R/utils_DRAC.R

In R-Lum/Luminescence: Comprehensive Luminescence Dating Data Analysis

## FUNCTIONS -------------------------------------------------------------------

#' @title Subset the DRAC reference
#'
#' @param x [data.frame] or [DRAC.list]
#'
#'
#' @md
#' @noRd
.get_DRAC_references <- function(x) {
  refs <- DRAC_refs()
  refs_names <- names(refs)

  used <- list(refs = NULL, desc = NULL)

  # TI:4 - Conversion factors
  ref_tmp <- unique(x[[.search_key(x, "TI:4")]])
  for (i in 1:length(ref_tmp)) {
    if (ref_tmp[i] == "X")
      next()

    used$refs <- c(used$refs, refs[refs_names %in% ref_tmp[i]])
    used$desc <- c(used$desc, "Conversion factors")
  }

  # TI:13 - External Rubidium
  ref_tmp <- unique(x[[.search_key(x, "TI:13")]])
  if (any(ref_tmp == "Y")) {
    used$refs <- c(used$refs, refs["Mejdahl1987"])
    used$desc <- c(used$desc, "External rubidium")
  }

  # TI:22 - Internal Rubidium
  ref_tmp <- unique(x[[.search_key(x, "TI:22")]])
  if (any(ref_tmp == "Y")) {
    used$refs <- c(used$refs, refs["Mejdahl1987"])
    used$desc <- c(used$desc, "Internal rubidium")
  }

  # TI:31 - Gamma dose rate scaling
  ref_tmp <- unique(x[[.search_key(x, "TI:31")]])
  if (any(ref_tmp == "Y")) {
    used$refs <- c(used$refs, refs["Aitken1985"])
    used$desc <- c(used$desc, "Gamma dose rate scaling")
  }

  # TI:34 - alpha grain size attenuation
  ref_tmp <- unique(x[[.search_key(x, "TI:34")]])
  for (i in 1:length(ref_tmp)) {
    if (ref_tmp[i] == "X")
      next
    used$refs <- c(used$refs, refs[refs_names %in% ref_tmp[i]])
    used$desc <- c(used$desc, "Alpha grain size attenuation factors")
  }

  # TI:35 - Beta grain size attenuation
  ref_tmp <- unique(x[[.search_key(x, "TI:35")]])
  for (i in 1:length(ref_tmp)) {
    if (ref_tmp[i] == "X")
      next
    used$refs <- c(used$refs, refs[refs_names %in% ref_tmp[i]])
    used$desc <- c(used$desc, "Beta grain size attenuation factors")
  }

  # TI:38 - beta etch attenuation factor
  ref_tmp <- unique(x[[.search_key(x, "TI:38")]])
  for (i in 1:length(ref_tmp)) {
    if (ref_tmp[i] == "X")
      next
    used$refs <- c(used$refs, refs[refs_names %in% ref_tmp[i]])
    used$desc <- c(used$desc, "Beta etch attenuation factor")
  }

  # TI:50 - Cosmic dose rate
  ref_tmp <- unique(x[[.search_key(x, "TI:50")]])
  if (any(ref_tmp == "X")) {
    used$refs <- c(used$refs, refs[c("PrescottHutton1994", "PrescottStephan1982")])
    used$desc <- c(used$desc, c("Cosmic dose rate", "Cosmic dose rate"))
  }

  return(used)
}

## REFERENCE LIST --------------------------------------------------------------
DRAC_refs <- function() {

  list(
    Aitken1985 = bibentry(
      bibtype = "Book",
      author = person("M.J.", "Aitken"),
      title = "Thermoluminescence Dating",
      year = "1985",
      publisher = "Academic Press",
      adress = "London"
    ),

    AitkenXie1990 = bibentry(
      bibtype = "Article",
      author = c(
        person("M.J.", "Aitken"),
        person("J.", "Xie")
      ),
      title = "Moisture correction for annual gamma dose",
      year = "1990",
      journal = "Ancient TL",
      volume = "8",
      pages = "6-9"
    ),

    AdamiecAitken1998 = bibentry(
      bibtype = "Article",
      author = c(
        person("G.", "Adamiec"),
        person("M.J.", "Aitken")
      ),
      title = "Dose-rate conversion factors: update",
      year = "1998",
      journal = "Ancient TL",
      volume = "16",
      pages = "37-46"
    ),

    Guerinetal2011 = bibentry(
      bibtype = "Article",
      author = c(
        person("G.", "Guerin"),
        person("N.", "Mercier"),
        person("G.", "Adamiec")
      ),
      title = "Dose-rate conversion factors: update",
      year = "2011",
      journal = "Ancient TL",
      volume = "29",
      pages = "5-8",
      url = "http://ancienttl.org/ATL_29-1_2011/ATL_29-1_Guerin_p5-8.pdf"
    ),

