NBSI {NicheBarcoding} | R Documentation |
Niche-model-Based Species Identification (NBSI)
Description
Species identification using DNA barcoding integrated with niche model.
Usage
NBSI(
ref.seq,
que.seq,
model = "RF",
independence = TRUE,
ref.add = NULL,
variables = "ALL",
en.vir = NULL,
bak.vir = NULL
)
Arguments
ref.seq |
DNAbin, the reference dataset containing sample IDs, taxon information,longitude and latitude, and barcode sequences of samples. |
que.seq |
DNAbin, the query dataset containing sample IDs, longitude and latitude, and barcode sequences of samples. |
model |
Character, string indicating which niche model will be used. Must be one of "RF" (default) or "MAXENT". "MAXENT" can only be applied when the java program paste(system.file(package="dismo"), "/java/maxent.jar", sep=”) exists. |
independence |
Logical. Whether the barcode sequences are related to the ecological variables? |
ref.add |
Data.frame, the additional coordinates collected from GBIF or literatures. |
variables |
Character, the identifier of selected bioclimate variables. Default of "ALL" represents to use all the layers in en.vir; the alternative option of "SELECT" represents to randomly remove the highly-correlated variables (|r| larger than 0.9) with the exception of one layer. |
en.vir |
RasterBrick, the global bioclimate data output from "raster::getData" function. |
bak.vir |
Matrix, bioclimate variables of random background points. |
Value
A dataframe of barcoding identification result for each query sample and corresponding niche model-based probability.
Author(s)
Cai-qing YANG (Email: yangcq_ivy(at)163.com) and Ai-bing ZHANG (Email:zhangab2008(at)cnu.edu.cn), Capital Normal University (CNU), Beijing, CHINA.
References
Breiman, L. 2001. Random forests. Machine Learning 45(1):5-32.
Liaw, A. and M. Wiener. 2002. Clasification and regression by randomForest. R News, 2/3:18-22.
Phillips, S.J., R.P. Anderson and R.E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190:231-259.
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 in Ecology and Evolution, 8:627-634.
Jin, Q., H.L. Han, X.M. Hu, X.H. Li, C.D. Zhu, S.Y.W. Ho, R.D. Ward and 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.
Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25(15):1965-1978.
Examples
data(en.vir)
data(bak.vir)
#envir<-raster::getData("worldclim",download=FALSE,var="bio",res=2.5)
#en.vir<-raster::brick(envir)
#back<-dismo::randomPoints(mask=en.vir,n=5000,ext=NULL,extf=1.1,
# excludep=TRUE,prob=FALSE,
# cellnumbers=FALSE,tryf=3,warn=2,
# lonlatCorrection=TRUE)
#bak.vir<-raster::extract(en.vir,back)
library(ape)
data(LappetMoths)
ref.seq<-LappetMoths$ref.seq[1:50,]
que.seq<-LappetMoths$que.seq[1:5,]
NBSI.out<-NBSI(ref.seq,que.seq,ref.add=NULL,
independence=TRUE,
model="RF",variables="SELECT",
en.vir=en.vir,bak.vir=bak.vir)
NBSI.out
### Add a parameter when additional reference coordinates are available ###
#ref.add<-LappetMoths$ref.add
#NBSI.out2<-NBSI(ref.seq,que.seq,ref.add=ref.add,
# independence=TRUE,
# model="RF",variables="SELECT",
# en.vir=en.vir,bak.vir=bak.vir)
#NBSI.out2