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remake.yml
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remake.yml
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sources:
- createlookup.R
packages:
- taxize
- R6
- yaml
- digest
- devtools
- downloader
targets:
all:
depends:
- plant_lookup.csv
- R/sysdata.rda
VascularPlantFamilies:
command: getTplVascularPlantFamilies()
downloadTPL:
command: downloadPlantList(VascularPlantFamilies)
tplGenera:
command: combineGeneraLists(downloadTPL,VascularPlantFamilies)
additions:
command: read_csv(file="source_data/Additions.csv",row.names=1)
tplGenera_patched:
command: patchTPL(tplGenera,additions)
lookupRaw:
command: matchPlantListFamiliesToApweb(tplGenera_patched)
lookupPatch:
command: read_csv("source_data/genus_order_lookup_fae.csv")
badTPL:
command: read_csv("source_data/badGeneraFamilyPairs.csv")
lookupFixed:
command: fixFernsAndOtherProblems(lookupRaw, lookupPatch, badTPL)
plant_lookup.csv:
command: outputFlatFile(lookupFixed, target_name)
source_data/Spermatophyta_Genera.csv:
download: http://datadryad.org/bitstream/handle/10255/dryad.59001/Spermatophyta_Genera.csv?sequence=2
higherOrderTaxonomy:
command: readHigherOrderTaxonomy("source_data/Spermatophyta_Genera.csv", lookupFixed)
R/sysdata.rda:
command: packageData(higherOrderTaxonomy, target_name)