    Liritzisetal2013 = bibentry(
      bibtype = "Article",
      author = c(
        person("I.", "Liritzis"),
        person("K.", "Stamoulis"),
        person("C.", "Papachristodoulou"),
        person("K.", "Ioannides")
      ),
      title = "A re-evaluation of radiation dose-rate conversion factors. ",
      year = "2013",
      journal = "Mediterranean Archaeology and Archaeometry",
      volume = "13",
      pages = "1-15",
      url = "http://maajournal.com/Issues/2012/pdf/FullTextLiritzis.pdf"
    ),

    Bell1979 = bibentry(
      bibtype = "Article",
      author = c(
        person("W.T.", "Bell")
      ),
      title = "Attenuation factors for the absorbed radiation dose in quartz inclusions for thermoluminescence dating",
      year = "1979",
      journal = "Ancient TL",
      volume = "8",
      pages = "1-12"
    ),

    Bell1980 = bibentry(
      bibtype = "Article",
      author = c(
        person("W.T.", "Bell")
      ),
      title = "Alpha attenuation in Quartz grains for Thermoluminescence Dating",
      year = "1980",
      journal = "Ancient TL",
      volume = "12",
      pages = "4-8"
    ),

    Brennanetal1991 = bibentry(
      bibtype = "Article",
      author = c(
        person("B.J.", "Brennan"),
        person("R.G.", "Lyons"),
        person("S.W.", "Phillips")
      ),
      title = "Attenuation of alpha particle track dose for spherical grains",
      year = "1991",
      journal = "International Journal of Radiation Applications and Instrumentation. Part D. Nuclear Tracks and Radiation Measurements",
      volume = "18",
      pages = "249-253"
    ),

    Cresswelletal2018 = bibentry(
      bibtype = "Article",
      author = c(
        person("A.J.", "Cresswell"),
        person("J.", "Carter"),
        person("D.C.W.", "Sanderson")
      ),
      title = "Dose rate conversion parameters: Assessment of nuclear data",
      year = "2008",
      journal = "Radiation Measurements",
      volume = "120",
      pages = "195-201",
      doi = "10.1016/j.radmeas.2018.02.007"
    ),

    Mejdahl1979 = bibentry(
      bibtype = "Article",
      author = c(
        person("V.", "Mejdahl")
      ),
      title = "Thermoluminescence Dating: Beta-Dose Attenuation in Quartz Grains",
      year = "1979",
      journal = "Archaeometry",
      volume = "21",
      pages = "61-72"
    ),

    Mejdahl1987 = bibentry(
      bibtype = "Article",
      author = c(
        person("V.", "Mejdahl")
      ),
      title = "Internal radioactivity in quartz and feldspar grains",
      year = "1987",
      journal = "Ancient TL",
      volume = "5",
      pages = "10-17"
    ),

    Brennan2003 = bibentry(
      bibtype = "Article",
      author = c(
        person("B.J.", "Brennan")
      ),
      title = "Beta doses to spherical grains",
      year = "2003",
      journal = "Radiation Measurements",
      volume = "37",
      pages = "299-303"
    ),

    `Guerinetal2012-Q` = bibentry(
      bibtype = "Article",
      author = c(
        person("G.", "Guerin"),
        person("N.", "Mercier"),
        person("R.", "Nathan"),
        person("G.", "Adamiec"),
        person("Y.", "Lefrais")
      ),
      title = "On the use of the infinite matrix assumption and associated concepts: A critical review",
      year = "2012",
      journal = "Radiation Measurements",
      volume = "47",
      pages = "778-785"
    ),

    `Guerinetal2012-F` = bibentry(
      bibtype = "Article",
      author = c(
        person("G.", "Guerin"),
        person("N.", "Mercier"),
        person("R.", "Nathan"),
        person("G.", "Adamiec"),
        person("Y.", "Lefrais")
      ),
      title = "On the use of the infinite matrix assumption and associated concepts: A critical review",
      year = "2012",
      journal = "Radiation Measurements",
      volume = "47",
      pages = "778-785"
    ),

    PrescottHutton1994 = bibentry(
      bibtype = "Article",
      author = c(
        person("J.R.", "Prescott"),
        person("J.T.", "Hutton")
      ),
      title = "Cosmic ray contributions to dose rates for luminescence and ESR dating: Large depths and long-term time variations",
      year = "1994",
      journal = "Radiation Measurements",
      volume = "23",
      pages = "497-500"
    ),

    PrescottStephan1982 = bibentry(
      bibtype = "Article",
      author = c(
        person("J.R.", "Prescott"),
        person("L.G.", "Stephan")
      ),
      title = "The contribution of cosmic radiation to the environmental dose for thermoluminescence dating",
      year = "1982",
      journal = "PACT",
      volume = "6",
      pages = "17-25"
    ),

    Readhead2002 = bibentry(
      bibtype = "Article",
      author = c(
        person("M.L.", "ReadHead")
      ),
      title = "Absorbed dose fraction for 87Rb beta particles",
      year = "2002",
      journal = "Ancient TL",
      volume = "20",
      pages = "25-29"
    )
  )
}

## internal helper to search key from the DRAC table
.search_key <- function(x, key) {
  if(inherits(x, "DRAC.list"))
    which(vapply(x, function(i) attr(i, "key") == key, logical(1)))
  else
    which(colnames(x) == key)
}