final reproducible environment

vignettes/.Rprofile

@@ -0,0 +1,40 @@
+### File generated by `rix::rix_init()` ###
+# 1. Currently, system RStudio does not inherit environmental variables
+#   defined in `$HOME/.zshrc`, `$HOME/.bashrc` and alike. This is workaround to
+#   make the path of the nix store and hence basic nix commands available
+#   in an RStudio session
+# 2. For nix-R session, remove `R_LIBS_USER`, system's R user library.`.
+#   This guarantees no user libraries from the system are loaded and only
+#   R packages in the Nix store are used. This makes Nix-R behave in pure manner
+#   at run-time.
+{
+    is_rstudio <- Sys.getenv("RSTUDIO") == "1"
+    is_nix_r <- nzchar(Sys.getenv("NIX_STORE"))
+    if (isFALSE(is_nix_r) && isTRUE(is_rstudio)) {
+        cat("{rix} detected RStudio R session")
+        old_path <- Sys.getenv("PATH")
+        nix_path <- "/nix/var/nix/profiles/default/bin"
+        has_nix_path <- any(grepl(nix_path, old_path))
+        if (isFALSE(has_nix_path)) {
+            Sys.setenv(PATH = paste(old_path, nix_path, sep = ":"))
+        }
+        rm(old_path, nix_path)
+    }
+    if (isTRUE(is_nix_r)) {
+        install.packages <- function(...) {
+            stop("You are currently in an R session running from Nix.\n", "Don't install packages using install.packages(),\nadd them to ", "the default.nix file instead.")
+        }
+        update.packages <- function(...) {
+            stop("You are currently in an R session running from Nix.\n", "Don't update packages using update.packages(),\n", "generate a new default.nix with a more recent version of R. ", "If you need bleeding edge packages, read the", "'Understanding the rPackages set release cycle and using ", "bleeding edge packages' vignette.")
+        }
+        remove.packages <- function(...) {
+            stop("You are currently in an R session running from Nix.\n", "Don't remove packages using `remove.packages()``,\ndelete them ", "from the default.nix file instead.")
+        }
+        current_paths <- .libPaths()
+        user_dir <- grep(paste(userlib_paths, collapse = "|"), current_paths, fixed = TRUE)
+        new_paths <- current_paths[-user_dir]
+        .libPaths(new_paths)
+        rm(current_paths, userlib_paths, user_dir, new_paths)
+    }
+    rm(is_rstudio, is_nix_r)
+}

vignettes/Power_analysis_REACTIV.Rmd

@@ -2,6 +2,7 @@
 title: "Reproducing power analysis based on REACTIV validation studies of publication"
 author: "Inka Marie Spyridonov"
 date: "2024-12-17"
+output: rmarkdwon::html_vignette
 vignette: >
   %\VignetteIndexEntry{Power analysis based on REACTIV validation studies}
   %\VignetteEngine{knitr::rmarkdown}

vignettes/Running_RADAR_analysis.Rmd

@@ -2,6 +2,7 @@
 title: "Analysis of all RADAR validation studies"
 author: "Inka Marie Spyridonov"
 date: "2024-12-17"
+output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Analysis of all RADAR validation studies}
   %\VignetteEngine{knitr::rmarkdown}
@@ -21,7 +22,7 @@ rix::rix(
   tex_pkgs = c("amsmath"),
   git_pkgs = list(package_name = "xeredar",
                   repo_url = "https://github.com/basf/xeredar",
-                  commit = "2b85763"),
+                  commit = "ca1d789"),
   ide = "rstudio",
   project_path = "./vignettes",
   overwrite = TRUE

vignettes/User_guide.Rmd

@@ -1,5 +1,6 @@
 ---
 title: "User guide"
+output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{User guide}
   %\VignetteEngine{knitr::rmarkdown}

vignettes/creating_REACTIV_data.Rmd

@@ -2,6 +2,7 @@
 title: "Creating simulated REACTIV data for power analysis of publication"
 author: "Inka Marie Spyridonov"
 date: "2024-12-17"
+output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{Creating simulated REACTIV data for power analysis}
   %\VignetteEngine{knitr::rmarkdown}

vignettes/default.nix

@@ -1,4 +1,4 @@
-# This file was generated by the {rix} R package v0.12.4 on 2025-01-07
+# This file was generated by the {rix} R package v0.12.4 on 2025-01-08
 # with following call:
 # >rix::rix(r_ver = "6f3340bf0f888d0fda9a3b91dd5b3a9b05d08212",
 #  > r_pkgs = c("tidyverse",
@@ -15,7 +15,7 @@
 #  > system_pkgs = NULL,
 #  > git_pkgs = list(package_name = "xeredar",
 #  > repo_url = "https://github.com/basf/xeredar",
-#  > commit = "2b85763"),
+#  > commit = "ca1d789"),
 #  > tex_pkgs = c("amsmath"),
 #  > ide = "rstudio",
 #  > project_path = "./vignettes",
@@ -46,13 +46,11 @@ let
       name = "xeredar";
       src = pkgs.fetchgit {
         url = "https://github.com/basf/xeredar";
-        rev = "2b85763";
-        sha256 = "sha256-Yxbp8Qi3TOXFhdgZ2shRNSuN0gkermY8OEAMVwhIlp8=";
+        rev = "ca1d789";
+        sha256 = "sha256-OzTJkNdThqK9lI3IagtBD6MWt27Qo3oIObOCHBN75qA=";
       };
       propagatedBuildInputs = builtins.attrValues {
         inherit (pkgs.rPackages) 
-          Matrix
-          ARTool
           broom
           bslib
           car
@@ -61,20 +59,17 @@ let
           fBasics
           ggplot2
           ggpubr
-          gt
           lme4
-          magrittr
           MASS
           multcomp
           parameters
           performance
-          readxl
           rlang
+          tibble
+          tidyr
           shiny
           shinydashboard
-          shinyWidgets
-          tibble
-          tidyr;
+          shinyWidgets;
       };
     })
    ];