read rst file from paml (both baseml and codeml) output

read.paml_rst(rstfile, type = "Joint")

Arguments

rstfile

rst file

type

one of 'Marginal' or 'Joint'

Value

A treedata object

Author

Guangchuang Yu https://guangchuangyu.github.io

Examples

rstfile <- system.file("extdata/PAML_Baseml", "rst", package="treeio")
read.paml_rst(rstfile)
#> 'treedata' S4 object that stored information
#> of
#> 	'/usr/local/lib/R/site-library/treeio/extdata/PAML_Baseml/rst'.
#> 
#> [email protected] phylo:
#> 
#> 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:
#>   'subs', 'AA_subs'.
#> 
#> # The associated data tibble abstraction: 28 × 5
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#>     node label isTip subs                            AA_subs                    
#>    <dbl> <chr> <lgl> <chr>                           <chr>                      
#>  1     1 A     TRUE  C214T / G294T / G785A / T966C … "R262K / K603R"            
#>  2     2 B     TRUE  C222T / G555A / C732A / G785A … "R262K"                    
#>  3     3 C     TRUE  A204G / C222T / G504A / A815G … "N272S / I354T"            
#>  4     4 D     TRUE  A111G / A168G / T211C / A213G … "K104R / F105L / E382D / F…
#>  5     5 E     TRUE  C174T / G243A / G321A / A622T … "T208S / V379I / K609R"    
#>  6     6 F     TRUE  T829C / C1353T / A1443G / T154… "S277P / L549I"            
#>  7     7 G     TRUE  A5T / A69G / G106T / C156T / C… "E2V / A36S / G99R / E101Q…
#>  8     8 H     TRUE  A112G / C132A / G774T / A792C … "I38V / E258D / T570I"     
#>  9     9 I     TRUE  T211C / C582T / C891T / A894G … ""                         
#> 10    10 J     TRUE  G295A / A618G / A783C / C996T … "G99R"                     
#> # … with 18 more rows