BAMMtools-data {BAMMtools} | R Documentation |
BAMMtools datasets
Description
Example datasets and sample BAMM
output for the
package BAMMtools
.
Details
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
).
Source
Vos R.A., A.O. Mooers. 2006. A new dated supertree of the Primates. Chapter 5. In Inferring large phylogenies: the big tree problem (R Vos, Ph.D. thesis) Simon Fraser University.
Redding D.W., C. DeWolff, A.O. Mooers. 2010. Evolutionary distinctiveness, threat status and ecological oddity in primates. Conservation Biology 24: 1052-1058. DOI: 10.1111/j.1523-1739.2010.01532.x
Steeman, M.E., M.B. Hebsgaard, R.E. Fordyce, S.W.Y. Ho, D.L. Rabosky, R. Nielsen, C. Rahbek, H. Glenner, M.V. Sorensen, E. Willerslev. 2009. Radiation of Extant Cetaceans Driven by Restructuring of the Oceans. Systematic Biology. 58: 573-585. DOI: 10.1093/sysbio/syp060
Rabosky, D. L., F. Santini, J.T. Eastman, S. . Smith, B.L. Sidlauskas, J. Chang, and M.E. Alfaro. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications DOI: 10.1038/ncomms2958.