R/itis.lookup.exhaustive.search.r

In AtlanticR/bio.taxonomy: Package that interacts with bio and associated projects to ...

    itis.lookup.exhaustive.search = function( X, vnames, vtypes ) {
      
      # requires itis.tsn, tolookup as variables in X
      
      iToLookup = which( X$tolookup & !is.finite(X$itis.tsn )) 

			kingdoms = itis.db( DS="kingdoms")
			kingdoms = sort( kingdoms$kingdom_name )  
      
      # this makes sure Animalia is first .. speeds things up

      for ( k in kingdoms ) { 

				print (k)
				itaxa = itis.db( "itaxa", itis.kingdom=k )

        for ( i in 1: length(vnames) ) {
            vn = vnames[i]
            vt = vtypes[i]
            lookup = intersect( iToLookup, which( !is.finite( X$itis.tsn ) ) )
            for ( ii in lookup ) {
              jj = itis.lookup( ii, tx=X[,vn], itaxa=itaxa, type=vt )          
              if (length(jj) == 1) {
                X$itis.tsn[ii] = jj
                print( X[ii,] )
              }
            }
			    }
        } # end for
      
      return (X) 
    }