get_node_support: Get node support from a tree produced with IQTREE

In harrietr: Wrangle Phylogenetic Distance Matrices and Other Utilities

Description

In IQTREE it is possible to obtain node support values by SH aproximate likelihood ratio tests (SH-aLRT), and ultrafast bootstraps (uBS). Often, we do both, which IQTREE encodes as two numbers separated by a '/' as the internal node label. This function will return a data.frame with the number of the internal nodes, and the support values for each.

Usage

get_node_support(tree)

Arguments

tree	An object of type phylo generated using IQTREE

Value

A data.frame with internal node information, plus two columns: (1) SH-aLRT; and (2) uBS

Examples

## Not run: 
data(woodmouse_iqtree)
get_node_support(woodmouse_iqtree)

## End(Not run)

Example output

Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
# A tibble: 13 x 10
   parent  node branch.length `SH-aLRT`   uBS isTip       x     y  branch angle
    <int> <int>         <dbl>     <dbl> <int> <lgl>   <dbl> <dbl>   <dbl> <dbl>
 1     16    16      0             NA      NA FALSE 0        3.49 0        83.9
 2     16    17      0.00389       85.7    84 FALSE 0.00389  7.48 0.00195 180. 
 3     17    18      0.00215       84.6    77 FALSE 0.00604 10.3  0.00497 248. 
 4     18    19      0.00216       91.9    91 FALSE 0.00820  8.75 0.00712 210  
 5     19    20      0.00273       86.8    89 FALSE 0.0109   9.5  0.00957 228  
 6     18    21      0.000002       0      47 FALSE 0.00605 11.9  0.00605 286. 
 7     21    22      0.00105       38.9    61 FALSE 0.0071  12.9  0.00657 309  
 8     22    23      0.00108       77.3    80 FALSE 0.00818 13.8  0.00764 330  
 9     23    24      0.00227       87.5    93 FALSE 0.0105  14.5  0.00932 348  
10     17    25      0.00225       82.5    81 FALSE 0.00614  4.62 0.00502 111  
11     25    26      0.00776       99.1   100 FALSE 0.0139   5.75 0.0100  138  
12     26    27      0.00107        0      50 FALSE 0.0150   6.5  0.0144  156  
13     25    28      0.000002       0      68 FALSE 0.00615  3.5  0.00614  84  
Warning messages:
1: `mutate_()` is deprecated as of dplyr 0.7.0.
Please use `mutate()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: `filter_()` is deprecated as of dplyr 0.7.0.
Please use `filter()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

harrietr documentation built on May 2, 2019, 3:37 p.m.