Example datasets and sample BAMM output for the
package BAMMtools.
This includes both the raw data and the BAMM output for
three example analyses. The first is an analysis of speciation and
extinction rates during the radiation of modern whales, using a
time-calibrated tree from Steeman et al. (2009). The second is a
BAMM analysis of phenotypic evolutionary rates (body mass)
during the radiation of extant primates, taken from Vos and Mooers
(2006) and Redding et al. (2010).The third is a BAMM analysis
of speciation and extinction rates for a 300-species subset of
ray-finned fishes, along with body size data for these species from
Rabosky et al. (2013).
Dataset whales is the raw time-calibrated tree that was
analyzed with BAMM, primates is the corresponding
time-calibrated phylogeny of 233 primate species, and fishes
is the time-calibrated phylogeny of 300 fish species. Log-transformed
body masses for primates are in dataset mass.primates, and fish
body sizes are in dataset traits.fishes.
The MCMC output files (mcmc.whales and mcmc.primates)
are dataframes containing the raw MCMC output as generated by
BAMM. Column headers in the dataframes includes the sampling
generation, the current number of shifts in the simulation
(N_shifts), the log-prior density of the parameters
(logPrior), the log-likelihood of the data (logLik), the
current parameter of the Poisson process governing the number of
regime shifts (eventRate), and the MCMC acceptance rate
(acceptRate). This is the file that would typically be analyzed
as a first step towards assessing MCMC convergence (e.g., analyzing
effective sample sizes of logLik and N_shifts).
The "core" BAMM output is included in the event data
files (events.whales, events.primates and
events.fishes). These are all the parameters sampled with MCMC
that are relevant to reconstructing the nature and location of
evolutionary rate dynamics across a phylogeny. Please refer to
BAMM documentation for a detailed overview of this output, but
a brief description is as follows:
generation: The index value of the state in the MCMC simulation
(the "generation").
leftchild, rightchild: This defines a unique topological
location where a rate shift was sampled. Specifically, for given
right-left pair, the shift is sampled on the branch leading to the
node from which rightchild and leftchild are descended
(these two taxa are part of the spanning set of taxa for the node). If
leftchild is "NA", this simply means that the shift was sampled
on a terminal branch.
abstime: The absolute occurrence time of the shift, assuming
that the time of the root node is 0.0.
lambdainit, lambdashift: For speciation extinction model, the
initial speciation rate and rate change parameter for the process.
muinit: For speciation extinction model, the extinction rate
(time-invariant).
betainit, betashift: For phenotypic evolutionary model, the
initial (betainit) rate of phenotypic evolution and the rate
change parameter (betashift).