Small additions to thermochronometry docs and uniform function name.

R-Lum · Dec 17, 2024 · 7a3c9cb · 7a3c9cb
1 parent 21e75e4
commit 7a3c9cb
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Showing 6 changed files with 41 additions and 34 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -143,7 +143,7 @@ export(extract_ROI)
 export(fit_CWCurve)
 export(fit_DoseResponseCurve)
 export(fit_EmissionSpectra)
-export(fit_IsoThermalHolding)
+export(fit_IsothermalHolding)
 export(fit_LMCurve)
 export(fit_OSLLifeTimes)
 export(fit_SurfaceExposure)

diff --git a/R/analyse_ThermochronometryData.R b/R/analyse_ThermochronometryData.R
@@ -5,31 +5,33 @@
 #'
 #' @details ##TODO
 #'
-#' @param object [character] (**required**): path to a CSV file with;
+#' @param object [character] (**required**): path to a CSV file ##TODO;
 #' alternatively a [vector] of paths
 #'
 #' @param ITL_model [character] (*with default*): type of model to fit,
-#' either `"GOK"` or `"BTS"`
+#' either `"GOK"` (default) or `"BTS"`
 #'
 #' @param plot [logical] (*with default*): enable/disable plot output
 #'
 #' @param verbose [logical] (*with default*): enable/disable terminal output
 #'
-#' @param ... further arguments passed to ...
+#' @param ... currently unused
 #'
 #' @section Function version: 0.1.0
 #'
-#' @author Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany), Svenja Riedesel, DTU Risø (Denmark)
+#' @author
+#' Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany),
+#' Svenja Riedesel, DTU Risø (Denmark)
 #'
 #' @keywords datagen
 #'
 #' @return
 #' An [RLum.Results-class] object is returned: ##TODO
 #'
-#' @seealso [analyse_FadingMeasurement], ## TODO
+#' @seealso [analyse_FadingMeasurement], [fit_IsothermalHolding]
 #'
 #' @examples
-#' # example code ##TOD
+#' # example code ##TODO
 #'
 #' @md
 #' @export
@@ -89,7 +91,7 @@ analyse_ThermochronometryData <- function(
 
     # (2) ITL Data ------------------------------------------------------------
     df_ITL <- object@data$ITL[object@data$ITL$SAMPLE == sample_names[i],]
-    results_ITL <- fit_IsoThermalHolding(
+    results_ITL <- fit_IsothermalHolding(
       data = df_ITL,
       ITL_model = ITL_model,
       rhop = results_FAD,
@@ -148,7 +150,7 @@ analyse_ThermochronometryData <- function(
     class = "RLum.Results",
     data = list(
       FAD = results_combined[["analyse_FadingMeasurement"]],
-      ITL = results_combined[["fit_IsoThermalHolding"]],
+      ITL = results_combined[["fit_IsothermalHolding"]],
       DRC = results_combined[["fit_DoseResponseCurve"]]),
     info = list(
       call = sys.call()

diff --git a/R/fit_IsothermalHolding.R b/R/fit_IsothermalHolding.R
@@ -1,4 +1,4 @@
-#' @title Fit ISO-Thermal Holding Data
+#' @title Fit Isothermal Holding Data
 #'
 #' @description ##TODO
 #'
@@ -17,29 +17,31 @@
 #'
 #' @section Function version: 0.1.0
 #'
-#' @author Svenja Riedesel, DTU Risø (Denmark),  Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
+#' @author
+#' Svenja Riedesel, DTU Risø (Denmark)
+#' Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany)
 #'
 #' @keywords datagen
 #'
 #' @return
 #' An [RLum.Results-class] object is returned: ##TODO
 #'
-#' @seealso ##TODO
+#' @seealso [analyse_ThermochronometryData], [analyse_FadingMeasurement]
 #'
 #' @examples
 #' # example code ##TOD
 #'
 #'
 #' @md
 #' @export
-fit_IsoThermalHolding <- function(
+fit_IsothermalHolding <- function(
     data,
     ITL_model = 'GOK',
     rhop,
     plot = TRUE,
     ...
 ) {
-  .set_function_name("fit_IsoThermalHolding")
+  .set_function_name("fit_IsothermalHolding")
   on.exit(.unset_function_name(), add = TRUE)
 
   ## TODOs

diff --git a/man/analyse_ThermochronometryData.Rd b/man/analyse_ThermochronometryData.Rd
diff --git a/man/fit_IsoThermalHolding.Rd → man/fit_IsothermalHolding.Rd b/man/fit_IsoThermalHolding.Rd → man/fit_IsothermalHolding.Rd
diff --git a/tests/testthat/test_fit_IsoThermalHolding.R → tests/testthat/test_fit_IsothermalHolding.R b/tests/testthat/test_fit_IsoThermalHolding.R → tests/testthat/test_fit_IsothermalHolding.R
@@ -1,30 +1,31 @@
+## load data
 input.csv <- file.path(test_path("_data"),
                        paste0("CLBR_IR", c(50, 100, 150, 225), ".csv"))
 
 test_that("input validation", {
   testthat::skip_on_cran()
 
-  expect_error(fit_IsoThermalHolding(list()),
+  expect_error(fit_IsothermalHolding(list()),
                "'data' should be of class 'character', 'RLum.Results' or")
-  expect_error(fit_IsoThermalHolding("error"),
+  expect_error(fit_IsothermalHolding("error"),
                "File does not exist")
-  expect_error(fit_IsoThermalHolding(set_RLum("RLum.Results", data = list(1))),
+  expect_error(fit_IsothermalHolding(set_RLum("RLum.Results", data = list(1))),
                "'data' has unsupported originator")
-  expect_error(fit_IsoThermalHolding(iris),
+  expect_error(fit_IsothermalHolding(iris),
                "'data' has the wrong column headers")
-  expect_error(fit_IsoThermalHolding(input.csv[1], ITL_model = "error"),
+  expect_error(fit_IsothermalHolding(input.csv[1], ITL_model = "error"),
                "'ITL_model' should be one of 'GOK' or 'BTS'")
-  expect_error(fit_IsoThermalHolding(test_path("_data/CLBR.xlsx")),
+  expect_error(fit_IsothermalHolding(test_path("_data/CLBR.xlsx")),
                "XLS/XLSX format is not supported, use CSV instead")
 })
 
 test_that("check functionality", {
   testthat::skip_on_cran()
 
-  expect_s4_class(fit_IsoThermalHolding(input.csv[1], rhop = -7),
+  expect_s4_class(fit_IsothermalHolding(input.csv[1], rhop = -7),
                   "RLum.Results")
 
   data <- .import_ThermochronometryData(input.csv[1])
-  expect_s4_class(fit_IsoThermalHolding(data, rhop = -7, mfrow = c(2, 2)),
+  expect_s4_class(fit_IsothermalHolding(data, rhop = -7, mfrow = c(2, 2)),
                   "RLum.Results")
 })