write simulation output analysis into a notebook

flake.nix

@@ -127,8 +127,16 @@
             buildInputs = [
               pkgs.R
               pkgs.rPackages.tidyverse
-              pkgs.rPackages.multidplyr
-              pkgs.rPackages.gaussplotR
+              pkgs.rPackages.viridis
+            ];
+          };
+          r-notebook = pkgs.mkShell {
+            buildInputs = [
+              pkgs.pandoc
+              pkgs.R
+              pkgs.rPackages.rmarkdown
+              pkgs.rPackages.knitr
+              pkgs.rPackages.tidyverse
               pkgs.rPackages.viridis
             ];
           };

notebooks/run-rmarkdown-notebook.R

+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+
+if (length(args) == 1) {
+  library(rmarkdown)
+  rmarkdown::render(args[1])
+} else {
+  write("usage: run-rmarkdown-notebook <NOTEBOOK-FILE>", stderr())
+  invokeRestart("abort")
+}