duplicated.nex: Find duplicate or overlapping characters in nexus files

In celiason/phenotools: Tools for the analysis and assembly of phenomic data in R

Find duplicate or overlapping characters in nexus files

Description

Function uses fuzzy text matching to output a list of potentially overlapping characters in a 'nex' object

Usage

## S3 method for class 'nex'
duplicated(
  x,
  incomparables = FALSE,
  opt = c("fuzzy", "terms", "comments", "traitcor"),
  method = NULL,
  within_dataset = FALSE,
  commasep = FALSE,
  weighting = c(1, 1, 1),
  K = 1,
  cluster = c("infomap", "fast_greedy", "walktrap", "label_prop", "leading_eigen",
    "louvain", "optimal", "spinglass"),
  cores = 1,
  latin = TRUE,
  ...
)

Arguments

x	(required) a 'nex' object
incomparables	unused argument
opt	method to use for finding duplicates
method	specific method arguments to pass to functions
within_dataset	whether to limit search to only among-dataset characters (e.g., useful if you are certain the individual matrices do not contain duplicates)
commasep	whether characters should be split into parts based on commas
weighting	vector for parts of character (before comma, after comma, character states)
K	number of clusters (if 1 cluster are found automatically according to method specified with 'cluster=')
cluster	clustering algorithm to use for finding overlapping characters
cores	how many cores to use (for parallel processing in traitcor option)
latin	whether to use Schinke Latin stemmer (logical)
...	additional arguments (unused)

Value

an object of class nex for use in further phenotools functions

Author(s)

Chad Eliason [e-mail]

Examples

## Not run: 
x1 <- read.nex(system.file("extdata", "clarke_2006.nex", package = "phenotools"))
x2 <- read.nex(system.file("extdata", "nesbitt_2015.nex", package = "phenotools"))
x <- concat(list(x1, x2))
x.dup <- duplicated.nex(x, opt = "terms")
# printout(x.dup, file="testprintout.html")

## End(Not run)

celiason/phenotools documentation built on Sept. 29, 2024, 5:43 p.m.