adding REACTIV and RADAR data adding scripts as vignettes

basf · Dec 17, 2024 · 0fae81b · 0fae81b
1 parent a41cdca
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -52,7 +52,7 @@ Imports:
     shinyWidgets,
     tibble,
     tidyr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends:
     R (>= 4.3),
     Matrix

diff --git a/R/data.R b/R/data.R
@@ -48,176 +48,24 @@
 #' in the correct way.
 "testDataUnspiked"
 
-#' Negative_Amant_IDEA_RADAR data used for testing the functions.
-#' It contains spiked and unspiked data.The column Conc is a factor with
-#' specified levels, as the Williams test will otherwise not order the
-#' concentrations in the correct way. This dataset is from the RADAR study
-#' validation in the lab IDEA with an inert chemical .
-"Negative_Amant_IDEA_RADAR"
-
-#' Negative_Amant_IDEA_RADAR_Spiked data used for testing the functions.
-#' It contains only spiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' IDEA with an inert chemical.
-"Negative_Amant_IDEA_RADAR_Spiked"
-
-#' Negative_Amant_IDEA_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' IDEA with an inert chemical .
-"Negative_Amant_IDEA_RADAR_Unspiked"
-
-
-#' Negative_Amant_Watchfrog_RADAR data used for testing the functions.
-#' It contains spiked and unspiked data.The column Conc is a factor with
-#' specified levels, as the Williams test will otherwise not order the
-#' concentrations in the correct way. This dataset is from the RADAR study
-#'  validation in the lab Watchfrog with an inert chemical.
-"Negative_Amant_Watchfrog_RADAR"
-
-#' Negative_Amant_Watchfrog_RADAR_Spiked data used for testing the functions.
-#' It contains only spiked data.The column Conc is a factor with specified
+#' RADAR_valid_data_table_spiked_unspiked list of data used for testing the
+#' functions.
+#' It contains spiked and unspiked data from all substances and labs from the
+#' RADAR validation studies.
+#' For all datasets the column Conc is a factor with specified
 #' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' Watchfrog with an inert chemical .
-"Negative_Amant_Watchfrog_RADAR_Spiked"
-
-#' Negative_Amant_Watchfrog_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' Watchfrog with an inert chemical .
-"Negative_Amant_Watchfrog_RADAR_Unspiked"
-
-#' Negative_Amant_FIWI_RADAR data used for testing the functions.
-#' It contains spiked and unspiked data.The column Conc is a factor with
-#' specified levels, as the Williams test will otherwise not order the
-#' concentrations in the correct way. This dataset is from the RADAR study
-#' validation in the lab FIWI with an inert chemical.
-"Negative_Amant_FIWI_RADAR"
-
-#' Negative_Amant_FIWI_RADAR_Spiked data used for testing the functions. It
-#' contains only spiked data.The column Conc is a factor with specified levels,
-#' as the Williams test will otherwise not order the concentrations in the
-#' correct way. This dataset is from the RADAR study validation in the lab
-#' FIWI with an inert chemical.
-"Negative_Amant_FIWI_RADAR_Spiked"
-
-#' Negative_Amant_FIWI_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.
-#' The column Conc is a factor with specified levels, as the Williams test will
-#' otherwise not order the concentrations in the correct way. This dataset is
-#' from the RADAR study validation in the lab FIWI with an inert chemical.
-"Negative_Amant_FIWI_RADAR_Unspiked"
-
-#' Pos_Anas_CEFAS_RADAR data used for testing the functions. It contains spiked
-#' and unspiked data.The column Conc is a factor with specified levels, as the
-#' Williams test will otherwise not order the concentrations in the correct way.
-#' This dataset is from the RADAR study validation in the lab Cefas with an
-#' androgen axis active chemical.
-"Pos_Anas_CEFAS_RADAR"
-
-#' Pos_Anas_CEFAS_RADAR_Spiked data used for testing the functions.
-#' It contains only spiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations
-#' in the correct way. This dataset is from the RADAR study validation in the
-#' lab Cefas with an androgen axis active chemical.
-"Pos_Anas_CEFAS_RADAR_Spiked"
-
-#' Pos_Anas_CEFAS_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' Cefas with an androgen axis active chemical.
-"Pos_Anas_CEFAS_RADAR_Unspiked"
-
+#' the correct way.
+"RADAR_valid_data_table_spiked_unspiked"
 
