From 39e36878453d4572e892f7542b2a469cf8660fac Mon Sep 17 00:00:00 2001
From: Joe Roe <git@joeroe.io>
Date: Thu, 17 Oct 2024 13:39:27 +0200
Subject: [PATCH] Add shub1_c14

As a less intensive example of aggregation. Moved from stratigraphr.
---
 NEWS.md                                   |   1 +
 R/cal_aggregate.R                         |   4 +-
 R/data.R                                  |  30 +++++++++
 data-raw/41598_2017_17096_MOESM2_ESM.xlsx | Bin 0 -> 16523 bytes
 data-raw/shub1_c14.R                      |  75 ++++++++++++++++++++++
 data/shub1_c14.rda                        | Bin 0 -> 991 bytes
 inst/REFERENCES.bib                       |  16 +++++
 man/cal_sum.Rd                            |   4 +-
 man/shub1_c14.Rd                          |  37 +++++++++++
 9 files changed, 163 insertions(+), 4 deletions(-)
 create mode 100644 data-raw/41598_2017_17096_MOESM2_ESM.xlsx
 create mode 100644 data-raw/shub1_c14.R
 create mode 100644 data/shub1_c14.rda
 create mode 100644 man/shub1_c14.Rd

diff --git a/NEWS.md b/NEWS.md
index e260695..e562e12 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -23,6 +23,7 @@
   * `c14_age()` for calculating a radiocarbon age from fraction modern.
   * `c14_f14c()` for reverse-calculating fraction modern from a radiocarbon age.
   * Decay constants `c14_decay_libby` and `c14_decay_cambridge`.
+* Added example datasets `ppnd` and `shub1_c14`
 
 # c14 0.0.0
 
diff --git a/R/cal_aggregate.R b/R/cal_aggregate.R
index 844a760..4e1481f 100644
--- a/R/cal_aggregate.R
+++ b/R/cal_aggregate.R
@@ -22,8 +22,8 @@
 #' @export
 #'
 #' @examples
-#' ppnd_cal <- c14_calibrate(ppnd$cra, ppnd$error)
-#' cal_sum(ppnd_cal)
+#' shub1_cal <- c14_calibrate(shub1_c14$c14_age, shub1_c14$c14_error)
+#' cal_sum(shub1_cal)
 cal_sum <- function(x, range = cal_age_common(x), ...) {
   # TODO: ensure x and range have the same era - or is this a job for cal validation?
   x <- cal_interpolate(x, range)
diff --git a/R/data.R b/R/data.R
index 834d54c..db98b8a 100644
--- a/R/data.R
+++ b/R/data.R
@@ -20,6 +20,36 @@
 #' @source \url{https://www.exoriente.org/associated_projects/ppnd.php} (Retrieved 2018-04-02)
 "ppnd"
 
