View source: R/setPreferredTaxonNomenclature.R
setPreferredTaxonNomenclature | R Documentation |
Sets (or resets) a preferred taxon nomenclature to the organism identities of a data set using a lookup table
setPreferredTaxonNomenclature( target, x, mapping, date.format = "%Y-%m-%d", missing.values = c(NA, ""), verbose = TRUE )
target |
The initial object of class |
x |
A data frame where each row corresponds to a different value of 'originalOrganismName'. |
mapping |
A named list whose elements are strings that correspond to column names in
|
date.format |
A character string specifying the input format of dates (see |
missing.values |
A character vector of values that should be considered as missing data (see details). |
verbose |
A boolean flag to indicate console output of the nomenclatural change process. |
The modified object of class VegX
.
Other organism identity functions:
setOriginalIdentificationConcepts()
# Load source data data(mokihinui) # Create new Veg-X document with aggregate organism observations mapping = list(plotName = "Plot", obsStartDate = "PlotObsStartDate", taxonName = "NVSSpeciesName", stratumName = "Tier", cover = "Category") coverscale = defineOrdinalScaleMethod(name = "Recce cover scale", description = "Recce recording method by Hurst/Allen", subject = "plant cover", citation = "Hurst, JM and Allen, RB. (2007) The Recce method for describing New Zealand vegetation – Field protocols. Landcare Research, Lincoln.", codes = c("P","1","2","3", "4", "5", "6"), quantifiableCodes = c("1","2","3", "4", "5", "6"), breaks = c(0, 1, 5, 25, 50, 75, 100), midPoints = c(0.05, 0.5, 15, 37.5, 62.5, 87.5), definitions = c("Presence", "<1%", "1-5%","6-25%", "26-50%", "51-75%", "76-100%")) strataDef = defineMixedStrata(name = "Recce strata", description = "Standard Recce stratum definition", citation = "Hurst, JM and Allen, RB. (2007) The Recce method for describing New Zealand vegetation – Field protocols. Landcare Research, Lincoln.", heightStrataBreaks = c(0, 0.3,2.0,5, 12, 25, 50), heightStrataNames = paste0("Tier ",1:6), categoryStrataNames = "Tier 7", categoryStrataDefinition = "Epiphytes") x = addAggregateOrganismObservations(newVegX(), moki_tcv, mapping = mapping, methods = c(cover=coverscale), stratumDefinition = strataDef) # Inspect the original organism identities head(showElementTable(x, "organismIdentity")) y = setPreferredTaxonNomenclature(x, moki_lookup, c(originalOrganismName = "NVSSpeciesName", preferredTaxonName = "PreferredSpeciesName")) # Inspect the modified organism identities head(showElementTable(y, "organismIdentity"))
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