update vignettes

vignettes/Power_analysis_REACTIV.Rmd

@@ -69,7 +69,7 @@ resultList
 
 ### Analysis
 
-```{r eval=TRUE, output=FALSE}
+```{r eval=TRUE, echo=TRUE, results='hide', message=FALSE}
 devtools::install_github("thomasp85/patchwork")
 #devtools::install_github("basf/xeredar")
 purrr::map(c("dplyr","tidyr", "purrr", "furrr", "gt","easystats","rlang","drc", "DHARMa", "devtools", "patchwork", "ggplot2"), require, character.only = TRUE)

vignettes/Running_RADAR_analysis.Rmd

@@ -1,6 +1,7 @@
 ---
 title: "Analysis of all RADAR validation studies"
-output: rmarkdown::html_vignette
+author: "Inka Marie Spyridonov"
+date: "2024-12-17"
 vignette: >
   %\VignetteIndexEntry{Analysis of RADAR validation studies}
   %\VignetteEngine{knitr::rmarkdown}
@@ -35,9 +36,7 @@ The following sections contain the code that needs to be executed to reproduce t
 
 
 ### Functions
-```{r}
-
-
+```{r eval=TRUE, echo=TRUE, results='hide', message=FALSE}
 decreasing_alpha <- function(df, vector){
   for(i in vector){
     result <- xeredar::data_prep(df, row=FALSE, alpha = i, trim=FALSE, outlier = FALSE)
@@ -111,14 +110,12 @@ significances <- function(df, Williams= FALSE){
   }
 }
 
-
-
 ```
 
 ### Checking all RADAR validation studies for ED activity
 
 
-```{r eval=TRUE, output=FALSE}
+```{r eval=TRUE, echo=TRUE, results='hide', message=FALSE}
 devtools::install_github("thomasp85/patchwork")
 #devtools::install_github("basf/xeredar")
 purrr::map(c("tidyverse","tidyr", "purrr", "furrr", "gt","easystats","rlang","drc", "DHARMa", "devtools", "patchwork"), require, character.only = TRUE)
@@ -127,14 +124,11 @@ library(patchwork)
 
 
 
-```{r eval = TRUE, output = FALSE}
+```{r eval=TRUE, echo=TRUE, results='hide', message=FALSE, warning=FALSE, fig.show='hide'}
 
 
 anovas <- purrr::imap(xeredar::RADAR_valid_data_table_spiked_unspiked, ~ check(.x, .y)) |> purrr::flatten()
 
-
-resultList <- 
-
 anovas_unspiked <- anovas[stringr::str_detect(names(anovas), "Unspiked")]
 anovas_spiked<- anovas[!stringr::str_detect(names(anovas), "Unspiked")]
 
@@ -203,7 +197,7 @@ Result_Radar_valid <- dplyr::full_join(significances_Spiked, significances_Unspi
 ```
 
 
-```{r eval=TRUE}
+```{r eval=TRUE, echo=TRUE, message=FALSE}
 gt::gt(Result_Radar_valid) |>
     gt::tab_style(
     style = list(

vignettes/Software_validation.Rmd

@@ -159,11 +159,6 @@ gt::gt(thyroid_active, rowname_col = "substance") |>
 ```
 
 
-##
-
-
-
-
 
 
 

vignettes/creating_REACTIV_data.qmd → vignettes/creating_REACTIV_data.Rmd

@@ -50,11 +50,11 @@ resultList
 
 ### Analysis
 
-```{r eval=TRUE}
+```{r eval=TRUE, echo=TRUE, results='hide', message=FALSE, warning=FALSE, fig.show='hide'}
 
 #devtools::install_git("https://gitlab.roqs.basf.net/WillmsIM/xetaana.git")
 #install.packages("easystats")
-lapply(c("tidyverse","xeredar","tidyr", "purrr", "furrr", "gt","easystats","rlang","drc", "DHARMa", "devtools"), require, character.only = TRUE)
+lapply(c("tidyverse","xeredar","tidyr", "purrr", "furrr", "gt","easystats","rlang","drc", "DHARMa", "devtools", "ggplot2"), require, character.only = TRUE)
 
 ```
 
@@ -106,12 +106,12 @@ gt::gt(xeredar::SimulationInfoWTzeroInflated) |> gt::tab_caption(caption = "Summ
 ```{r eval=TRUE}
 xeredar::SimulationInfoWTzeroInflated |> 
   dplyr::select(adj_ICC, Country, Spiked) |> 
-  dplyr::mutate(Spiked = if_else(Spiked == TRUE, "Spiked", "Unspiked")) |>
-  ggplot(aes(y= as.numeric(adj_ICC), x= Country, color = Spiked))+
-  geom_jitter(alpha= 0.5,  width = 0.2)+
-  geom_abline(slope=0, intercept= 0.1337804)+
-  labs(color='Spiked or Unspiked?')+
-  ylab(label="adjusted ICC value")+
+  dplyr::mutate(Spiked = dplyr::if_else(Spiked == TRUE, "Spiked", "Unspiked")) |>
+  ggplot2::ggplot(aes(y= as.numeric(adj_ICC), x= Country, color = Spiked)) +
+  geom_jitter(alpha= 0.5,  width = 0.2) +
+  geom_abline(slope=0, intercept= 0.1337804) +
+  labs(color='Spiked or Unspiked?') +
+  ylab(label="adjusted ICC value") +
   xlab(label="")
 ```
 
