R/getTaxaDepth.R

In HMPTrees: Statistical Object Oriented Data Analysis of RDP-Based Taxonomic Trees from Human Microbiome Data

getTaxaDepth <-
function(level){	
	if(tolower(level) == "kingdom" || tolower(level) == "k"){
		return(1)
	}else if(tolower(level) == "phylum" || tolower(level) == "p"){
		return(2)
	}else if(tolower(level) == "class" || tolower(level) == "c"){
		return(3)
	}else if(tolower(level) == "order" || tolower(level) == "o"){
		return(4)
	}else if(tolower(level) == "family" || tolower(level) == "f"){
		return(5)
	}else if(tolower(level) == "genus" || tolower(level) == "g"){
		return(6)
	}else if(tolower(level) == "species" || tolower(level) == "s"){
		return(7)
	}else if(tolower(level) == "subspecies" || tolower(level) == "ss"){
		return(8)
	}else{
		if(is.na(suppressWarnings(as.numeric(level))))
			stop(sprintf("%s isn't recognized.", as.character(level)))
		
		lvl <- as.numeric(level)
		if(lvl > 0)
			return(lvl)
		
		stop("'level' cannot be negative.")
	}
}