setOriginalIdentificationConcepts: Sets original identification taxon concepts

In miquelcaceres/VegX: Vegetation data in Veg-X

Sets original identification taxon concepts

Description

Sets (or resets) taxon concepts associated with the original identification of organisms

Usage

setOriginalIdentificationConcepts(
  target,
  citationStringAll = "",
  x = NULL,
  mapping = list(),
  date.format = "%Y-%m-%d",
  missing.values = c(NA, ""),
  verbose = TRUE
)

Arguments

target	The initial object of class VegX to be modified
citationStringAll	A string with the bibliographic citation to be applied to all organism identities of the VegX object (using the original organism names as taxon names), or to all original organism names listed in x.
x	A data frame where each row corresponds to one organism identity, given by a column that can be mapped to originalOrganismName.
mapping	A named list whose elements are strings that correspond to column names in x. Names of the list should be: originalOrganismName - A string with the original name given by the author of the data set (required). conceptName - A string with the taxon name forming the taxon concept, if different from originalOrganismName (optional). conceptCitation - A string with the bibliographic citation forming the taxon concept (optional). assertionDate - Date of taxon concept assertion (see date.format) (optional). assertionParty - Name of the party that undertook taxon concept assertion (optional).
date.format	A character string specifying the input format of dates (see as.Date).
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 concept identification process.

Value

The modified object of class VegX.

References

Wiser SK, Spencer N, De Caceres M, Kleikamp M, Boyle B & Peet RK (2011). Veg-X - an exchange standard for plot-based vegetation data

See Also

Other organism identity functions: setPreferredTaxonNomenclature()

Examples

# 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 = setOriginalIdentificationConcepts(x, citationStringAll="Allen 1998")

head(showElementTable(y, "organismIdentity"))

miquelcaceres/VegX documentation built on Sept. 18, 2022, 7:04 p.m.