R/coffee-package.R

In Maarten14C/coffee: Chronological Ordering for Fossils and Environmental Events

#' coffee
#' @description While individual calibrated radiocarbon dates can span several centuries, combining multiple dates together with any chronological constraints can make a chronology much more robust and precise. This package, an acronym of Chronological Ordering For Fossils and Environmental Events, uses Bayesian methods to enforce the chronological ordering of radiocarbon and other dates, for example for trees with multiple radiocarbon dates spaced at exactly known intervals (e.g., every 10 annual rings; Christen 2003). Another example is sites where the relative chronological position of the dates is taken into account - the ages of dates further down a site must be older than those of dates further up (e.g., Buck et al. 1991). MCMC runs are done using the t-walk (Christen and Fox 2010).
#'
#' Note that several R packages exist to run and/or extract results from OxCal (see OxcAAR and https://github.com/gavinsimpson/roxcal).
#' However, coffee is meant as a stand-alone package that doesn't rely on having OxCal installed. Additionally, the data files of coffee are meant to be more easily readable and writeable by humans.
#'
#' References
#'
#' Buck CE, Kenworthy JB, Litton CD, Smith AFM, 1991. Combining archaeological and radiocarbon information: a Bayesian approach to calibration. Antiquity 65, 808-821.
#'
#' Christen JA, 2003. Bwigg: An Internet facility for Bayesian radiocarbon wiggle-matching. Internet Archaeology 13. \doi{10.11141/ia.13.2}
#'
#' Christen JA, Fox C 2010. A General Purpose Sampling Algorithm for Continuous Distributions (the t-walk). Bayesian Analysis 5, 263-282
#' @docType package
#' @author Maarten Blaauw <maarten.blaauw@qub.ac.uk> J. Andres Christen <jac@cimat.mx>
#' @importFrom grDevices dev.cur dev.off pdf dev.copy2pdf grey rgb dev.list extendrange
#' @importFrom graphics abline box curve hist image layout legend lines par plot points polygon segments rect axis mtext text
#' @importFrom stats approx dbeta density dgamma dnorm dunif lm quantile rnorm weighted.mean coef median cor runif var as.ts na.omit
#' @importFrom utils read.csv read.table write.table packageName txtProgressBar setTxtProgressBar
#' @importFrom data.table fread fwrite
#' @importFrom rintcal ccurve glue.ccurves
#' @importFrom rice caldist BCADtocalBP draw.dates draw.ccurve hpd
#' @name coffee
#' @keywords internal
"_PACKAGE"

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