+# shub1_radiocarbon -------------------------------------------------------
+#' Radiocarbon dates from Shubayqa 1
+#'
+#' Radiocarbon dates from Shubayqa 1, an Epipalaeolithic site in eastern Jordan,
+#' from \insertCite{Richter2017;textual}{c14}.
+#'
+#' @format A data frame with 27 rows and 8 variables:
+#' \describe{
+#'   \item{lab_id}{character; standardised lab code uniquely identifying the dated sample.}
+#'   \item{context}{integer; schematic context number the sample was found in (see details).}
+#'   \item{phase}{character; phase the sample was assigned to.}
+#'   \item{sample}{character; description of the sample context, including its real context number.}
+#'   \item{material}{character; description of the sample material.}
+#'   \item{c14_age}{integer; conventional radiocarbon age of the sample in years cal BP.}
+#'   \item{c14_error}{integer; standard error associated with the radiocarbon measurement in ± years cal BP.}
+#'   \item{outlier}{logical; whether the sample is considered an outlier.}
+#' }
+#'
+#' @details
+#'
+#' `context` refers to the schematic stratigraphy included in [stratigraphr::shub1];
+#' the real context number is described in `sample`.
+#'
+#' @source \insertCite{Richter2017;textual}{c14}
+#'
+#' @references
+#' \insertAllCited{}
+"shub1_c14"
+
+
 #' Radiocarbon laboratories
 #'
 #' @description
diff --git a/data-raw/41598_2017_17096_MOESM2_ESM.xlsx b/data-raw/41598_2017_17096_MOESM2_ESM.xlsx
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diff --git a/data-raw/shub1_c14.R b/data-raw/shub1_c14.R
new file mode 100644
index 0000000..97d8c28
--- /dev/null
+++ b/data-raw/shub1_c14.R
@@ -0,0 +1,75 @@
+# shub1_c14.R
+# Prepare shub1_c14 dataset – radiocarbon dates from Shubayqa 1 (Richter et al.
+# 2017, ESM 2, "Radiocarbon Dates")
+#
+# Citation: Richter, T., Arranz-Otaegui, A., Yeomans, L. et al. High Resolution
+#   AMS Dates from Shubayqa 1, northeast Jordan Reveal Complex Origins of Late
+#   Epipalaeolithic Natufian in the Levant. Sci Rep 7, 17025 (2017).
+#   https://doi.org/10.1038/s41598-017-17096-5
+
+shub1_c14 <- readxl::read_xlsx("data-raw/41598_2017_17096_MOESM2_ESM.xlsx")
+
+# Discard unwanted columns and normalise the names of the rest
+shub1_c14 <- dplyr::select(shub1_c14,
+                           lab_id = `Laboratory Code`,
+                           phase = `Archaeological Phase`,
+                           sample = `Sample Context ID`,
+                           material = `Sample material`,
+                           age = `C-14 Age ±1σ year BP`
+)
+
+# Fill missing phases
+shub1_c14 <- tidyr::fill(shub1_c14, phase)
+
+# Discard non-data rows
+shub1_c14 <- tidyr::drop_na(shub1_c14, lab_id)
+
+# Normalise lab IDs
+shub1_c14 <- dplyr::mutate(shub1_c14,
+                           lab_id = stringr::str_remove(lab_id, "R_Date "))
+
+# Add an outlier column (marked with a "*" next to the lab ID in the original data)
+shub1_c14 <- dplyr::mutate(shub1_c14,
+                           outlier = stringr::str_detect(lab_id, stringr::coll("*")),
+                           lab_id = stringr::str_remove(lab_id, stringr::coll("*")))
+
+# Separate age and error in radiocarbon date
+shub1_c14 <- tidyr::separate(shub1_c14, age, c("c14_age", "c14_error"), " ±")
+shub1_c14$c14_age <- as.integer(shub1_c14$c14_age)
+shub1_c14$c14_error <- as.integer(shub1_c14$c14_error)
+
+# Add schematic context numbers to match "shub1" dataset from stratigraphr
+shub1_c14 <- dplyr::mutate(shub1_c14,
+                           context = dplyr::recode(lab_id,
+                                                   `RTD-7951` = 23,
+                                                   `Beta-112146` = 24,
+                                                   `RTD-7317` = 26,
+                                                   `RTD-7318` = 27,
+                                                   `RTD-7948` = 24,
+                                                   `RTD-7947` = 22,
+                                                   `RTD-7313` = 22,
+                                                   `RTD-7311` = 22,
+                                                   `RTD-7312` = 22,
+                                                   `RTD-7314` = 22,
+                                                   `RTD-7316` = 22,
+                                                   `RTD-7315` = 22,
+                                                   `RTK-6818` = 14,
+                                                   `RTK-6820` = 14,
+                                                   `RTK-6821` = 16,
+                                                   `RTK-6822` = 16,
+                                                   `RTK-6823` = 16,
+                                                   `RTK-6813` = 12,
+                                                   `RTK-6816` = 12,
+                                                   `RTK-6819` = 5,
+                                                   `RTK-6812` = 3,
+                                                   `RTK-6817` = 2,
+                                                   `RTD-8904` = 1,
+                                                   `RTK-6814` = 1,
+                                                   `RTD-8902` = 1,
+                                                   `RTD-8903` = 1,
+                                                   `RTK-6815` = 1))
+shub1_c14 <- dplyr::relocate(shub1_c14, context, .after = lab_id)
+shub1_c14$context <- as.integer(shub1_c14$context)
+
+# Export
+usethis::use_data(shub1_c14, overwrite = TRUE)
diff --git a/data/shub1_c14.rda b/data/shub1_c14.rda
new file mode 100644
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diff --git a/inst/REFERENCES.bib b/inst/REFERENCES.bib
index 2cc42ff..6da9580 100644
--- a/inst/REFERENCES.bib
+++ b/inst/REFERENCES.bib
@@ -225,6 +225,22 @@ @ARTICLE{Reimer2020
   doi       = "10.1017/RDC.2020.41"
 }
 
