R/get.IOdbseqs.R

In leondap/iodatabase: Integrated and Open Butterfly Database

get.IOdbseqs<-function(families=NULL, subfamilies=NULL, genera=NULL, species=NULL,
                   countries=NULL, xlim=NULL, ylim=NULL){
  	spetot<-checklist$Scientific_Name
  	speciesusefam<-NULL
  	speciesusesub<-NULL
  	speciesusegen<-NULL
  	speciesusesp<-NULL
  	uselong<-NULL
  	uselat<-NULL
  	usecou<-NULL
	res<-NULL
	if(!is.null(families)){
  		check<-which(families %in% checklist$Family)
  		failed<-families[-check]
  		if(length(failed)>0){
  			print(paste("The following families were not found in the checklist:",failed))
  		}
    		speciesusefam<-spetot[which(checklist$Family %in% families)]
	}
	if(!is.null(subfamilies)){
 		 check<-which(subfamilies %in% checklist$Subfamily)
  		failed<-subfamilies[-check]
  		if(length(failed)>0){
  			print(paste("The following subfamilies were not found in the checklist:",failed))
  		}
  		speciesusesub<-spetot[which(checklist$Subfamily %in% subfamilies)]
	}
	if(!is.null(genera)){
  		check<-which(genera %in% checklist$Genus)
  		failed<-genera[-check]
  		if(length(failed)>0){
  			print(paste("The following genera were not found in the checklist:",failed))
  		}
    		speciesusegen<-spetot[which(checklist$Genus %in% genera)]
	}
	if(!is.null(species)){
		check<-which(species %in% spetot)
		failed<-species[-check]
		if(length(failed)>0){
			print(paste("The following species were not found in the checklist:",failed))
		}
  		speciesusesp<-spetot[which(checklist$Scientific_Name %in% species)]
	}
	speciesuse<-unique(c(speciesusefam,speciesusesub,speciesusegen,speciesusesp))
	select<-which(iodb$Scientific_Name %in% speciesuse)

if(!is.null(xlim)){
  uselong<-which(iodb$Longitude>=xlim[1] & iodb$Longitude<=xlim[2])
}
if(!is.null(ylim)){
  uselat<-which(iodb$Latitude>=ylim[1] & iodb$Latitude>=xlim[2])
}
if(!is.null(countries)){
  usecoun<-which(iodb$Country %in% countries)
}
useall<-unique(c(uselong,uselat,usecou))
if (!is.null(useall)){
  select<-select[which(select %in% useall)]
}
#select<-c(1:100)
res$metadata<-iodb[select,-which(colnames(iodb)=="seqs")]
res$fasta<-makefasta(iodb[select,c("names","seqs")])
return(res)
}