Alignment entropy

Alignment entropy

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