bbsik {BarcodingR} | R Documentation |
Species identification using BP-based method for both protein-coding barcodes, for instance, COI, and non-coding barcodes, such as, ITS, using kmer statistics.
bbsik(ref, que, kmer = kmer, UseBuiltModel = FALSE, lr = 5e-05, maxit = 1e+06)
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. |
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).
Ai-bing ZHANG, Meng-di HAO, Cai-qing YANG, CNU, Beijing, CHINA. zhangab2008 (at) mail. cnu. edu.cn
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.
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