cal14C: Radiocarbon Calibration of Occurrences

In RRgeo: Species Distribution Modelling for Rare Species

Radiocarbon Calibration of Occurrences

Description

The function is meant to automatically apply the calibration process to conventional radiocarbon ages, relying on the package Bchron (Haslett & Parnell 2008). Specifically, the function internally selects the appropriate calibration curve based on the latitude associated with each occurrence and the nature of the sample (i.e marine or terrestrial samples).

Usage

cal14C(dataset,age=NULL,uncertainty=NULL,latitude=NULL,domain=NULL,
 bounds=c(0.025,0.975), clust=0.5, save=TRUE, output.dir=NULL)

Arguments

dataset	a data.frame containing all the occurrences to be calibrated.
age	character. Name of the column in dataset containing the conventional radiocarbon dates.
uncertainty	character. Name of the column in dataset containing the uncertainty associated to conventional radiocarbon dates.
latitude	character. Name of the column in dataset containing the latitude (in decimal degrees) of each occurrence.
domain	character. Name of the column in dataset indicating which occurrences are marine radiocarbon samples. If NULL, all the occurrences are assumed as "terrestrial" radiocarbon samples.
bounds	numeric. An upper and lower bound (in quantiles) to define the limits of the density probability created for each radiocarbon age (default: 95%).
clust	numeric. The proportion of cores used to train cal14C. If NULL, parallel computing is disabled.
save, output.dir	if save = TRUE, cal14C outputs are saved in output.dir.

Details

If dataset includes marine samples, the user should indicate it in the domain column by indicating "marine" for the corresponding occurrences. In this case, the function uses the marine20 curve to calibrate the related radiocarbon ages accordingly.

Value

The initial dataset with additional columns providing detailed calibration information for each occurrence. The new columns indicate the calibration curve used for each occurrence ("curve"), the calibrated radiocarbon ages ("cal_age"), and the values corresponding to the specified confidence limits derived from the density estimate of the calibrated radiocarbon ages. If save=TRUE, the dataframe is saved as xlsx file in output.dir.

Author(s)

Alessandro Mondanaro, Silvia Castiglione, Pasquale Raia

See Also

Bchron::BchronCalibrate

Examples

library(RRgeo)

## Create an example dataset with 100 random radiocarbon ages and errors
set.seed(2025)
data.frame(age=round(runif(100,20000,50000),0),
           uncertain=round(runif(100,20,300),0),
           latitude=round(runif(100,-90,90),2))->data
data$domain<-"domain"
rep("marine",5)-> data[sample(nrow(data),5),"domain"]

cal14C(dataset=data,
       age="age",
       uncertainty = "uncertain",
       latitude = "latitude",
       domain<-"domain",
       clust=NULL,
       save= FALSE)->res

RRgeo documentation built on July 2, 2025, 5:09 p.m.