inst/scripts/taxonomy.r

In jae0/bio.taxonomy: R package that does useful things with taxonomic hierarchies ...

  # taxonomy.db contains taxa/species codes that are internally (bio) consistent and parsimonious

  # require ( multicore ) # simple parallel interface (using threads) .. does not work well in MSWindows?

  project.library( "aegis", "aegis", "bio.taxonomy" )

  refresh.itis.tables = FALSE
  if ( refresh.itis.tables ) {
    itis.db( "make.snapshot", lnk="http://www.itis.gov/downloads/itisMySQLTables.tar.gz")
    itis.db( "main.redo")     # assemble all itis tables into a coherent and usable form
  }

  bootstrap.new.data.system = FALSE
  if ( bootstrap.new.data.system) {

    # first. refresh BIO's species codes from Oracle -- done also from groundfish update
    taxonomy.db( "spcodes.redo" )

    # bootstrap an initial set of tables .. these will be incomplete as a parsimonious tree needs to be created first but it depends upon the last file created taxonomy.db("complete") .. so ...
    taxonomy.db( "groundfish.itis.redo" )  ## link itis with groundfish tables using taxa names, vernacular, etc
    taxonomy.db( "full.taxonomy.redo" )  # merge full taxonomic hierrachy (limit to animalia and resolved to species)
    taxonomy.db( "life.history.redo" ) # add life history data (locally maintained in groundfish.lifehistory.manually.maintained.{csv/rda} )
    taxonomy.db( "complete.redo" )
    taxonomy.db( "parsimonious.redo" )
  }



### NOTE:: taxonomy db is creating wrong lookup for some species .. turtles  <<<<<<<<<<<<<<<<<<<

## TODO:: add Worms database
## links to observer database species codes




  example.usage = FALSE
  if (example.usage) {

    # -------------------------------
    # example usage to extract TSN's

		tx="Microgadus tomcod"

    tx="cod"

			taxonomy.recode( from="taxa.fast", tolookup=tx) # lookup only from local taxonomy db
			taxonomy.recode( from="taxa", tolookup=tx ) # look up species id from both itis and local taxonomy.db

      lu = taxonomy.recode( from="taxa", tolookup="AMMODYTES" ) # look up species id from both itis and local taxonomy.db
      taxonomy.recode( from="tsn", to="taxa", tolookup= lu[[1]]$tsn )

      taxonomy.recode( from="spec", to="taxa", tolookup=taxonomy.recode( from="taxa.fast", tolookup="AMMODYTES" ) )


      itis.taxa.to.tsn( tx) # look up only from itis

			o = taxonomy.recode( from="taxa", tolookup=tx )
				o
				taxonomy.recode( from="spec", tolookup=o[[1]]$spec )
				taxonomy.recode( from="tsn", to="taxa", tolookup= o[[1]]$tsn )
				itis.extract( o[[1]]$tsn[1], itis.db( "itaxa" ))


		taxonomy.recode( from="spec", tolookup=c(10,20) )

		itaxa = itis.db( "itaxa" )

		tx = "Microgadus tomcod"
			itis.taxa.to.tsn(  tx=tx, itaxa=itaxa )

    tx = "ling"
			txids = itis.vernacular.to.tsn( tx=tx, itaxa=itaxa )
      taxonomy.recode( from="tsn", to="taxa", tolookup=txids )

    # ITIS data from tsn's
    tsn = c(164714:164780)
			itis.extract( tsn, itaxa)

    # -------------------------------

    kid = itis.code.extract( DS="kingdom", value="Animalia")
    tid = itis.code.extract( DS="taxon.unit.types", value="species" )
    sid = itis.code.extract( DS="itaxa", value="Gadus morhua" )
    sid = itis.code.extract( DS="itaxa.vernacular", value="atlantic cod" )

  }