Finish renaming of NumberIterations.MC to n.MC in plot_GrowthCurve().

This completes the work started in fcb3404, adding the deprecation of the old name in plot_GrowthCurve() and fixing up the tests.
R-Lum · Dec 17, 2024 · cbf7328 · cbf7328
1 parent fcb3404
commit cbf7328
Show file tree

Hide file tree

Showing 16 changed files with 118 additions and 96 deletions.
diff --git a/NEWS.Rmd b/NEWS.Rmd
@@ -49,6 +49,14 @@ sometimes under a slightly different name, has now been renamed to
 also this function conforms to the rest of the package. The use of the
 older names is now deprecated and will produce a warning (#351, fixed in #408).
 
+* The `NumberIterations.MC` option of `plot_GrowthCurve()` has now been
+renamed to `n.MC` for consistency with other functions. Potentially affected
+are also `analyse_Al2O3C_ITC()`, `analyse_baSAR()`, `analyse_SAR.CWOSL()`,
+`analyse_SAR.TL()`, `calc_Huntley2006()`, `calc_Lamothe2003()`,
+as they may pass that option `plot_GrowthCurve()` via their `...` argument.
+The use of the older name is now deprecated and will produce a warning (#546,
+fixed in #547).
+
 ## Removed functions and deprecations
 * Function `Analyse_SAR.OSLdata()` is now officially deprecated,
 `analyse_SAR.CWOSL()` should be used instead (#216, fixed in #264).
@@ -94,8 +102,9 @@ within the `method_control` argument (#521, fixed in #522).
 
 ### `analyse_SAR.CWOSL()`
 * The function crashed for a list input that led to `NULL` for various
-reasons (e.g., unsuitable set of curves). Here the self-call attempted to extract information 
-from the results that did not exist in the first place instead of returning `NULL`; fixed.
+reasons (e.g., unsuitable set of curves). Here the self-call attempted to
+extract information from the results that did not exist in the first place
+instead of returning `NULL`; fixed.
 
 ### `analyse_FadingMeasurement()`
 * The function now checks for the version of the BIN-file that originated the
@@ -247,8 +256,7 @@ calls itself on each element of the list and produces a list of `RLum.Results`
 as output (#405, fixed in #434).
 * The function reported negative dose values in the MC runs plot when using
 `fit.method = "QDR"` and `mode = "extrapolation"` (#504, fixed in #505).
-* New argument added `n.MC`, this is identical to `NumberIterations.MC`. The latter
-will be deprecated in v1.1.0 and later defunct.
+* Argument `NumberIterations.MC` has been renamed to `n.MC` (#546, fixed in #547).
 
 ### `plot_RLum.Analysis()`
 * Option `plot.single` has been renamed to `plot_singlePanels` (#351, fixed

diff --git a/NEWS.md b/NEWS.md
@@ -5,7 +5,7 @@
 
 <!-- NEWS.md was auto-generated by NEWS.Rmd. Please DO NOT edit by hand!-->
 
-# Changes in version 0.9.26.9000-96 (2024-12-17)
+# Changes in version 0.9.26.9000-95 (2024-12-17)
 
 ## New functions
 
@@ -54,6 +54,15 @@
   the older names is now deprecated and will produce a warning (#351,
   fixed in \#408).
 
+- The `NumberIterations.MC` option of `plot_GrowthCurve()` has now been
+  renamed to `n.MC` for consistency with other functions. Potentially
+  affected are also `analyse_Al2O3C_ITC()`, `analyse_baSAR()`,
+  `analyse_SAR.CWOSL()`, `analyse_SAR.TL()`, `calc_Huntley2006()`,
+  `calc_Lamothe2003()`, as they may pass that option
+  `plot_GrowthCurve()` via their `...` argument. The use of the older
+  name is now deprecated and will produce a warning (#546, fixed in
+  \#547).
+
 ## Removed functions and deprecations
 
 - Function `Analyse_SAR.OSLdata()` is now officially deprecated,
@@ -296,8 +305,8 @@
 - The function reported negative dose values in the MC runs plot when
   using `fit.method = "QDR"` and `mode = "extrapolation"` (#504, fixed
   in \#505).
-- New argument added `n.MC`, this is identical to `NumberIterations.MC`.
-  The latter will be deprecated in v1.1.0 and later defunct.
+- Argument `NumberIterations.MC` has been renamed to `n.MC` (#546, fixed
+  in \#547).
 
