standardize_traits: Standardize trait names and harmonize measured values and...

In EcologicalTraitData/traitdataform: Formatting and Harmonizing Ecological Trait-Data

Standardize trait names and harmonize measured values and reported facts

Description

Adds columns to a traitdata table with standardized trait names and relates them to globally unique identifiers via URIs. Optionally converts units of values and renames factor levels into accepted terms.

Usage

standardize_traits(
  x,
  thesaurus = attributes(x)$thesaurus,
  rename = NULL,
  categories = c("No", "Yes"),
  output = "logical",
  ...
)

Arguments

x	a traitdata object (as returned by as.traitdata()) or a data table containing at least the column 'verbatimScientificName.
thesaurus	an object of class 'thesaurus' (as returned by as.thesaurus()).
rename	a named vector to map user-provided names to thesaurus object names (see Details).
categories	target categories for binary/logical traits harmonization.
output	behaviour of fixlogical(). see fixlogical().
...	parameters to be ignored, forwarded from wrapper function standardize().

Details

The function matches the trait names provided in 'verbatimTraitName' to the traits provided in the thesaurus (in field 'trait'). Matching must be exact (case sensitive). Fuzzy matching may be provided in a later version of the package.

The function parameter 'rename' should be provided to map trait names where user-provided names and thesaurus names are different. In this case, rename should be a named vector with the target names used in the thesaurus as names, and the original names as provided in 'verbatimTraitName' as value. E.g. rename = c()

Value

A traidata object with standardized trait names according to a provided thesaurus.

See Also

Other standardize: standardize_taxa(), standardize()

Other standardize: standardize_taxa(), standardize()

Examples

pulldata("carabids")

dataset1 <- as.traitdata(carabids,
  taxa = "name_correct",
  traits = c("body_length", "antenna_length", "metafemur_length"),
  units = "mm",
  keep = c(datasetID = "source_measurement", measurementRemark = "note"),
  metadata = list(
    bibliographicCitation = attributes(carabids)$citeAs,
    author = "Fons van der Plas",
    license = "http://creativecommons.org/publicdomain/zero/1.0/"
    )
)

traitlist <- as.thesaurus(
body_length = as.trait("body_length", expectedUnit = "mm", valueType = "numeric",
   identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Body_length"),
antenna_length = as.trait("antenna_length", expectedUnit = "mm", valueType = "numeric",
   identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Antenna_length"),
metafemur_length = as.trait("metafemur_length", expectedUnit = "mm", valueType = "numeric",
   identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length")
)

dataset1Std <- standardize_traits(dataset1, thesaurus = traitlist)



## Example: matching of original names to thesaurus

pulldata("heteroptera_raw")

dataset2 <- as.traitdata(heteroptera_raw,
  taxa = "SpeciesID",
  traits = c("Body_length", "Antenna_Seg1", "Antenna_Seg2",
    "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5", "Hind.Femur_length"),
  units = "mm",
  keep = c(sex = "Sex", references = "Source", lifestage = "Wing_development"),
  metadata = list(
    bibliographicCitation = attributes(heteroptera_raw)$citeAs,
    license = "http://creativecommons.org/publicdomain/zero/1.0/"
    )
)


traits2 <- as.thesaurus(
    Body_length = as.trait("Body_length",
            expectedUnit = "mm", valueType = "numeric",
            traitDescription = "From the tip of the head to the end of the abdomen"),
    Antenna_Seg1 = as.trait("Antenna_Seg1",
            expectedUnit = "mm", valueType = "numeric",
            traitDescription = "Length of first antenna segment",
            broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
    Antenna_Seg2 = as.trait("Antenna_Seg2",
            expectedUnit = "mm", valueType = "numeric",
            traitDescription = "Length of second antenna segment",
            broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
    Antenna_Seg3 = as.trait("Antenna_Seg3",
            expectedUnit = "mm", valueType = "numeric",
            traitDescription = "Length of third antenna segment",
            broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
    Antenna_Seg4 = as.trait("Antenna_Seg4",
            expectedUnit = "mm", valueType = "numeric",
            traitDescription = "Length of fourth antenna segment",
            broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
    Antenna_Seg5 = as.trait("Antenna_Seg5",
            expectedUnit = "mm", valueType = "numeric",
            traitDescription = "Length of fifth antenna segment (only Pentatomoidea)",
            broaderTerm = "http://ecologicaltraitdata.github.io/TraitDataList/Antenna_length"),
    Hind.Femur_length = as.trait("Hind.Femur_length",
            expectedUnit = "mm", valueType = "numeric",
            traitDescription = "Length of the femur of the hind leg",
            broaderTerm = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length")
    )

dataset2Std <- standardize_traits(dataset2,
    thesaurus = traits2
    )

EcologicalTraitData/traitdataform documentation built on June 12, 2022, 5:57 a.m.