BarcodingR (version 1.0-3)

barcoding.spe.identify: Species Identification using Protein-coding Barcodes

Description

Species identification using protein-coding barcodes with different methods,including BP-based method (Zhang et al. 2008), fuzzy-set based method (Zhang et al. 2012), Bayesian-based method (Jin et al. 2013).

Usage

barcoding.spe.identify(ref, que, method = "bpNewTraining")

Arguments

ref

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

que

object of class "DNAbin", whose identities (species names) need to be inferred.

method

a character string indicating which method will be used to train model and/or infer species membership. One of these methods ("fuzzyId", "bpNewTraining", "bpNewTrainingOnly", "bpUseTrained","Bayesian") should be specified.

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 / FMF values for fuzzy set theory based method / posterior probability for Bayesian method) when available.

References

Zhang, A. B., M. D. Hao, C. Q. Yang, and Z. Y. Shi. (2017). BarcodingR: an integrated R package for species identification using DNA barcodes. Methods Ecol Evol. 8(5):627-634. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12682.

Jin,Q., H.L. Han, X.M. Hu, X.H. Li,C.D. Zhu,S. Y. W. Ho, R. D. Ward, A.B. Zhang . (2013). Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau. PloS One 8: e644. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064428.

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. https://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05235.x

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://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12682

Examples

# NOT RUN {
data(TibetanMoth)
ref<-as.DNAbin(as.character(TibetanMoth[1:5,]))
que<-as.DNAbin(as.character(TibetanMoth[50:55,]))
bsi<-barcoding.spe.identify(ref, que, method = "fuzzyId")
bsi
bsi<-barcoding.spe.identify(ref, que, method = "bpNewTraining")
bsi
bsi<-barcoding.spe.identify(ref, que, method = "Bayesian")
bsi
# }