-#' Pos_Anas_FIWI_RADAR data used for testing the functions. It contains spiked
-#' and unspiked data.The column Conc is a factor with specified levels, as the
-#' Williams test will otherwise not order the concentrations in the correct way.
-#' This dataset is from the RADAR study validation in the lab FIWI with an
-#' androgen axis active chemical.
-"Pos_Anas_FIWI_RADAR"
-
-#' Pos_Anas_FIWI_RADAR_Spiked data used for testing the functions.
-#' It contains only spiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations
-#' in the correct way. This dataset is from the RADAR study validation in the
-#' lab FIWI with an androgen axis active chemical.
-"Pos_Anas_FIWI_RADAR_Spiked"
-
-#' Pos_Anas_FIWI_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' FIWI with an androgen axis active chemical.
-"Pos_Anas_FIWI_RADAR_Unspiked"
-
-
-#' Pos_Anas_IDEA_RADAR data used for testing the functions.
-#' It contains spiked and unspiked data.The column Conc is a factor with
-#' specified levels, as the Williams test will otherwise not order the
-#' concentrations in the correct way. This dataset is from the RADAR study
-#' validation in the lab IDEA with an androgen axis active chemical.
-"Pos_Anas_IDEA_RADAR"
-
-#' Pos_Anas_IDEA_RADAR_Spiked data used for testing the functions.
-#' It contains only spiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' IDEA with an androgen axis active chemical.
-"Pos_Anas_IDEA_RADAR_Spiked"
-
-#' Pos_Anas_IDEA_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' IDEA with an androgen axis active chemical.
-"Pos_Anas_IDEA_RADAR_Unspiked"
-
-#' Pos_Anas_Watchfrog_RADAR data used for testing the functions.
-#' It contains spiked and unspiked data.The column Conc is a factor with
-#' specified levels, as the Williams test will otherwise not order the
-#' concentrations in the correct way. This dataset is from the RADAR study
-#' validation in the lab Watchfrog with an androgen axis active chemical.
-"Pos_Anas_Watchfrog_RADAR"
-
-#' Pos_Anas_Watchfrog_RADAR_Spiked data used for testing the functions.
-#' It contains only spiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' Watchfrog with an androgen axis active chemical.
-"Pos_Anas_Watchfrog_RADAR_Spiked"
-
-#' Pos_Anas_Watchfrog_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' Watchfrog with an androgen axis active chemical.
-"Pos_Anas_Watchfrog_RADAR_Unspiked"
-
-#' Pos_mDHT_Fraunhofer_RADAR data used for testing the functions.
-#' It contains spiked and unspiked data.The column Conc is a factor with
-#' specified levels, as the Williams test will otherwise not order the
-#' concentrations in the correct way. This dataset is from the RADAR study
-#' validation in the lab Fraunhofer with an androgen axis active chemical.
-"Pos_mDHT_Fraunhofer_RADAR"
-
-#' Pos_mDHT_Fraunhofer_RADAR_Spiked data used for testing the functions.
-#' It contains only spiked data.The column Conc is a factor with specified
-#' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' Fraunhofer with an androgen axis active chemical.
-"Pos_mDHT_Fraunhofer_RADAR_Spiked"
 
-#' Pos_mDHT_Fraunhofer_RADAR_Unspiked data used for testing the functions.
-#' It contains only unspiked data.The column Conc is a factor with specified
+#' REACTIV_valid_data_table_spiked_unspiked list of data used for testing the
+#' functions.
+#' It contains spiked and unspiked data from all substances and labs from the
+#' REACTIV validation studies.
+#' For all datasets the column Conc is a factor with specified
 #' levels, as the Williams test will otherwise not order the concentrations in
-#' the correct way. This dataset is from the RADAR study validation in the lab
-#' Fraunhofer with an androgen axis active chemical.
-"Pos_mDHT_Fraunhofer_RADAR_Unspiked"
+#' the correct way.
+"REACTIV_valid_data_table_spiked_unspiked"
 
 
 #' REACTIV data used for testing the functions.

