CalibDataBat2: Calibration datasets for bat species

In IsoriX: Isoscape Computation and Inference of Spatial Origins using Mixed Models

Calibration datasets for bat species

Description

These datasets contain hydrogen delta values of fur keratin from sedentary bat species captured between 2005 and 2009 from Popa-Lisseanu et al. (2012). These data can be used as an example to fit a calibration model using the function calibfit. The difference between CalibDataBat2 and CalibDataBat2Rev is that in the latter the bat fur isotope values were corrected to align with the current delta values for deuterium for keratin reference materials (Soto et al. 2017, https://doi.org/10.1002/rcm.7893) ensuring comparability between formerly and more recently normalized datasets of delta values for deuterium.

Format

Two dataframes with 178 observations and 6 variables:

site_ID	(factor)	Identification of the sampling site
long	(numeric)	Longitude coordinate (decimal degrees)
lat	(numeric)	Latitude coordinate (decimal degrees)
elev	(numeric)	Elevation asl (m)
sample_ID	(factor)	Identification of the sampled animal
sample_value	(numeric)	Hydrogen delta value of the tissue

Details

Users who wish to use their own dataset for calibration should create a dataframe of similar structure than these ones (only the column 'species' can be dropped). The columns should possess the same names as the ones described above. If the elevation is unknown at the sampling sites, elevation information can be extracted from a high resolution elevation raster using the function terra::extract (see Examples). Note that the original study used a different source of elevation data.

Source

data provided by Popa-Lisseanu AG et al.

References

Popa-Lisseanu AG, Soergel K, Luckner A, Wassenaar LI, Ibanez C, Kramer-Schadt S, Ciechanowski M, Goerfoel T, Niermann I, Beuneux G, Myslajek RW, Juste J, Fonderflick J, Kelm D & Voigt CC (2012). A triple isotope approach to predict the breeding origins of European bats. PLoS ONE 7(1):e30388.

Soto DX, Koehler G, Wassenaar LI & Hobson KA (2017). Re-evaluation of the hydrogen stable isotopic composition of keratin calibration standards for wildlife and forensic science applications. Rapid Commun Mass Spectrom. 31(14):1193-1203. doi: 10.1002/rcm.7893. PMID: 28475227.

See Also

CalibDataBat for another (related) calibration dataset

calibfit to fit a calibration model

Examples

head(CalibDataBat2)
str(CalibDataBat2)

## The following example require to have downloaded
## an elevation raster with the function getelev()
## and will therefore not run unless you uncomment it

# if (require(terra)){
#    ## We delete the elevation data
#    CalibDataBat2$elev <- NULL
#
#    ## We reconstruct the elevation data using an elevation raster
#    getelev(file = "elevBats.tif", z = 6,
#            lat_min = min(CalibDataBat2$lat),
#            lat_max = max(CalibDataBat2$lat),
#            long_min = min(CalibDataBat2$long),
#            long_max = max(CalibDataBat2$long))
#    ElevationRasterBig <- rast("elevBats.tif")
#    CalibDataBat2$elev <- extract(
#        ElevationRasterBig,
#        cbind(CalibDataBat2$long, CalibDataBat2$lat))
#    head(CalibDataBat2)
# }

IsoriX documentation built on Sept. 11, 2024, 8:22 p.m.