getAlignmentSupport: Rboretum Alignment Signal Support Mapper
In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

getAlignmentSupport

R Documentation

Rboretum Alignment Signal Support Mapper

Description

This function maps phylogenetic signal from one or more multiple-sequence alignments onto a rooted phylo or multiPhylo object, or a set of specified clades

Usage

getAlignmentSupport(
  signal,
  tree,
  include_root,
  clade,
  dataset_name,
  max_missing,
  separate_signal,
  only_parsinf,
  include_gap,
  only_gap,
  only_biallelic,
  only_triallelic,
  only_quadallelic,
  only_pentallelic,
  return_integer,
  return_table,
  existing_support
)

Arguments

`signal`	Output from getAlignmentSignal()
`tree`	OPTIONAL: Tree(s) onto which alignment signal will be mapped. Not considered if 'clade' argument is used. Tree options include: A rooted phylo object A rooted multiPhylo object where all trees share 3+ taxa
`include_root`	OPTIONAL: If TRUE and using a 'tree', return alignment support for root clades as well [Default: FALSE, don't include root clades]
`clade`	OPTIONAL: Character vector of semicolon-separted taxa specifying specific clades of interest (i.e. get support for specific clade(s) rather than a whole tree). Supercedes 'tree' argument
`dataset_name`	OPTIONAL: Character vector containing a new name for each alignment dataset in 'signal', [Default: Alignment name from signal dataframe + 'm_<MISSING>']
`max_missing`	OPTIONAL: Number of missing sites allowed in alignment column before it is not considered [Default: Taxa Count - 3]
`separate_signal`	OPTIONAL: If FALSE, return values as the sum of all datasets [Default: TRUE, return results separated by dataset]
`only_parsinf`	OPTIONAL: If TRUE, do not count sites with singletons as part of total support (i.e. parsimony-informative sites) [Default: FALSE, allow sites with singletons to contribute data]
`include_gap`	OPTIONAL: If FALSE, count sites with gap positions ('-') as missing data; otherwise, count gaps as valid indel data [Default: TRUE: Gaps are treated as indel signal]
`only_gap`	OPTIONAL: TRUE or FALSE; Only count sites with gap positions ('-') [Default: FALSE]
`only_biallelic`	OPTIONAL: If TRUE, only count sites with biiallelic variation as part of total support [Default: FALSE]
`only_triallelic`	OPTIONAL: If TRUE, only count sites with triallelic variation as part of total support [Default: FALSE]
`only_quadallelic`	OPTIONAL: If TRUE, only count sites with quadallelic variation as part of total support [Default: FALSE]
`only_pentallelic`	OPTIONAL: If TRUE, only count sites with pentallelic variation as part of total support [Default: FALSE]
`return_integer`	OPTIONAL: If TRUE, return the integer support summed across datasets [Default: FALSE, return results as a dataframe]
`return_table`	OPTIONAL: If TRUE, return entire table of filtered signal counts by clade [FALSE: Return clade support counts]
`existing_support`	OPTIONAL: Append these results to the output from getAlignmentSupport() run with the same 'tree' and different alignment options