diff --git a/data/Negative_Amant_FIWI_RADAR.rda b/data/Negative_Amant_FIWI_RADAR.rda
diff --git a/data/Negative_Amant_FIWI_RADAR_Spiked.rda b/data/Negative_Amant_FIWI_RADAR_Spiked.rda
diff --git a/data/Negative_Amant_FIWI_RADAR_Unspiked.rda b/data/Negative_Amant_FIWI_RADAR_Unspiked.rda
diff --git a/data/Negative_Amant_IDEA_RADAR.rda b/data/Negative_Amant_IDEA_RADAR.rda
diff --git a/data/Negative_Amant_IDEA_RADAR_Spiked.rda b/data/Negative_Amant_IDEA_RADAR_Spiked.rda
diff --git a/data/Negative_Amant_IDEA_RADAR_Unspiked.rda b/data/Negative_Amant_IDEA_RADAR_Unspiked.rda
diff --git a/data/Negative_Amant_Watchfrog_RADAR.rda b/data/Negative_Amant_Watchfrog_RADAR.rda
diff --git a/data/Negative_Amant_Watchfrog_RADAR_Spiked.rda b/data/Negative_Amant_Watchfrog_RADAR_Spiked.rda
diff --git a/data/Negative_Amant_Watchfrog_RADAR_Unspiked.rda b/data/Negative_Amant_Watchfrog_RADAR_Unspiked.rda
diff --git a/data/Pos_Anas_CEFAS_RADAR.rda b/data/Pos_Anas_CEFAS_RADAR.rda
diff --git a/data/Pos_Anas_CEFAS_RADAR_Spiked.rda b/data/Pos_Anas_CEFAS_RADAR_Spiked.rda
diff --git a/data/Pos_Anas_CEFAS_RADAR_Unspiked.rda b/data/Pos_Anas_CEFAS_RADAR_Unspiked.rda
diff --git a/data/Pos_Anas_FIWI_RADAR.rda b/data/Pos_Anas_FIWI_RADAR.rda
diff --git a/data/Pos_Anas_FIWI_RADAR_Spiked.rda b/data/Pos_Anas_FIWI_RADAR_Spiked.rda
diff --git a/data/Pos_Anas_FIWI_RADAR_Unspiked.rda b/data/Pos_Anas_FIWI_RADAR_Unspiked.rda
diff --git a/data/Pos_Anas_IDEA_RADAR.rda b/data/Pos_Anas_IDEA_RADAR.rda
diff --git a/data/Pos_Anas_IDEA_RADAR_Spiked.rda b/data/Pos_Anas_IDEA_RADAR_Spiked.rda
diff --git a/data/Pos_Anas_IDEA_RADAR_Unspiked.rda b/data/Pos_Anas_IDEA_RADAR_Unspiked.rda
diff --git a/data/Pos_Anas_Watchfrog_RADAR.rda b/data/Pos_Anas_Watchfrog_RADAR.rda
diff --git a/data/Pos_Anas_Watchfrog_RADAR_Spiked.rda b/data/Pos_Anas_Watchfrog_RADAR_Spiked.rda
diff --git a/data/Pos_Anas_Watchfrog_RADAR_Unspiked.rda b/data/Pos_Anas_Watchfrog_RADAR_Unspiked.rda
diff --git a/data/Pos_mDHT_Fraunhofer_RADAR.rda b/data/Pos_mDHT_Fraunhofer_RADAR.rda
diff --git a/data/Pos_mDHT_Fraunhofer_RADAR_Spiked.rda b/data/Pos_mDHT_Fraunhofer_RADAR_Spiked.rda
diff --git a/data/Pos_mDHT_Fraunhofer_RADAR_Unspiked.rda b/data/Pos_mDHT_Fraunhofer_RADAR_Unspiked.rda
diff --git a/data/RADAR_valid_data_table_spiked_unspiked.rda b/data/RADAR_valid_data_table_spiked_unspiked.rda
diff --git a/data/REACTIV_valid_data_table_spiked_unspiked.rda b/data/REACTIV_valid_data_table_spiked_unspiked.rda
diff --git a/man/Negative_Amant_FIWI_RADAR.Rd b/man/Negative_Amant_FIWI_RADAR.Rd
diff --git a/man/Negative_Amant_FIWI_RADAR_Spiked.Rd b/man/Negative_Amant_FIWI_RADAR_Spiked.Rd
diff --git a/man/Negative_Amant_FIWI_RADAR_Unspiked.Rd b/man/Negative_Amant_FIWI_RADAR_Unspiked.Rd
diff --git a/man/Negative_Amant_IDEA_RADAR.Rd b/man/Negative_Amant_IDEA_RADAR.Rd
diff --git a/man/Negative_Amant_IDEA_RADAR_Spiked.Rd b/man/Negative_Amant_IDEA_RADAR_Spiked.Rd
diff --git a/man/Negative_Amant_IDEA_RADAR_Unspiked.Rd b/man/Negative_Amant_IDEA_RADAR_Unspiked.Rd
diff --git a/man/Negative_Amant_Watchfrog_RADAR.Rd b/man/Negative_Amant_Watchfrog_RADAR.Rd
diff --git a/man/Negative_Amant_Watchfrog_RADAR_Spiked.Rd b/man/Negative_Amant_Watchfrog_RADAR_Spiked.Rd