Method for function rbind() to append objects of class 'traitdata' to each
other.
Usage
# S3 method for 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")
#> 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", 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/"
)
)
#> Input is taken to be a species -- trait matrix. If this is not the case, please provide parameters!
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")
#> 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 = 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/"
)
)
#> 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!
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"))
#> Warning: There seems to be no overlap in taxon names of the provided datasets!
#> It is recommended to map 'ScientificNameStd' of each dataset to the same thesaurus or ontology!
head(database)
#> traitID traitName traitValue traitUnit verbatimScientificName
#> 1 1 Body_length 7.29 mm Adelphocoris quadripunctatus
#> 2 1 Body_length 8.61 mm Adelphocoris quadripunctatus
#> 3 1 Body_length 2.35 mm Acalypta nigrina
#> 4 1 Body_length 2.10 mm Acalypta nigrina
#> 5 1 Body_length 2.17 mm Acalypta nigrina
#> 6 1 Body_length 2.15 mm Acalypta nigrina
#> verbatimTraitName verbatimTraitValue verbatimTraitUnit measurementID
#> 1 Body_length 7.29 mm 20
#> 2 Body_length 8.61 mm 21
#> 3 Body_length 2.35 mm 1
#> 4 Body_length 2.10 mm 2
#> 5 Body_length 2.17 mm 3
#> 6 Body_length 2.15 mm 4
#> occurrenceID references measurementRemarks sex
#> 1 20 Zoological State Collection Munich <NA> f
#> 2 21 Zoological State Collection Munich <NA> m
#> 3 1 Zoological State Collection Munich <NA> f
#> 4 2 Zoological State Collection Munich <NA> f
#> 5 3 Zoological State Collection Munich <NA> m
#> 6 4 Zoological State Collection Munich <NA> m
#> lifeStage datasetID author
#> 1 m gossner15 Martin Gossner
#> 2 m gossner15 Martin Gossner
#> 3 m gossner15 Martin Gossner
#> 4 b gossner15 Martin Gossner
#> 5 m gossner15 Martin Gossner
#> 6 b gossner15 Martin Gossner
#>
#> This trait-dataset contains 10 traits for 299 taxa ( 2586 measurements in total).
#> $vanderplas17
#>
#> vanderplas17 : by Fons van der Plas .
#>
#> When using these data, you must acknowledge the following usage policies:
#>
#> Cite this trait dataset as:
#> [1] "van der Plas et al. (2017) Methods in Ecol. & Evol., doi: 10.1111/2041-210x.12728"
#>
#> Published under: http://creativecommons.org/publicdomain/zero/1.0/
#>
#> This dataset conforms to: [1] "Ecological Trait-data Standard (ETS) v0.10"
#>
#>
#> $gossner15
#>
#> gossner15 : by Martin Gossner .
#>
#> When using these data, you must acknowledge the following usage policies:
#>
#> Cite this trait dataset as:
#> [1] "Gossner et al. (2015) Ecology, 96:1154. doi: 10.1890/14-2159.1"
#>
#> Published under: http://creativecommons.org/publicdomain/zero/1.0/
#>
#> This dataset conforms to: [1] "Ecological Trait-data Standard (ETS) v0.10"
#>
#>