BarcodingR (version 1.0-3)

bbsik: Bp Barcoding Species Identify using Kmer

Description

Species identification using BP-based method for both protein-coding barcodes, for instance, COI, and non-coding barcodes, such as, ITS, using kmer statistics.

Usage

bbsik(ref, que, kmer = kmer, UseBuiltModel = FALSE, lr = 5e-05, maxit = 1e+06)

Arguments

ref

object of class "DNAbin" used as a reference dataset, which contains taxon information.

que

object of class "DNAbin", which needs to be inferred.

kmer

a numeric indicating the length of kmer used.

UseBuiltModel

logic value to indicate whether a built model is used or not.

lr

parameter for weight decay. Default 5e-5.

maxit

maximum number of iterations. Default 1e+6.

Value

a list containing model parameters used, species identification success rates using references, query sequences, species inferred, and corresponding confidence levels (bp probability for BP-based method).

References

Zhang, A. B., D. S. Sikes, C. Muster, S. Q. Li. (2008). Inferring Species Membership using DNA sequences with Back-propagation Neural Networks. Systematic Biology, 57(2):202-215. https://academic.oup.com/sysbio/article/57/2/202/1622290

Examples

# NOT RUN {
data(TibetanMoth) 
ref<-as.DNAbin(as.character(TibetanMoth[1:50,]))
que<-as.DNAbin(as.character(TibetanMoth[51:60,]))
out<-bbsik(ref, que, kmer = 1, UseBuiltModel = FALSE)
out
out$convergence
out$success.rates.ref

data(pineMothITS2) 
ref<-pineMothITS2
que<-pineMothITS2
out<-bbsik(ref, que, kmer = 1, UseBuiltModel = FALSE)
out
out$convergence
out$success.rates.ref



# }