locmin_tbl: Turns Local Minima Results into a Tibble

In delimtools: Helper Functions for Species Delimitation Analysis

Turns Local Minima Results into a Tibble

Description

locmin_tbl() processes output from tclust into an object of class tbl_df.

Usage

locmin_tbl(distobj, threshold = 0.01, haps = NULL, delimname = "locmin")

Arguments

distobj	A distance object (usually from dist.dna).
threshold	Distance cutoff for clustering. Default of 0.01. See localMinima for details.
haps	Optional. A vector of haplotypes to keep into the tbl_df.
delimname	Character. String to rename the delimitation method in the table. Default to 'locmin'.

Details

spider package uses localMinima to determine possible thresholds for any distance matrix and tclust to cluster samples within a given threshold into species partitions. locmin_tbl() turns these inputs into a tibble which matches the output from gmyc_tbl and bgmyc_tbl.

Value

An object of class tbl_df.

Author(s)

Samuel Brown.

Source

Brown S.D.J., Collins R.A., Boyer S., Lefort M.-C., Malumbres-Olarte J., Vink C.J., Cruickshank, R.H. 2012. Spider: An R package for the analysis of species identity and evolution, with particular reference to DNA barcoding. Molecular Ecology Resources, 12: 562-565.

Examples

# create a distance matrix
mat <- ape::dist.dna(geophagus, model = "raw", pairwise.deletion = TRUE)

# run Local Minima
locmin_res <- spider::localMinima(mat)

# create a tibble
locmin_df <- locmin_tbl(mat, 
                        threshold = locmin_res$localMinima[1], 
                        haps = ape::as.phylo(geophagus_beast)$tip.label)

# check
locmin_df 

delimtools documentation built on April 3, 2025, 9:28 p.m.