+@ARTICLE{Richter2017,
+  title   = "High Resolution {AMS} Dates from Shubayqa 1, northeast Jordan
+             Reveal Complex Origins of Late Epipalaeolithic Natufian in the
+             Levant",
+  author  = "Richter, Tobias and Arranz-Otaegui, Amaia and Yeomans, Lisa and
+             Boaretto, Elisabetta",
+  journal = "Scientific reports",
+  volume  =  7,
+  number  =  1,
+  pages   = "17025",
+  month   =  dec,
+  year    =  2017,
+  issn    = "2045-2322",
+  doi     = "10.1038/s41598-017-17096-5"
+}
+
 @TECHREPORT{Stenstrom2011,
   title       = "A guide to radiocarbon units and calculations",
   author      = "Stenstr{\"o}m, Kristina Eriksson and Skog, G{\"o}ran and
diff --git a/man/cal_sum.Rd b/man/cal_sum.Rd
index 54b7b6b..d0eadc5 100644
--- a/man/cal_sum.Rd
+++ b/man/cal_sum.Rd
@@ -26,7 +26,7 @@ This function can be evaluated in parallel using \code{\link[future:plan]{future
 substantially speeds up the computation for large sets of dates.
 }
 \examples{
-ppnd_cal <- c14_calibrate(ppnd$cra, ppnd$error)
-cal_sum(ppnd_cal)
+shub1_cal <- c14_calibrate(shub1_c14$c14_age, shub1_c14$c14_error)
+cal_sum(shub1_cal)
 }
 \concept{functions for aggregating calendar probability distributions}
diff --git a/man/shub1_c14.Rd b/man/shub1_c14.Rd
new file mode 100644
index 0000000..6737b94
--- /dev/null
+++ b/man/shub1_c14.Rd
@@ -0,0 +1,37 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{shub1_c14}
+\alias{shub1_c14}
+\title{Radiocarbon dates from Shubayqa 1}
+\format{
+A data frame with 27 rows and 8 variables:
+\describe{
+\item{lab_id}{character; standardised lab code uniquely identifying the dated sample.}
+\item{context}{integer; schematic context number the sample was found in (see details).}
+\item{phase}{character; phase the sample was assigned to.}
+\item{sample}{character; description of the sample context, including its real context number.}
+\item{material}{character; description of the sample material.}
+\item{c14_age}{integer; conventional radiocarbon age of the sample in years cal BP.}
+\item{c14_error}{integer; standard error associated with the radiocarbon measurement in ± years cal BP.}
+\item{outlier}{logical; whether the sample is considered an outlier.}
+}
+}
+\source{
+\insertCite{Richter2017;textual}{c14}
+}
+\usage{
+shub1_c14
+}
+\description{
+Radiocarbon dates from Shubayqa 1, an Epipalaeolithic site in eastern Jordan,
+from \insertCite{Richter2017;textual}{c14}.
+}
+\details{
+\code{context} refers to the schematic stratigraphy included in \link[stratigraphr:shub1]{stratigraphr::shub1};
+the real context number is described in \code{sample}.
+}
+\references{
+\insertAllCited{}
+}
+\keyword{datasets}