BCI data: refine slow species lookup loop

merge.data.BCI.R

@@ -29,11 +29,8 @@ data.bci <- big.bci; rm(big.bci)
 species.clean <- read.table("./data/raw/DataBCI/TaxonomyDataReport.txt",stringsAsFactors=FALSE, header = T, sep = "\t")
 
 ## Try to relate SpeciesID in species.clean species names in data.bci
-data.bci$sp <- rep(NA,nrow(data.bci))
-for(k in 1:nrow(species.clean)) {
-	latin.name <- apply(species.clean[k,2:3],1,paste,collapse=" ")[1]
-	data.bci$sp[which(data.bci$Latin == latin.name)] <- species.clean$SpeciesID[k] }
-	
+data.bci$sp2 = species.clean$SpeciesID[match(data.bci$Latin,
+	paste(species.clean[["Genus"]], species.clean[["species"]]))]
 length(unique(data.bci$sp))
 
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