read.codeml: read.codeml

In treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

Description

read baseml output

Usage

read.codeml(rstfile, mlcfile, tree = "mlc", type = "Joint")

Arguments

rstfile	rst file
mlcfile	mlc file
tree	one of 'mlc' or 'rst'
type	one of 'Marginal' or 'Joint'

Value

A treedata object

Author(s)

Guangchuang Yu

Examples

rstfile <- system.file("extdata/PAML_Codeml", "rst", package="treeio")
mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio")
read.codeml(rstfile, mlcfile)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:treeio':

    mask

The following object is masked from 'package:base':

    strsplit

'codeml' S4 object that stored information of
	 '/usr/local/lib/R/site-library/treeio/extdata/PAML_Codeml/rst' and 
	'/usr/local/lib/R/site-library/treeio/extdata/PAML_Codeml/mlc'. 

...@ tree:
Phylogenetic tree with 15 tips and 13 internal nodes.

Tip labels:
	A, B, C, D, E, F, ...
Node labels:
	16, 17, 18, 19, 20, 21, ...

Unrooted; includes branch lengths.

with the following features available:
	'marginal_subs',	'joint_subs',	'marginal_AA_subs',	'joint_AA_subs',	't',	'N',
	'S',	'dN_vs_dS',	'dN',	'dS',	'N_x_dN',	'S_x_dS'.

treeio documentation built on Nov. 21, 2020, 2:01 a.m.