assignR (version 1.2.0)

subOrigData: Extract known origin sample data

Description

This function subsets the known-origin isotope dataset included in this package.

Usage

subOrigData(marker = "d2H", taxon = NULL, group = NULL, reference = NULL, 
  age_code = NULL, mask = NULL)

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.

reference

character string or string vector. Bibliographic reference for data to be extracted.

age_code

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

mask

SpatialPolygons or SpatialPolygonsDataFrame. Constrains the geographic area from which data are extracted. If not provided, global.

Value

SpatialPointsDataFrame including the location and a single feature corresponding to the marker for each selected sample. Output is formatted for use in calRaster or QA functions.

Examples

# NOT RUN {
## WITHOUT mask
# extract d2H data for Jackdaw, Partridge and Willow Grouse
d1 = subOrigData(taxon = c("Danaus plexippus", "Setophaga ruticilla", "Turdus migratorius"))
summary(d1)

# extract d2H data for insects and birds
d2 = subOrigData(group = c("insect","bird"))
summary(d2)

# extract d18O data for humans
d3 = subOrigData(marker = "d18O", group = "human")
summary(d3)

# extract d2H data for humans using taxon
d4 = subOrigData(marker = "d2H", taxon = "Homo sapiens")
summary(d4)

## WITH mask
# error - no samples found
# }
# NOT RUN {
d5 = subOrigData(taxon = "Turdus philomelos", mask = naMap)
# }
# NOT RUN {
# these work OK
d6 = subOrigData(taxon = c("Danaus plexippus", "Setophaga ruticilla", 
  "Turdus migratorius"), mask = naMap)
d7 = subOrigData(group = "human", mask = naMap)
# }