Description Usage Arguments Details Value Author(s) References See Also Examples
Provides a wrapper for Bayesian phylogenetic tree search through MrBayes (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003).
1 2 |
x |
An object of class |
file |
A character string, giving the name of the MrBayes input file. |
lset |
A list as returned by |
prset |
A list as returned by |
mcmc |
A list as returned by |
unlink |
|
constraint |
|
burnin |
An integer; the number of samples from the MCMC to be discarded prior to further analysis. |
contype |
A character string; the type of consensus tree calculated from the posterior distribution of trees: either |
exec |
A character string giving the full path of the MrBayes program. |
run |
Logical; |
mrbayes
was last updated and tested with MrBayes v3.2.2 under R 3.1.0 on a x86_64-apple-darwin10.8.0 (64-bit) platform. It is intended to offer a simply parameterized building block for larger scripts.
None; a NEXUS file with MrBayes block is written to a file and, if run = TRUE
, the MCMC runs in MrBayes are started.
Christoph Heibl
J. P. Huelsenbeck & Ronquist F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
Ronquist F. & J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Biometrics 19: 1572-1574.
MrBayes website: http://mrbayes.sourceforge.net/.
mafft
and prank
for sequence alignment; raxml for maximum likelihood tree search.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
data(ips.cox1)
x <- ips.cox1[, 100:140] # tiny alignment
mrbayes(x, file = "", mcmc = mrbayes.mcmc(ngen = 100), run = FALSE)
## Not run:
library(phangorn)
tree <- rtree(10)
Y1 <- simSeq(tree, l = 20)
Y2 <- simSeq(tree, l = 20, type = "USER", levels=c("0", "1"))
Y <- cbind(as.character(Y1), as.character(Y2))
mrbayes(Y, file = "", run = FALSE)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.