R/extractSpeInfo.R

In NicheBarcoding: Niche-model-Based Species Identification

#' Extraction of taxon/species  and distribution information
#'
#' @description Split comma-separated sample information into different columns
#' of a data frame.
#'
#' @param  seqID.full Character, sample ID, taxon information and longitude and
#' latitude data that splitted by comma in class character.
#'
#' @return A data frame of splitted sample ID, taxon information and longitude 
#' and latitude data for further analysis.
#'
#' @keywords extractSpeInfo
#' @export
#'
#' @author 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.
#'
#'
#' @examples
#' data(LappetMoths)
#' ref.seq<-LappetMoths$ref.seq
#' seqID.full<-rownames(ref.seq)
#'
#' infor<-extractSpeInfo(seqID.full)
#' head(infor)


extractSpeInfo<-function(seqID.full){
  pattern.ref<-"^[-\\.[:alnum:][:space:]_]+,[-\\.[:alnum:][:digit:][:space:]_]+,[-\\.[:digit:][:space:]]+$"
  pattern.que<-"^[-\\.[:alnum:][:space:]_]+,[-\\.[:digit:][:space:]]+$"

  seqID.full.as.list<-as.list(seqID.full)
  seqID.ok.ref<-sapply(seqID.full.as.list,grepl,pattern=pattern.ref)
  seqID.ok.que<-sapply(seqID.full.as.list,grepl,pattern=pattern.que)

  if(!(all(seqID.ok.ref)==TRUE)&&!(all(seqID.ok.que)==TRUE)){
    cat("bad format:",seqID.full[which(seqID.ok.ref==FALSE)],"\n")
    #stop ("The input data must BE like \n (ref):>ABLRP543-09,Agamidae_Phrynocephalus_helioscopus,61.367 46.228 !\n or (que):>ABLRP543-09,61.367 46.228 !\n")
  }else{### format is ok!
    if(all(seqID.ok.ref)==TRUE){
      SppDistrRef<-gsub("^[-\\.[:alnum:]]+,","",seqID.full)
      mpattern<-",[-\\.[:alnum:][:space:]_]+$" ##
      seqIDs<-gsub(mpattern,"",seqID.full)
      seqIDs<-gsub(mpattern,"", seqIDs)
      strTmp<-strsplit(SppDistrRef,",")
      strTmp2<-unlist(strTmp)
      strTmp3<-as.data.frame(strTmp2)
      id.index<-seq(1,dim(strTmp3)[1],by=2)
      coor.index<-seq(2,dim(strTmp3)[1],by=2)
      spe<-strTmp3$strTmp2[id.index]
      spe<-as.vector(spe)
      longLat<-strTmp3$strTmp2[coor.index]
      longLat<-as.vector(longLat)
      longLat2<-unlist(strsplit(longLat," "))
      long<-as.numeric(longLat2[id.index])
      lat<-as.numeric(longLat2[coor.index])
      SppDistrRef<-data.frame(no.= c(1:length(spe)),
                              seqIDs =  seqIDs,
                              species = spe,
                              Lon = long,
                              Lat = lat
                              )
      return(SppDistrRef)

    }else{### for query:

      SppDistrQue<-gsub("^[-\\.[:alnum:]]+,","",seqID.full)
      mpattern<-",[-\\.[:alnum:][:space:]_]+$" ##
      seqIDs<-gsub(mpattern,"",seqID.full)

      id.index<-seq(1,length(SppDistrQue)*2,by=2)
      coor.index<-seq(2,length(SppDistrQue)*2,by=2)

      longLat<-SppDistrQue
      longLat<-as.vector(longLat)
      longLat2<-unlist(strsplit(longLat," "))
      long<-as.numeric(longLat2[id.index])
      lat<-as.numeric(longLat2[coor.index])
      SppDistrQue<-data.frame(no.= c(1:length(seqIDs)),
                              seqIDs =  seqIDs,
                              species = "unknown",
                              Lon = long,
                              Lat = lat
      )
      return(SppDistrQue)
    }
  } ### the end of else-loop
}

# The end of extractSpeInfo #