subOrigData {assignR}

Extract known origin sample data

Description

This function subsets the known-origin isotope dataset included in this package and conducts optional transformations to convert isotope measurements to a common reference scale.

Usage

subOrigData(marker = "d2H", taxon = NULL, group = NULL, dataset = NULL, 
  age_code = NULL, mask = NULL, ref_scale = "VSMOW_H", niter = 5000, genplot = TRUE)

Arguments

marker

character string. Column name for isotopic data to be extracted, either “d2H” or “d18O”.

taxon

character string or string vector. Species name(s) for data to be extracted.

group

character string or string vector. Taxonomic groups for data to be extracted.

dataset

integer or integer vector. Dataset_ID(s) for data to be extracted. See knownOrig feature sources.

age_code

character string or string vector. Animal age code for data to be extracted.

mask

SpatVector. Polygon layer used to constrain the geographic area from which data are extracted. If not provided, global.

ref_scale

character string. Text identifier for reference scale to which all isotope values will be transformed. See stds. Use “NULL” to obtain untransformed values on the originally reported scale.

niter

integer. Number of random samples used to propagate uncertainty in calibration hierarchy transformations.

genplot

logical. Plot results in R.

Value

Returns an object of class “subOrigData”, formatted for use in calRaster or QA functions.

data

SpatVector including one point feature for each selected sample. Data fields are described in knownOrig feature samples.

sources

data.frame. Information for all data sources for the selected samples. Fields are described in knownOrig feature sources

chains

list. Each item is a character string vector containing the hierarchy of calibrations used in the transformation for a set of selected samples. See stds.

marker

character string. The isotopic marker specified in the call to subOrigData

References

Magozzi, S. et al. (in press) Calibration chain transformation to improve the comparability of organic hydrogen and oxygen isotope data. Methods in Ecology and Evolution

Examples

## WITHOUT mask
# extract d2H data for Jackdaw, Partridge and Willow Grouse, transformed
# to the VSMOW/SLAP H reference scale by default
d1 = subOrigData(taxon = c("Danaus plexippus", "Setophaga ruticilla", 
  "Turdus migratorius"), niter = 100)
summary(d1)

# extract d2H data for insects and passerine birds without transformation
d2 = subOrigData(group = c("Insect","Passerine"), ref_scale = NULL, genplot = FALSE)
summary(d2)

# extract d18O data for all humans, transformed to the VSMOW/SLAP O reference scale
d3 = subOrigData(marker = "d18O", 
  group = c("Modern human", "Indigenous human"), ref_scale = "VSMOW_O", 
  niter = 100, genplot = FALSE)
summary(d3)

# extract d2H data for humans using taxon, transformed to the VSMOW/SLAP H reference scale
d4 = subOrigData(marker = "d2H", taxon = "Homo sapiens", ref_scale = 
  "VSMOW_H", niter = 100, genplot = FALSE)
summary(d4)

## WITH mask
# error - no samples found
## Not run: d5 = subOrigData(taxon = "Turdus philomelos", mask = naMap)
# this works OK
d6 = subOrigData(taxon = c("Danaus plexippus", "Setophaga ruticilla", 
  "Turdus migratorius"), mask = naMap, genplot = FALSE)