alignment_entropy: Alignment entropy

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

Alignment entropy

Description

Alignment entropy

Usage

alignment_entropy(
  x,
  mask_gaps = 0.2,
  count_gaps = FALSE,
  method = "ML",
  unit = "log",
  return_extra = FALSE
)

Arguments

x	A DNAbin or AAbin object
mask_gaps	The threshold of gaps allowed before a position in the alignment is masked
count_gaps	Whether gaps should be counted within entropy calculations. Default is FALSE.
method	the method employed by entropy::entropy to estimate alignment entropy. Accepts: "ML" : maximum likelihood "MM" : bias-corrected maximum likelihood, "Jeffreys" : Dirichlet with a=1/2 "Laplace" : Dirichlet with a=1 "SG" : Dirichlet with a=a=1/length(y) "minimax" : Dirichlet with a=sqrt(sum(y))/length(y) "CS" : ChaoShen "NSB": Nemenman, Shafee and Biale (2002) "shrink" : Shrinkage estimator See the help page of entropy::entropy for more information
unit	the unit in which entropy is measured. The default is "nats" (natural units). For computing entropy in "bits" set unit="log2".
return_extra	Whether to return a dataframe including extra columns including individual base counts, gap proportions and number of bases at each position

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