rbind.traitdata: Combine trait datasets

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

Combine trait datasets

Description

Method for function rbind() to append objects of class 'traitdata' to each other.

Usage

## S3 method for class 'traitdata'
rbind(
  ...,
  metadata = NULL,
  datasetID = NULL,
  metadata_as_columns = FALSE,
  drop = NULL
)

Arguments

...	two or more objects of class traitdata.
metadata	a list of metadata entries which are to be added as dataset-level information.
datasetID	a vector of the same length as number of objects. If NULL (default), object names will be returned as ID.
metadata_as_columns	logical (defaults to FALSE) or vector of columns to return. If TRUE , the output will contain the "author", "license", "datasetName" and (autogenerated) "datasetID" name, if those are provided. If character vector, the output will contain the listed columns.
drop	FALSE by default. If true, columns that are not present in all datasets will be dropped.

Details

Metadata are ideally already included in the datasets as attributes (see ?as.traitdata). The function rbind.traitdata() takes a list of lists as its metadata argument. The outer list must have the same length as the provided objects to combine, with each entry containing objects according to the terms of the Ecological Traitdata Standard (http://ecologicaltraitdata.github.io/ETS/#metadata-vocabulary).

A lookup table for dataset details will be appended as an attribute to the output dataset, linked to each entry via the field datasetID. It can be accessed by calling attributes(<dataset>)$datasets.

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", measurementRemarks = "note"),
  metadata = as.metadata(
    bibliographicCitation = c(
        "van der Plas et al. (2017) Methods in Ecol. & Evol., doi: 10.1111/2041-210x.12728"
       ),
    author = "Fons van der Plas",
    license = "http://creativecommons.org/publicdomain/zero/1.0/"
    )
)


traits1 <- 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 = traits1)

# occurrence table:

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 = as.metadata(
    bibliographicCitation = "Gossner et al. (2015) Ecology, 96:1154. doi: 10.1890/14-2159.1",
    author = "Martin Gossner",
    license = "http://creativecommons.org/publicdomain/zero/1.0/"
    )
)

dataset2 <- mutate.traitdata(dataset2,
  antenna_length = Antenna_Seg1 + Antenna_Seg2 + Antenna_Seg3 + Antenna_Seg4 + Antenna_Seg5
  )


traits2 <- 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"),
 Hind.Femur_length = as.trait("metafemur_length",
   expectedUnit = "mm", valueType = "numeric",
   identifier = "http://t-sita.cesab.org/BETSI_vizInfo.jsp?trait=Femur_length")
)

dataset2Std <- standardize_traits(dataset2, thesaurus = traits2)

database <- rbind(dataset1Std, dataset2Std, 
                   datasetID = c("vanderplas17", "gossner15"),
                   metadata_as_columns = c("author"))
head(database)

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