The calibration model is a linear mixed-effects model (LMM) that fits the isotopic values of sedentary organisms as a linear function of the isotopic values in their environment (e.g. precipitation).This function considers that the isotopic values from the environment (e.g. from precipitation) at the locations at which organisms were sampled are not known. The function therefore predicts these isotopic values from the geostatistical model fitted by the function Isofit, which is provided to Calibfit using the argument isofit.
The LMM used to fit the calibration function has a simple fixed-effect structure: an intercept and a slope. The random effect is more complex: it is normally distributed with mean zero, a certain variance between locations proportional to the squared fixed slope, and a covariance structure defined by the prediction covariance matrix of the isoscape model between the calibration locations. All models used in IsoriX will be soon detailed in an additional document.
This function is only needed in the case for which the assignment of organisms has to be performed within an isoscape that was built using another source of isotopic values (e.g., precipitation). This implies that if the isoscape had been fitted using isotopic ratios from sedentary animals, then this calibration step is not needed.
If source isotopic values are known at the locations where sedentary organisms were sampled, users should calibrate their data directly using the function lm by fitting tissue isotopic values as a function of source isotopic values.