lca_probs: Probabilitys of sharing a rank as a function of sequence...

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

Probabilitys of sharing a rank as a function of sequence identity

Description

Probabilitys of sharing a rank as a function of sequence identity

Usage

lca_probs(
  x,
  method = "mbed",
  k = 5,
  nstart = 20,
  ranks = c("kingdom", "phylum", "class", "order", "family", "genus", "species"),
  delim = ";"
)

Arguments

x	a DNAbin object or an object coercible to DNAbin
method	The distance matrix computation method to use, accepts "mbed" which computes a distance matrix from each sequence to a subset of 'seed' sequences using the method outlined in Blacksheilds et al (2010). This scales well to big datasets, alternatively "kdist" computes the full n * n distance matrix.
k	integer giving the k-mer size used to generate the input matrix for k-means clustering.
nstart	value passed to nstart passed to kmeans. Higher increases computation time but can improve clustering accuracy considerably.
ranks	The taxonomic ranks currently assigned to the names
delim	The delimiter used between ranks

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.