| TDR2 {BarcodingR} | R Documentation |
TDR2 Species Membership Value
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