Turns wide-table formats (species-traits matrix and occurrence table) into long-table format. As input, the function requires information about which columns contain traits, given as a list of trait-names, and which column contains the taxon name. For tables containing repeated measurements of traits within the same taxon, an occurrenceID should be given or will be created.

as.traitdata(x, traits = attributes(x)$traits, taxa = attributes(x)$taxa,
  individuals = attributes(x)$individuals, occurrences = individuals,
  datasetID = attributes(x)$datasetID,
  measurements = attributes(x)$measurements, units = attributes(x)$units,
  keep = attributes(x)$keep, drop = NULL, na.rm = TRUE,
  id.vars = names(x)[names(x) %in% keep & !names(x) %in% drop],
  mutate = NULL, thesaurus = attributes(x)$thesaurus,
  metadata = attributes(x)$metadata, ...)

Arguments

x

data.frame object, containing at least a column of taxa, and one or more columns of trait measurements.

traits

a vector of column names containing traits.

taxa

the name of the column containing taxon names.

individuals

identical to occurrence. (old term kept for clarification)

occurrences

either a column name containing identifiers for each individual specimen on which several traits were measured, i.e. an occurrence of this taxon, or a vector of occurrence identifiers which must be of the same length as the number of rows of the table. See 'Details'.

datasetID

a unique name for this dataset (optional). Will be prepended to the occurrence ID and measurement ID.

measurements

either a column name containing identifiers for each individual measurement, or a vector of measurement identifiers. This applies, if single trait measurements span across multiple columns of data, e.g. multivariate traits like quantitative measures of chemical compounds, wavelengths or x-y-z coordinates. In most cases, a measurementID will link the data across rows in the longtable format. Make sure that the traitnames given reflect the different dimensions of the trait measurement. If measurement remains blank, sequential identifiers will be auto-generated for each measured value.

units

a single character string or named vector giving the units that apply to the traits. If only one unit type is given, it will be applied to all traits.

keep

a vector or named vector containing the names of the input columns to be kept in the output. Vector names will be used to rename the columns. It is recommended to use accepted column names of the traitdata standard for renaming!

drop

a vector acting as the inverse of keep. All columns listed will be removed from the output dataset.

na.rm

logical defaults to TRUE. If FALSE, all measured Values containing NA will be kept in the output table. This is not reccomended for most data.

metadata

a list of class metadata, as created by function as.metadata(). Metadata will be added as attributes to the data table. Possible parameters to the function call are: rightsHolder, bibliographicCitation, license, author, datasetID, datasetName, version. (see 'Details')

...

Details

If occurrence is left blank, the script will check for the structure of the input table. If several entries are given for the same taxon, it assumes that input is an occurrence table and assigns identifiers.

Metadata will be stored as attributes to the data frame and can be accessed via attributes(). It is not necessary but highly recommended to provide metadata when working with multiple trait data files. When appending datasets using rbind(), the metadata information will be added as additional columns and dataset attribution will be listed in attributes.

Examples

# species-trait matrix: pulldata(carabids)
#> Error in source(system.file("extdata", paste0(x, ".R"), package = "traitdataform")): cannot coerce type 'closure' to vector of type 'character'
dataset1 <- as.traitdata(carabids, taxa = "name_correct", traits = c("body_length", "antenna_length", "metafemur_length"), units = "mm", keep = c(basisOfRecordDecription = "source_measurement", measurementRemark = "note") )
#> Input is taken to be a species -- trait matrix. If this is not the case, please provide parameters!
# occurrence table: pulldata("heteroptera_raw")
#> loading dataset 'heteroptera_raw' from original data source! #> When using this data, please cite the original publication: #> Gossner MM, Simons NK, Höck L and Weisser WW (2015). Morphometric #> measures of Heteroptera sampled in grasslands across three regions of #> Germany. _Ecology_, *96*, pp. 1154. doi: 10.1890/14-2159.1 (URL: #> http://doi.org/10.1890/14-2159.1). #> The dataset 'heteroptera_raw' is now available for use!
dataset2 <- as.traitdata(heteroptera_raw, taxa = "SpeciesID", traits = c("Body_length", "Body_width", "Body_height", "Thorax_length", "Thorax_width", "Head_width", "Eye_width", "Antenna_Seg1", "Antenna_Seg2", "Antenna_Seg3", "Antenna_Seg4", "Antenna_Seg5", "Front.Tibia_length", "Mid.Tibia_length", "Hind.Tibia_length", "Front.Femur_length", "Hind.Femur_length", "Front.Femur_width", "Hind.Femur_width", "Rostrum_length", "Rostrum_width", "Wing_length", "Wing_widt"), units = "mm", keep = c(sex = "Sex", references = "Source", lifestage = "Wing_development"), metadata = as.metadata( author = "Gossner MM, Simons NK, Höck L and Weisser WW", datasetName = "Morphometric traits Heteroptera", bibliographicCitation = attributes(heteroptera_raw)$citeAs, license = "http://creativecommons.org/publicdomain/zero/1.0/" ) )
#> it seems you are providing repeated measures of traits on multiple specimens of the same species (i.e. an occurrence table)! Sequential identifiers for the occuences will be added. If your dataset contains user-defined occurrenceIDs you may specify the column name in parameter 'occurrences'.