TDR2: TDR2 Species Membership Value

In BarcodingR: Species Identification using DNA Barcodes

Description

To calculate TDR value for a set of queries and one potential species. Its value is in the range of [0,1], 0 indicates extremly weak species membership, values close 1 indicating strong species membership.

Usage

TDR2(oneSpe, que, boot, boot2)

Arguments

oneSpe	object of class "DNAbin" which contains DNA sequences from one species
que	object of class "DNAbin" which contains DNA sequences different samples
boot	a numeric value indicating times of resampling along sequence columns
boot2	a numeric value indicating times of resampling along sequence rows (different samples)

Value

a numeric vector represents TDR values for each query against the species

Note

oneSpe and que should be the same in sequence length, i.e., they should be aligned in prior. It's strongly recommended that oneSpe should have large enough sample size,e.g., 20.

Author(s)

Ai-bing ZHANG, PhD. CNU, Beijing, CHINA, contact at zhangab2008(at)mail.cnu.edu.cn

References

Jin Q, L,J.He, A.B. Zhang* (2012). A Simple 2D Non-Parametric Resampling Statistical Approach to Assess Confidence in Species Identification in DNA Barcoding-An Alternative to Likelihood and Bayesian Approaches. PLoS ONE 7(12): e50831. doi:10.1371/ journal. pone. 0050831. http://dx.plos.org/ 10.1371/ journal. pone. 0050831.

Examples

data(TibetanMoth)  
sampleSpeNames<-NAMES(TibetanMoth)
Spp<-gsub(".+,","",sampleSpeNames)
oneSpe<-TibetanMoth[grep("Macdunnoughia_crassisigna", Spp, value = FALSE,fixed = TRUE),] 
oneSpe<-as.DNAbin(as.character(oneSpe[1:5,]))
que<-TibetanMoth[grep("Agrotis_justa", Spp, value = FALSE,fixed = TRUE),] 
que2<-oneSpe[1:2,]
out<-TDR2(oneSpe,que, boot=10,boot2=10) ### true false identification

BarcodingR documentation built on April 14, 2020, 6:04 p.m.