 ### `plot_RLum.Analysis()`
 

diff --git a/R/analyse_baSAR.R b/R/analyse_baSAR.R
@@ -151,7 +151,7 @@
 #' `background.count.distribution` \tab [calc_OSLLxTxRatio] \tab `"non-poisson"` \tab set assumed count distribution\cr
 #' `fit.weights` \tab [plot_GrowthCurve] \tab `TRUE` \tab enables / disables fit weights\cr
 #' `fit.bounds` \tab [plot_GrowthCurve] \tab `TRUE` \tab enables / disables fit bounds\cr
-#' `NumberIterations.MC` \tab [plot_GrowthCurve] \tab `100` \tab number of MC runs for error calculation\cr
+#' `n.MC` \tab [plot_GrowthCurve] \tab `100` \tab number of MC runs for error calculation\cr
 #' `output.plot` \tab [plot_GrowthCurve] \tab `TRUE` \tab enables / disables dose response curve plot\cr
 #' `output.plotExtended` \tab [plot_GrowthCurve] \tab `TRUE` \tab enables / disables extended dose response curve plot\cr
 #' `recordType` \tab [get_RLum] \tab `c(OSL (UVVIS), irradiation (NA)` \tab helps for the curve selection\cr
@@ -811,7 +811,7 @@ analyse_baSAR <- function(
     ## plot_GrowthCurve()
     fit.weights = TRUE,
     fit.bounds = TRUE,
-    NumberIterations.MC = 100,
+    n.MC = 100,
     output.plot = plot,
     output.plotExtended = plot,
 
@@ -1598,7 +1598,7 @@ analyse_baSAR <- function(
           fit.weights = additional_arguments$fit.weights,
           fit.includingRepeatedRegPoints = fit.includingRepeatedRegPoints,
           fit.bounds = additional_arguments$fit.bounds,
-          NumberIterations.MC = additional_arguments$NumberIterations.MC,
+          n.MC = additional_arguments$n.MC,
           output.plot = additional_arguments$output.plot,
           output.plotExtended = additional_arguments$output.plotExtended,
           txtProgressBar = FALSE,

diff --git a/R/fit_DoseResponseCurve.R b/R/fit_DoseResponseCurve.R
@@ -141,12 +141,8 @@
 #' with the fit methods `EXP`, `EXP+LIN`, `EXP OR LIN`, `GOK`, `LambertW`
 #' Argument to be inserted for experimental application only!
 #'
-#' @param NumberIterations.MC [integer] (*with default*):
-#' number of Monte Carlo simulations for error estimation. See details.
-#'
 #' @param n.MC [integer] (*with default*):  number of Monte Carlo simulations
-#' for error estimation. Similar to `NumberIterations.MC`, which will be become deprecated
-#' at some point.
+#' for error estimation, see details.
 #'
 #' @param txtProgressBar [logical] (*with default*):
 #' enables or disables `txtProgressBar`. If `verbose = FALSE` also no
@@ -289,8 +285,7 @@ fit_DoseResponseCurve <- function(
   fit.NumberRegPoints = NULL,
   fit.NumberRegPointsReal = NULL,
   fit.bounds = TRUE,
-  NumberIterations.MC = 100,
-  n.MC = NumberIterations.MC,
+  n.MC = 100,
   txtProgressBar = TRUE,
   verbose = TRUE,
   ...
@@ -338,7 +333,6 @@ fit_DoseResponseCurve <- function(
   .validate_class(fit.bounds, "logical")
   .validate_positive_scalar(fit.NumberRegPoints, int = TRUE, null.ok = TRUE)
   .validate_positive_scalar(fit.NumberRegPointsReal, int = TRUE, null.ok = TRUE)
-  .validate_positive_scalar(NumberIterations.MC, int = TRUE)
   .validate_positive_scalar(n.MC, int = TRUE)
 
