taxonomy.filter.taxa = function ( spcode, method=c("direct", "complete"), taxafilter="all", outtype="internalcodes" ) {
out = data.frame(spcode=spcode, sortindex=1:length(spcode), keep=FALSE )
if ( outtype %in% c( "spec_bio", "internalcodes", "parsimonious", "spec.parsimonious") ) outcode="spec.parsimonious"
if ( outtype %in% c( "spec", "bio.groundfishcodes") ) outcode ="spec"
taxalist = taxonomy.codes( taxa=taxafilter,method=method, outcode=outcode ) # these are still groundfish codes
##taxalist = taxonomy.codes( method=taxafilter, outcode=outcode ) # making a change AMC for species composition
f = which( is.finite( out$spcode ) )
k = which(( out$spcode %in% taxalist) )
keep = intersect( f, k )
return( keep )
}
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