R/QL.R

In ZhuLeZi/leplant: Description of community characteristics

QL<-function(com,cp,n=5){
  com<-jz_data(com)
  cp<-cp
  cp<-data.frame(sp=cp$TAXA_NAME,D=cp$D)
  cat<-n+1
  new_com<-merge(com,cp,by = 'sp')

  ####按层片，物种数总数
  sum_cp<-tapply(new_com$sp,list(new_com$site,new_com$D),length)%>%jz_data()
  names(sum_cp)<-c("site","D","物种数","xh")
  sum_cp<-sum_cp[,-4]
  ####按层片，重要值总数
  iv_cp<-tapply(new_com$iv, list(new_com$site,new_com$D), sum)%>%jz_data()
  names(iv_cp)<-c("site","D","D_iv","xh")
  ###层片内最大的IV值
  max_cp_sp<-tapply(new_com$iv,list(new_com$site,new_com$D),max)%>%jz_data()
  names(max_cp_sp)<-c("site","D","iv","xh")

  cs<-merge(max_cp_sp,new_com,by=c("site","D","iv"))%>%merge(.,iv_cp,by=c("site","D")) %>%merge(.,sum_cp,by=c("site","D"))

  cs<-data.frame(site=cs$site,D=cs$D,D_xh=cs$xh,D_iv=cs$D_iv,物种数=cs$物种数,sp=cs$sp,sp_iv=cs$iv,sp_iv=cs$xh.y)%>%arrange(.,site,D_xh)

  #new_com<-arrange(new_com,site,xh)


  newcom1<-new_com
  newcom1$cs<-paste(newcom1$site,newcom1$D)

  newcom1<-arrange(newcom1,cs,xh)
  newcom1<-transform(newcom1,nxh=unlist(tapply(cs,cs,index)))

  #newcom2<-subset(newcom1,nxh<cat)
  newcom2<-filter(newcom1,nxh<cat)
  newcom2<-arrange(newcom2,site,xh)

  cx<-tapply(newcom2$sp,list(newcom2$site,newcom2$D),function(x)paste(x,collapse="、"))%>%as.data.frame()
  cx<-cbind(site=row.names(cx), cx)

  ca<-melt(cx,id.vars=c("site"),variable.name="D",
           value.name="物种",na.rm = TRUE)

  re<-merge(cs,ca,by=c("site","D"))%>%arrange(.,site,D_xh)

  re
}