   ## convert input to data.frame

diff --git a/R/plot_DoseResponseCurve.R b/R/plot_DoseResponseCurve.R
@@ -380,7 +380,7 @@ plot_DoseResponseCurve <- function(
             axes = FALSE,
             ylim = c(0, max(norm.curve.y)),
             sub = paste0("valid fits = ", length(na.exclude(x.natural)),
-                         "/", fit.args$NumberIterations.MC),
+                         "/", fit.args$n.MC),
             col = "grey"
         ), silent = TRUE)
 

diff --git a/R/plot_GrowthCurve.R b/R/plot_GrowthCurve.R
@@ -55,9 +55,12 @@
 #' @param verbose [logical] (*with default*):
 #' enables or disables terminal feedback.
 #'
+#' @param n.MC [integer] (*with default*):
+#' number of MC runs for error calculation.
+#'
 #' @param ... Further arguments to [fit_DoseResponseCurve] (`fit_weights`,
 #' `fit_bounds`, `fit.force_through_origin`, `fit.includingRepeatedRegPoints`,
-#' `fit.NumberRegPoints`, `fit.NumberRegPointsReal`, `NumberIterations.MC`,
+#' `fit.NumberRegPoints`, `fit.NumberRegPointsReal`, `n.MC`,
 #' `txtProgressBar`) and graphical parameters to be passed (supported:
 #' `xlim`, `ylim`, `main`, `xlab`, `ylab`).
 #'
@@ -132,17 +135,24 @@ plot_GrowthCurve <- function(
   plot_singlePanels = FALSE,
   cex.global = 1,
   verbose = TRUE,
+  n.MC = 100,
   ...
 ) {
   .set_function_name("plot_GrowthCurve")
   on.exit(.unset_function_name(), add = TRUE)
 
   ## deprecated argument
-  if ("output.plotExtended.single" %in% names(list(...))) {
-    plot_singlePanels <- list(...)$output.plotExtended.single
+  extraArgs <- list(...)
+  if ("output.plotExtended.single" %in% names(extraArgs)) {
+    plot_singlePanels <- extraArgs$output.plotExtended.single
     .throw_warning("'output.plotExtended.single' is deprecated, use ",
                    "'plot_singlePanels' instead")
   }
+  if ("NumberIterations.MC" %in% names(extraArgs)) {
+    n.MC <- extraArgs$NumberIterations.MC
+    .throw_warning("'NumberIterations.MC' is deprecated, use ",
+                   "'n.MC' instead")
+  }
 
   ## input validation
   .validate_class(output.plot, "logical")
@@ -153,7 +163,8 @@ plot_GrowthCurve <- function(
 
   ## remaining input validation occurs inside the fitting function
   fit <- fit_DoseResponseCurve(sample, mode, fit.method,
-                               verbose = verbose, ...)
+                               verbose = verbose, n.MC = n.MC, ...)
+
   if (is.null(fit)) {
     if (verbose)
       message("[plot_GrowthCurve()] Fitting failed, no plot possible")

diff --git a/man/analyse_SAR.CWOSL.Rd b/man/analyse_SAR.CWOSL.Rd
diff --git a/man/analyse_baSAR.Rd b/man/analyse_baSAR.Rd
diff --git a/man/fit_DoseResponseCurve.Rd b/man/fit_DoseResponseCurve.Rd
diff --git a/man/plot_GrowthCurve.Rd b/man/plot_GrowthCurve.Rd
diff --git a/tests/testthat/_snaps/fit_DoseResponseCurve.md b/tests/testthat/_snaps/fit_DoseResponseCurve.md
@@ -111,7 +111,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -352,7 +352,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -593,7 +593,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -834,7 +834,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -1075,7 +1075,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -1316,7 +1316,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -1557,7 +1557,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -1798,7 +1798,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -2039,7 +2039,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -2280,7 +2280,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [
@@ -2521,7 +2521,7 @@
                 "names": {
                   "type": "character",
                   "attributes": {},
-                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "NumberIterations.MC"]
+                  "value": ["object", "fit.method", "mode", "fit.force_through_origin", "fit.includingRepeatedRegPoints", "fit.NumberRegPoints", "fit.NumberRegPointsReal", "fit.weights", "fit.bounds", "n.MC"]
                 }
               },
               "value": [