Standardize trait names and harmonize measured values and reported facts

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().

Value

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

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()

Examples



pulldata("carabids")
#> Direct call to data source failed. Please check internet connectivity and re-load data!
#> The dataset 'carabids' has successfully been downloaded! 

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/"
    )
)
#> Input is taken to be a species -- trait matrix. If this is not the case, please provide parameters!

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")
#> The dataset 'heteroptera_raw' has successfully been downloaded! 

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/"
    )
)
#> Input is taken to be an occurrence table/an observation -- trait matrix 
#> (i.e. with individual specimens per row and multiple trait measurements in columns). 
#> If this is not the case, please provide parameters! 


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
    )