@@ -451,45 +451,5 @@ resultsUnspiked_power_reactive  <- dplyr::bind_rows(resultsUnspiked_power_reacti
 
 resultsUnspiked_power_reactive <- dplyr::left_join(resultsUnspiked_power_reactive, perc_effect_e_dose_Unspiked)
 
-usethis::use_data(resultsUnspiked_power_reactive, overwrite = TRUE)
 ```
 
-```{r eval=TRUE}
-breaks=c("mixedDunnett","PooledDunnetts","pooledDunns" ,"mixedWilliamsIncrease")
-
-labels=c("mixed Dunnett", "Pooled Dunnetts","Pooled Dunns","mixed Williams")
-
-type1_error_Spiked <- xeredar::resultsSpiked_power_reactive |> dplyr::arrange(e, percEffect) |> filter(percEffect <= 1) |>
-  ggplot2::ggplot(aes(x=PercentSign, color=Test))+
-  geom_boxplot( alpha= 0.5)+
-  scale_x_continuous(labels = scales::percent, trans = "log10")+
-  xlab("% significant tests")
-
-power_Spiked <- xeredar::resultsSpiked_power_reactive |> dplyr::arrange(e, percEffect) |>  dplyr::filter(Conc==100) |>
-  ggplot2::ggplot(ggplot2::aes(x=percEffect, y=PercentSign, color=Test))+
-  ggplot2::geom_line(linewidth=1.2)+
-  ggplot2::geom_hline(x=as.numeric(0:300), yintercept=0.8)+
-  ggplot2::scale_color_discrete(name  ="Tests",
-                      breaks = breaks,
-                      labels = labels)+
-  ggplot2::ylab("% significant")+
-  ggplot2::xlab("% effect")
-
-power_Unspiked <- xeredar::resultsUnspiked_power_reactive |> dplyr::arrange(e, percEffect) |>  dplyr::filter(Conc==100) |>
-  ggplot2::ggplot(ggplot2::aes(x=percEffect, y=PercentSign, color=Test))+
-  ggplot2::geom_line(linewidth=1.2)+
-  ggplot2::geom_hline(x=as.numeric(0:300), yintercept=0.8)+
-  ggplot2::scale_color_discrete(name  ="Tests",
-                      breaks = breaks,
-                      labels = labels)+
-  ggplot2::ylab("% significant")+
-  ggplot2::xlab("% effect")
-
-type1_error_Spiked <- xeredar::resultsSpiked_power_reactive |> dplyr::arrange(e, percEffect) |> filter(percEffect <= 1) |>
-  ggplot2::ggplot(aes(x=PercentSign, color=Test))+
-  geom_boxplot( alpha= 0.5)+
-  scale_x_continuous(labels = scales::percent, trans = "log10")+
-  xlab("% significant tests")
-
-power_Spiked + power_Unspiked
-```

vignettes/default.nix

@@ -1,6 +1,6 @@
-# This file was generated by the {rix} R package v0.12.4 on 2024-12-19
+# This file was generated by the {rix} R package v0.12.4 on 2025-01-06
 # with following call:
-# >rix::rix(r_ver = "4989a246d7a390a859852baddb1013f825435cee",
+# >rix::rix(r_ver = "bf689c40d035239a489de5997a4da5352434632e",
 #  > r_pkgs = c("tidyverse",
 #  > "tidyr",
 #  > "purrr",
@@ -20,11 +20,11 @@
 #  > ide = "rstudio",
 #  > project_path = "./vignettes",
 #  > overwrite = TRUE)
-# It uses nixpkgs' revision 4989a246d7a390a859852baddb1013f825435cee for reproducibility purposes
+# It uses nixpkgs' revision bf689c40d035239a489de5997a4da5352434632e for reproducibility purposes
 # which will install R version latest.
 # Report any issues to https://github.com/ropensci/rix
 let
- pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/4989a246d7a390a859852baddb1013f825435cee.tar.gz") {};
+ pkgs = import (fetchTarball "https://github.com/NixOS/nixpkgs/archive/bf689c40d035239a489de5997a4da5352434632e.tar.gz") {};
 
   rpkgs = builtins.attrValues {
     inherit (pkgs.rPackages)