Merge pull request #257 from R-Lum/issue_252

Set calc_Kars2008() as defunct [skip ci]

NAMESPACE

@@ -101,7 +101,6 @@ export(calc_FuchsLang2001)
 export(calc_HomogeneityTest)
 export(calc_Huntley2006)
 export(calc_IEU)
-export(calc_Kars2008)
 export(calc_Lamothe2003)
 export(calc_MaxDose)
 export(calc_MinDose)

NEWS.Rmd

@@ -10,6 +10,9 @@ header-includes:
 
 ## New functions
 
+## Removed functions
+* Function `calc_Kars2008()` (deprecated since version 0.8.1) is now officially defunct,
+`calc_Huntley2006()` should be used instead (#252, fixed in #257).
 
 ## Bugfixes
 

R/calc_Kars2008.R

@@ -1,91 +1,6 @@
-#' Apply the Kars et al. (2008) model (deprecated)
-#'
-#' A function to calculate the expected sample specific fraction of saturation
-#' following Kars et al. (2008) and Huntley (2006). This function is deprecated
-#' and will eventually be removed. Please use `calc_Huntley2006()` instead.
-#'
-#' This function applies the approach described in Kars et al. (2008),
-#' developed from the model of Huntley (2006) to calculate the expected sample
-#' specific fraction of saturation of a feldspar and also to calculate fading
-#' corrected age using this model. \eqn{\rho}' (`rhop`), the density of recombination
-#' centres, is a crucial parameter of this model and must be determined
-#' separately from a fading measurement. The function [analyse_FadingMeasurement]
-#' can be used to calculate the sample specific \eqn{\rho}' value.
-#'
-#' @param fit.method [character] (*with default*):
-#' Fit function of the dose response curve. Can either be `EXP` (the default)
-#' or `GOK`. Note that `EXP` (single saturating exponential) is the original
-#' function the model after Huntley (2006) and Kars et al. (2008) was
-#' designed to use. The use of a general-order kinetics function (`GOK`)
-#' is an experimental adaption of the model and should only be used
-#' with great care.
-#'
-#' @param ... Parameters passed to [calc_Huntley2006].
-#'
-#' @return An [RLum.Results-class] object is returned:
-#'
-#' @section Function version: 0.4.0
-#'
-#' @author
-#' Georgina E. King, University of Bern (Switzerland) \cr
-#' Christoph Burow, University of Cologne (Germany)
-#'
-#' @note **This function is deprecated and will eventually be removed from the package.**
-#' **Please use the function [calc_Huntley2006()] instead** 
-#' **(use `fit.method = "EXP"` to apply the model after Kars et al., 2008).**
-#'
-#' @keywords datagen
-#'
-#' @references
-#'
-#' Kars, R.H., Wallinga, J., Cohen, K.M., 2008. A new approach towards anomalous fading correction for feldspar
-#' IRSL dating-tests on samples in field saturation. Radiation Measurements 43, 786-790. doi:10.1016/j.radmeas.2008.01.021
-#'
-#' Huntley, D.J., 2006. An explanation of the power-law decay of luminescence.
-#' Journal of Physics: Condensed Matter 18, 1359-1365. doi:10.1088/0953-8984/18/4/020
-#'
-#' King, G.E., Herman, F., Lambert, R., Valla, P.G., Guralnik, B., 2016.
-#' Multi-OSL-thermochronometry of feldspar. Quaternary Geochronology 33, 76-87. doi:10.1016/j.quageo.2016.01.004
-#'
-#'
-#' **Further reading**
-#'
-#' Morthekai, P., Jain, M., Cunha, P.P., Azevedo, J.M., Singhvi, A.K., 2011. An attempt to correct
-#' for the fading in million year old basaltic rocks. Geochronometria 38(3), 223-230.
-#'
-#' @examples
-#'
-#' ## Load example data (sample UNIL/NB123, see ?ExampleData.Fading)
-#' data("ExampleData.Fading", envir = environment())
-#'
-#' ## (1) Set all relevant parameters
-#' # a. fading measurement data (IR50)
-#' fading_data <- ExampleData.Fading$fading.data$IR50
-#'
-#' # b. Dose response curve data
-#' data <- ExampleData.Fading$equivalentDose.data$IR50
-#'
-#' ## (2) Define required function parameters
-#' ddot <- c(7.00, 0.004)
-#' readerDdot <- c(0.134, 0.0067)
-#'
-#' # Analyse fading measurement and get an estimate of rho'.
-#' # Note that the RLum.Results object can be directly used for further processing.
-#' # The number of MC runs is reduced for this example
-#' rhop <- analyse_FadingMeasurement(fading_data, plot = TRUE, verbose = FALSE, n.MC = 10)
-#'
-#' ## (3) Apply the Kars et al. (2008) model to the data
-#' kars <- suppressWarnings(
-#'   calc_Kars2008(data = data,
-#'                 rhop = rhop,
-#'                 ddot = ddot,
-#'                 readerDdot = readerDdot,
-#'                 n.MC = 25)
-#' )
-#'
-#' @md
-#' @export
 calc_Kars2008 <- function(fit.method = "EXP", ...) {
-  .Deprecated("calc_Huntley2006")
+  # nocov start
+  .Defunct("calc_Huntley2006")
   calc_Huntley2006(fit.method = fit.method, ...)
-}
+  # nocov end
+}

tests/testthat/test_calc_Huntley2006.R

@@ -111,59 +111,6 @@ test_that("check values from calc_Huntley2008()", {
   expect_equal(round(sum(residuals(huntley$fits$unfaded)),2),  0)
 })
 
-## COMPARE calc_Kars2008 (deprecated) vs. re-named calc_Huntley2006
-test_that("compare deprecated calc_Kars2008 and calc_Huntley2006", {
-  testthat::skip_on_cran()
-
-  expect_identical({
-    set.seed(1)
-    calc_Huntley2006(
-      data = data,
-      rhop = rhop,
-      ddot = ddot,
-      readerDdot = readerDdot,
-      n.MC = 50,
-      fit.method = "EXP",
-      plot = FALSE, verbose = FALSE)$results
-  }, {
-    set.seed(1)
-    suppressWarnings(
-    calc_Kars2008(
-      data = data,
-      rhop = rhop,
-      ddot = ddot,
-      readerDdot = readerDdot,
-      n.MC = 50,
-      fit.method = "EXP",
-      plot = FALSE, verbose = FALSE)$results
-    )
-  })#EndOf::expect_identical
-
-  expect_identical({
-    set.seed(1)
-    calc_Huntley2006(
-      data = data,
-      rhop = rhop,
-      ddot = ddot,
-      readerDdot = readerDdot,
-      n.MC = 500,
-      fit.method = "GOK",
-      plot = FALSE, verbose = FALSE)$results
-  }, {
-    set.seed(1)
-    suppressWarnings(
-      calc_Kars2008(
-        data = data,
-        rhop = rhop,
-        ddot = ddot,
-        readerDdot = readerDdot,
-        n.MC = 500,
-        fit.method = "GOK",
-        plot = FALSE, verbose = FALSE)$results
-    )
-  })#EndOf::expect_identical
-})
-
 test_that("Further tests calc_Huntley2006", {
   testthat::skip_on_cran()