End-to-end reproducibility
- Clone this repo (make sure to start a new Rproject associated with it)
- Check that you have
GNU Makeon your device - Make sure you have these three packages installed:
here,tidyverse,modelsummary
We'll simulate everyone's nightmare:
- You have built your "coding pipeline" (see
scriptsanddraft.Rmd) and are ready to do something with it - Then, you (or a colleague) finds an error in the raw data (crisis!!!)
- You fix the error, and now have to rerun the ENTIRE analysis (which script did what, again? What depended on what?)
- By the time you are done figuring this out, you've also gotten your hands on more data so... gotta re-run everything again
The solution to this: one file (Makefile) and one command: Make
This repository contains everything we'll need for the session. Having git installed will make it easier (simply clone this repo). But, if you don't have it yet you can either follow this other tutorial or, simply download the entire thing as a compressed folder.
Open a terminal (or use the Terminal pane in RStudio) and type:
make -v #checks version of GNU make
Should show something like this (really, anything that is not an error should work):
>GNU Make 3.81
>Copyright (C) 2006 Free Software Foundation, Inc.
>This is free software; see the source for copying conditions.
>There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
>PARTICULAR PURPOSE.
Don't have it? This might help:
There are two options to make sure you have all the dependencies for this project.
Simply use the included renv environment:
renv::restore() # Follow the instructions
OR, manually install them if you don't already have them
renv::deactivate() # Deactivate the renv environment first
pkgs <- c("tidyverse", "here", "modelsummary") # List of packages needed
lapply(pkgs, install.packages) # Install all packages
- makefile2graph To convert your makefile into a graph
- graphviz To visualize that graph
To install both, follow the instructions here