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

Description Usage Arguments Value Author(s) Examples

View source: R/duplicated.nex.R

Description

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

Usage

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## S3 method for class 'nex'
duplicated(x, 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

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)

Value

an object of class nex for use in further phenotools functions

Author(s)

Chad Eliason celiason@fieldmuseum.org

Examples

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## 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. 12, 2019, 6:49 p.m.