion of the 'ints' option. ]

Note that the rvbd function is no longer suppored ('rate variable birth death').

Value

a dataframe with the number of rows equal to the number of candidate models. Columns include likelihoods,
parameters, and AIC scores for each model. The first column contains the model names. If a parameter
is not present in a particular model, it will have an entry of 'NA' in the column for that parameter.
Parameter names follow conventions for model descriptions in other parts of this document. For example,
parameter r1 is the initial net diversification rate for all models (note that this will be the
only rate for the pureBirth model).

The full set of columns if all available models are included in the candidate set will consist
of the following:

model

the model name for row i in the dataframe

params

the free parameters for model[i]

np

the number of free parameters in mode[i]

mtype

either 'RC' for rate-constant or 'RV' for rate-variable

LH

the log-likelihood under model[i]

r1, r2, r3

net diversification rates, as applicable; r1 is always the initial rate, and
r3 is always the final rate

a

the extinction fraction E/S if applicable

xp

the x-parameter from the DDX model

k

the k-parameter from the DDL model

st1, st2

shift-times, if applicable. st1 is always the first shift point

AIC

the Akaike Information Criterion for model[i]

dAIC

delta-AIC; the difference in AIC scores between model[i] and the overall best-fit model

Nee, S., R. M. May, and P. H. Harvey. 1994b. The reconstructed
evolutionary process. Philos. Trans. R. Soc. Lond. B 344:305-311.

Rabosky, D. L. 2006. Likelihood methods for inferring temporal shifts in
diversification rates. Evolution 60:1152-1164.

Examples

data(agamids)
agbtimes <- getBtimes(string = agamids)
#agbtimes is now a vector of branching times from the agamid phylogeny
#here we fit 2 rate-constant and 3 rate-variable models
# to the agamid data:
result <- fitdAICrc(agbtimes, modelset = c("pureBirth", "bd",
"DDX", "DDL", "yule2rate"), ints = 100)
# this outputs summaries of parameters and likelihoods to screen;
# object 'result' is a dataframe containing all parameter estimates,
# likelihoods, and AIC scores