Lposterior: Return a posterior of shift locations
In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies
Description
Usage
Arguments
Value
Description
Return a posterior of shift locations
Usage
1
Lposterior(chain, tree, burnin = 0, simpar = NULL, mag = TRUE)
Arguments
chain
A bayouMCMC chain
tree
A tree of class 'phylo'
burnin
A value giving the burnin proportion of the chain to be discarded
simpar
An optional bayou formatted parameter list giving the true values (if data were simulated)
mag
A logical indicating whether the average magnitude of the shifts should be returned
Value
A data frame with rows corresponding to postordered branches. pp indicates the
posterior probability of the branch containing a shift. magnitude of theta2 gives the average
value of the new optima after a shift. naive SE of theta2 gives the standard error of the new optima
not accounting for autocorrelation in the MCMC and rel location gives the average relative location
of the shift on the branch (between 0 and 1 for each branch).
bayou documentation built on May 2, 2019, 2:46 a.m.
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Description Usage Arguments Value
Description
Return a posterior of shift locations
Usage
1 | Lposterior(chain, tree, burnin = 0, simpar = NULL, mag = TRUE)
|
Arguments
chain |
A bayouMCMC chain |
tree |
A tree of class 'phylo' |
burnin |
A value giving the burnin proportion of the chain to be discarded |
simpar |
An optional bayou formatted parameter list giving the true values (if data were simulated) |
mag |
A logical indicating whether the average magnitude of the shifts should be returned |
Value
A data frame with rows corresponding to postordered branches. pp indicates the
posterior probability of the branch containing a shift. magnitude of theta2 gives the average
value of the new optima after a shift. naive SE of theta2 gives the standard error of the new optima
not accounting for autocorrelation in the MCMC and rel location gives the average relative location
of the shift on the branch (between 0 and 1 for each branch).
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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