Description Usage Arguments Details Value Note Author(s) References See Also Examples

`getEventData`

Reads shift configuration data (the
"event data" output) from a `BAMM`

analysis and creates a
`bammdata`

object. The `bammdata`

object is fundamental
for extracting information about macroevolutionary rate variation
through time and among lineages.

1 2 | ```
getEventData(phy, eventdata, burnin = 0, nsamples = NULL, verbose = FALSE,
type = "diversification")
``` |

`phy` |
An object of class |

`eventdata` |
A character string specifying the path to a |

`burnin` |
A numeric indicating the fraction of posterior samples to discard as burn-in. |

`nsamples` |
An integer indicating the number of posterior samples to
include in the |

`verbose` |
A logical. If |

`type` |
A character string. Either "diversification" or "trait"
depending on your |

In the `BAMM`

framework, an "event" defines a
macroevolutionary process of diversification or trait evolution. Every
sample from the posterior includes at least one process, defined by
such an "event". If a given sample includes just a single event, then
the dynamics of diversification or trait evolution can be described
entirely by a single time-constant or time-varying process that begins
at the root of the tree. Any sample from the posterior distribution
may include a complex mixture of distinct processes. To represent
temporal heterogeneity in macroevolutionary rates, `BAMM`

models
a rate *R*, e.g. speciation, as a function that changes
exponentially with time:

*R(t) = R(0)*exp(b*t)*.

Here *R(0)* is the initial rate and *b* is a parameter
determining how quickly that rate grows or decays with time.

The `eventdata`

file (or data frame) is a record of events and
associated parameters that were sampled with `BAMM`

during
simulation of the posterior with reversible jump MCMC. This complex,
information-rich file is processed into a `bammdata`

object,
which serves as the core data object for numerous downstream analyses.
From a `bammdata`

object, you can summarize rate variation
through time, among clades, extract locations of rate shifts,
summarize clade-specific rates of speciation and extinction, and more.

In general, the user does not need to be concerned with the details of
a `bammdata`

object. The object is used as input by a number of
`BAMMtools`

functions.

The parameter `nsamples`

can be used to reduce the total amount
of data included in the raw eventdata output from a `BAMM`

run.
The final `bammdata`

object will consist of all data for
`nsamples`

from the posterior. These `nsamples`

are equally
spaced after discarding some `burnin`

fraction as "burn-in". If
`nsamples`

is set to `NULL`

, the `bammdata`

object will
include all samples in the posterior after discarding the
`burnin`

fraction.

A list with many components:

edge See documentation for class

`phylo`

in package ape.Nnode See documentation for class

`phylo`

in package ape.tip.label See documentation for class

`phylo`

in package ape.edge.length See documentation for class

`phylo`

in package ape.begin The beginning time of each branch in absolute time (the root is set to time zero)

end The ending time of each branch in absolute time.

numberEvents An integer vector with the number of events contained in

`phy`

for each posterior sample. The length of this vector is equal to the number of posterior samples in the`bammdata`

object.eventData A list of dataframes. Each element is a single posterior sample. Each row in a dataframe holds the data for a single event. Data associated with an event are:

`node`

- a node number. This identifies the branch where the event originates.`time`

- this is the absolute time on that branch where the event originates (with the root at time 0).`lam1`

- an initial rate of speciation or trait evolution.`lam2`

- a decay/growth parameter.`mu1`

- an initial rate of extinction.`mu2`

- a decay/growth parameter.`index`

- a unique integer associated with the event. See 'Details'.eventVectors A list of integer vectors. Each element is a single posterior sample. For each branch in

`phy`

the index of the event that occurs along that branch. Branches are ordered increasing here and elsewhere.eventBranchSegs A list of matrices. Each element is a single posterior sample. Each matrix has four columns:

`Column 1`

identifies a node in`phy`

.`Column 2`

identifies the beginning time of the branch or segment of the branch that subtends the node in`Column 1`

.`Column 3`

identifies the ending time of the branch or segment of the branch that subtends the node in`Column 1`

.`Column 4`

identifies the index of the event that occurs along the branch or segment of the branch that subtends the node in`Column 1`

.tipStates A list of integer vectors. Each element is a single posterior sample. For each tip the index of the event that occurs along the branch subtending the tip. Tips are ordered increasing here and elsewhere.

tipLambda A list of numeric vectors. Each element is a single posterior sample. For each tip the rate of speciation or trait evolution at the end of the terminal branch subtending that tip.

tipMu A list of numeric vectors. Each element is a single posterior sample. For each tip the rate of extinction at the end of the terminal branch subtending that tip. Meaningless if working with

`BAMM`

trait results.meanTipLambda For each tip the mean of the marginal posterior density of the rate of speciation or trait evolution at the end of the terminal branch subtending that tip.

meanTipMu For each tip the mean of the marginal posterior density of the rate of extinction at the end of the terminal branch subtending that tip. Meaningless if working with

`BAMM`

trait results.type A character string. Either "diversification" or "trait" depending on your

`BAMM`

analysis.downseq An integer vector holding the nodes of

`phy`

. The order corresponds to the order in which nodes are visited by a pre-order tree traversal.lastvisit An integer vector giving the index of the last node visited by the node in the corresponding position in

`downseq`

.`downseq`

and`lastvisit`

can be used to quickly retrieve the descendants of any node. e.g. the descendants of node 89 can be found by`downseq[which(downseq==89):which(downseq==lastvisit[89])`

.

Currently the function does not check for duplicate tip labels in
`phy`

, which may cause the function to choke.

Dan Rabosky, Mike Grundler

`summary.bammdata`

, `plot.bammdata`

,
`dtRates`

.

1 2 3 4 5 6 7 8 9 10 | ```
data(primates, events.primates)
xx <- getEventData(primates, events.primates, burnin=0.25, nsamples=500,
type = 'trait')
# compute mean phenotypic rate for primate body size evolution:
brates <- getCladeRates(xx)
mean(brates$beta)
# Plot rates:
plot(xx)
``` |

BAMMtools documentation built on May 29, 2017, 5:47 p.m.

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