final package

DESCRIPTION

@@ -28,7 +28,6 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Imports:
-    ARTool,
     broom,
     bslib,
     car,
@@ -37,30 +36,30 @@ Imports:
     fBasics,
     ggplot2,
     ggpubr, 
-    gt,
     lme4 (>= 1.1-35.5),
-    magrittr,
     MASS,
     methods,
     multcomp,
     parameters,
     performance,
-    readxl,
     rlang,
+    tibble,
+    tidyr,
     shiny,
     shinydashboard,
-    shinyWidgets,
-    tibble,
-    tidyr
+    shinyWidgets
 RoxygenNote: 7.3.2
 Depends:
-    R (>= 4.3),
-    Matrix
+    R (>= 4.3)
 Suggests: 
+    ARTool,
+    gt,
     rmarkdown,
     testthat (>= 3.0.0),
     purrr,
     stringr,
-    knitr
+    knitr,
+    devtools,
+    readxl
 Config/testthat/edition: 3
 VignetteBuilder: knitr

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(ana)
 export(anova_assumpts)
 export(box_plots_ana)
@@ -21,7 +20,6 @@ export(williamsTest)
 import(shiny)
 import(shinyWidgets)
 import(shinydashboard)
-importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(rlang,.data)
 importFrom(shiny,runApp)

R/XETAfunctions.R

@@ -341,35 +341,43 @@ anova_assumpts <- function(dagostino, mixedaov, alpha) {
 #'  row = FALSE)
 #'
 #' # RADAR example androgen axis active chemical (data from validation studies)
-#' result4_1 <- data_prep(xeredar::Pos_Anas_CEFAS_RADAR_Unspiked,
+#' result4_1 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrozoleCEFAS_Unspiked"]],
 #'   row = FALSE, dagostino = TRUE, trimming = TRUE, outlier = TRUE,
 #'   boxcox = FALSE, artc = FALSE, alpha = 0
 #' )
-#' result4_2 <- data_prep(xeredar::Pos_Anas_CEFAS_RADAR_Spiked,
+#' result4_2 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrozoleCEFAS_Spiked"]],
 #'   row = FALSE, dagostino = TRUE, trimming = FALSE, outlier = FALSE,
 #'   boxcox = FALSE, alpha = 0
 #' )
-#' result5_1 <- data_prep(xeredar::Pos_Anas_FIWI_RADAR_Unspiked,
+#' result5_1 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrozoleFIWI_Unspiked"]],
 #'   row = FALSE,
 #'   dagostino = TRUE, trimming = TRUE, outlier = FALSE,
 #'   boxcox = FALSE, artc = FALSE, alpha = 0.05
 #' )
-#' result5_2 <- data_prep(xeredar::Pos_Anas_FIWI_RADAR_Spiked,
+#' result5_2 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrozoleFIWI_Spiked"]],
 #'   row = FALSE,
 #'   dagostino = TRUE, trimming = FALSE
 #' )
-#' result6_1 <- data_prep(xeredar::Pos_Anas_IDEA_RADAR_Unspiked,
+#' result6_1 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrozoleFIWI_Unspiked"]],
 #'   row = FALSE,
 #'   dagostino = TRUE, trimming = FALSE
 #' )
-#' result6_2 <- data_prep(xeredar::Pos_Anas_IDEA_RADAR_Spiked,
+#' result6_2 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrozoleIDEA_Spiked"]],
 #'   row = FALSE,
 #'   dagostino = TRUE, trimming = FALSE
 #' )
-#' result7_1 <- data_prep(xeredar::Pos_Anas_Watchfrog_RADAR_Unspiked,
+#' result7_1 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrazoleWATCHFR_Unspiked"]],
 #'   row = FALSE, dagostino = TRUE, trimming = FALSE
 #' )
-#' result7_2 <- data_prep(xeredar::Pos_Anas_Watchfrog_RADAR_Spiked,
+#' result7_2 <- data_prep(
+#' xeredar::RADAR_valid_data_table_spiked_unspiked[["AnastrazoleWATCHFR_Spiked"]],
 #'   row = FALSE,
 #'   dagostino = TRUE, trimming = FALSE
 #' )

R/data.R

@@ -73,3 +73,27 @@
 #' levels, as the Williams test will otherwise not order the concentrations in
 #' the correct way. This dataset is an artificiald dataset.
 "reactiv_data"
+
+#' Mean values for each concentration group, compound and concentration for the power analysis 
+#' based on REACTIV validation data. Based on these mean values, the simulation is carried out.
+"MeansAllStudiesperConcSpiked"
+
+#' Mean values for each concentration group, compound and concentration for the power analysis 
+#' based on REACTIV validation data. Based on these mean values, the simulation is carried out.
+"MeansAllStudiesperConcUnspiked"
+
+#' Data containing information from variance analysis of original REACTIV validation studies. 
+#' Based on this data, and on MeansAllStudiesperConcSpiked and MeansAllStudiesperConcUnspiked the simualted data is created.
+"Simulation_Info"
+
+
+#' Data containing information from variance analysis of original REACTIV validation studies only that the zero inflated studies were filtered out. 
+#' Based on this data, and on MeansAllStudiesperConcSpiked and MeansAllStudiesperConcUnspiked the simualted data is created.
+"SimulationInfoWTzeroInflated"
+
+#' Results  of power analysis of simulated spiked REACTIV data
+"resultsSpiked_power_reactive"
+
+
+#' Results  of power analysis of simulated unspiked REACTIV data
+"resultsUnspiked_power_reactive"

README.md

@@ -1,4 +1,4 @@
-Background
+
 # xeredar <a href="https://dplyr.tidyverse.org"><img src="man/figures/logo.png" align="right" height="138" /></a>
 
 <!-- badges: start -->
@@ -7,7 +7,7 @@ Background
 <!-- badges: end -->
 
 
-
+Background
 ==========
 
 The package xeredar is an R-package for analysis of the New Approach