phymltest(seqfile, format = "interleaved", itree = NULL,
exclude = NULL, execname = NULL, path2exec = NULL)
## S3 method for class 'phymltest':
print(x, ...)
## S3 method for class 'phymltest':
summary(object, ...)
## S3 method for class 'phymltest':
plot(x, ...)
"interleaved"
(the default), or
"sequential"
.NULL
(the default), PHYML uses a ``BIONJ'' tree.NULL
and the operating system is ``windows'',
the default name "phyml_w32"
is used, otherwise the name must
be given.NULL
the file must be accessible to R (either
it is in the computer path, or it is in R's working directory)."phymltest"
."phymltest"
.phymltest
returns an object of class "phymltest"
: a
numeric vector with the models as names.
The print
method prints an object of class "phymltest"
as matrix with the name of the models, the number of free parameters,
the log-likelihood value, and the value of the Akaike information
criterion (AIC = -2 * loglik + 2 * number of free parameters)
The summary
method prints all the possible likelihood ratio
tests for an object of class "phymltest"
.
The plot
method plots the values of AIC of an object of class
"phymltest"
on a vertical scale.dist.dna
.
When a gamma distribution of substitution rates is specified, four
categories are used (which is PHYML's default behaviour), and the
``alpha'' parameter is estimated from the data.
For the models with a different substition rate for transitions and
transversions, these rates are left free and estimated from the data
(and not constrained with a ratio of 4 as in PHYML's default).read.tree
, write.tree
,
dist.dna
### A "fake" example with random likelihood values: it does not
### make sense, but does not need PHYML and gives you a flavour
### of how the output looks like:
x <- runif(28, -100, -50)
names(x) <- .phymltest.model
class(x) <- "phymltest"
x
summary(x)
plot(x)
### This example needs PHYML, copy/paste or type the
### following commands if you want to try them, eventually
### changing setwd() and the options of phymltest()
setwd("D:/phyml_v2.4/exe") # under Windows
data(woodmouse)
write.dna(woodmouse, "woodmouse.txt")
X <- phymltest("woodmouse.txt")
X
summary(X)
plot(X)
Run the code above in your browser using DataCamp Workspace