createTransects.r generates transects for 6 canadian cities and writes out transect data to data/transects/*.rds
gbifDL.r generates MasterSpeciesList.csv using data/transects/*.rds
MasterSpeciesList.csv cleaned with OpenRefine to generate MasterSpeciesList_clean.csv
matchGbifTry.R identifies all the species from our transects that occur in the TRY database
getTRY_ids.r combines all of the species and the TRY AccCodes (output is Specieslist_joined) but there are lots of duplicate species because of subsp. and var.
The output of the species lists & TRY codes, with duplicates (Specieslist_Joined) is then brought into OpenRefine whereTRY spp. list OpenRefine removes all duplicate values and creates Specieslist_TRY_join.csv
getTRY_ids.r takes Specieslist_TRY_join.csv and builds a file (data/tryAccession/accessionMaster_clean.csv) where each row represents 1000 species (3) and one represents 190 species. Each row needs to be converted into the TRY format which is a list separated by commas.
- Easy way to do this is to take it into word (copy & paste text) and find replace " " with ", "
- Copy and paste the word file into TRY
- You can also open
accessionMaster.csvin any text editor. It will be a 4 line file - 1 line per TRY request.
tidying_TRYtraits.r takes the large files obtained from TRY, reads them in, and summarizes them by mean trait value for each species. It then writes out the tidied trait values to data/traitData.csv
buildSpeciesTraitData.r takes data/traitData.csv from TRY and combines it with the GBIF occurrance data MasterSpeciesList_clean.csv to create a list of species with their associate mean trait values in species_and_their_traits.csv
generate_percentiles.r builds list of species with a trait value in the tails of its distribution across all cities, within each city, and within each quadrat within each city