FMFtheta12: Calculate Intraspecific and Interspecific Variation

In BarcodingR: Species Identification using DNA Barcodes

Description

Calculation intraspecific variation (sd) of the potential species theta1, and mean interspecific distance (here, the mean distance between the potential species and its nearest neighbor theta2) (fuzzy-set based method,slightly modified from Zhang et al. 2012). The calculation was done for all species in the reference dataset.

Usage

FMFtheta12(ref)

Arguments

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

Value

a data frame containing intraspecific (sd, theta1) and interspefic variation (mean) of all species, and their corresponding nearest neighbor (NN).

Author(s)

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

References

Zhang, A. B., C. Muster, H.B. Liang, C.D. Zhu, R. Crozier, P. Wan, J. Feng, R. D. Ward.(2012). A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Molecular Ecology, 21(8):1848-63.

Examples

data(TibetanMoth) 
ref<-as.DNAbin(as.character(TibetanMoth[1:50,]))
FMF.theta12<-FMFtheta12(ref)
FMF.theta12

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