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Prepare occurrence, taxonomy, and checklist data for diversity estimation

Source: R/diversityPrepR.R
diversityPrepR.Rd

Takes your occurrence dataset along with a taxonomy and checklist in order to produce a file that's ready to be passed into the richnessEstimateR() function in order to estimate species richness using iChao and iNEXT (hill numbers) for countries, continents, or the entire globe.

Usage

diversityPrepR(
  data = NULL,
  taxonomyFile = BeeBDC::beesTaxonomy(),
  checklistFile = BeeBDC::beesChecklist(),
  curveFunction = function(x) (228.7531 * x * x^-log(12.1593)),
  sampleSize = 10000,
  countryColumn = "country_suggested",
  limitGlobal = NULL,
  outPath = tempdir()
)

Arguments

data

A data frame or tibble. Occurrence records as input. Needs to include the scientificName column and a "country" column (see countryColumn)

taxonomyFile

A data frame or tibble. The taxonomy file to use. Default = beesTaxonomy() but see taxadbToBeeBDC() for other taxa.

checklistFile

A data frame or tibble. The taxonomy to use. Default = beesChecklist(); use this as a template to convert other taxa checklists.

curveFunction

A function. The mathematical function that describes the curve used to randomly sample from in order to fill empty sample sizes for species present in the checklist but not present in the occurrence dataset. Default is function(x) (228.7531 * x * x^-log(12.1593)), which is taken from the paper "How many bee species are there? A quantitative global estimate" by Dorey et al. Models can be fit using mosaic::fitModel().

sampleSize

Numeric. The size of the sample randomly drawn from the provided curve. See curveFunction. Default = 10000.

countryColumn

Character. The column from which country names should be sought.

limitGlobal

Character vector. A character vector of the countries to filter the data to in order limit the extent of the global-level analysis. Defualt = NULL.

outPath

Character. The output path where the curve plot (curvePlot.pdf) and the output Rdata (richnessInputs.Rda) file will be saved. Default = tempdir().

Value

Saves an Rdata file with the data needed to feed into the richnessEstimateR() function. The richnessEstimateR() function will then use iChao and/or iNEXT to estimate species richness for countries, continents, and the globe. Also returns the RData file to the environment.

See also

countryHarmoniseR() to harmonise country names based on a short list.

Examples


if (FALSE) { # \dontrun{
data(beesCountrySubset)

estimateDataExample <- diversityPrepR(
  data = beesCountrySubset,
  # Download the taxonomy
  taxonomyFile = BeeBDC::beesTaxonomy(),
  # Download the checklist
  checklistFile = BeeBDC::beesChecklist(),
  curveFunction = function(x) (228.7531 * x * x^-log(12.1593)),
  sampleSize = 10000,
  countryColumn = "country_suggested",
  limitGlobal = NULL,
  outPath = tempdir()
)
} # }