View source: R/evol.rate.mcmc.R
evol.rate.mcmc | R Documentation |
Estimates the phylogenetic location of a single rate shift on the tree using Bayesian MCMC (as described in Revell et al., 2012b).
evol.rate.mcmc(tree, x, ngen=10000, control=list(), ...)
## S3 method for class 'evol.rate.mcmc'
print(x, ...)
## S3 method for class 'evol.rate.mcmc'
summary(object, ...)
## S3 method for class 'summary.evol.rate.mcmc'
print(x, ...)
## S3 method for class 'summary.evol.rate.mcmc'
plot(x, ...)
tree |
an object of class |
x |
a vector of tip values for species in which |
ngen |
an integer value indicating the number of generations for the MCMC. |
control |
a list of control parameters containing the following elements: |
object |
for the S3 |
... |
other optional arguments. |
This function takes a phylogenetic tree and data for a single continuously valued character and uses a Bayesian MCMC approach to identify the phylogenetic location of a shift in the evolutionary rate through time.
Default values of control
are given in Revell et al. (2012b).
An object of class "evol.rate.mcmc"
consisting of at least the following elements:
mcmc |
results from the MCMC run. |
tips |
list of tips in rate |
Liam Revell liam.revell@umb.edu
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
Revell, L. J., D. L. Mahler, P. Peres-Neto, and B. D. Redelings (2012) A new method for identifying exceptional phenotypic diversification. Evolution, 66, 135-146.
anc.Bayes
, brownie.lite
, evol.vcv
, minSplit
, posterior.evolrate
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