Rigor and Reproducibility in Experimental Design: Setup

Installation

This lesson assumes you have the R and RStudio software installed on your computer.

R can be downloaded from CRAN.

RStudio is an environment for developing using R. It can be downloaded here. You will need the Desktop version for your computer.

Data files and project organization

  1. Make a new folder in your Desktop called experimental_design. Move into this new folder.

  2. Create a data folder to hold the data, a scripts folder to house your scripts, and a results folder to hold results.

Alternatively, you can use the R console to run the following commands for steps 1 and 2.

setwd("~/Desktop")
dir.create("./experimental_design")
setwd("~/Desktop/experimental_design")
dir.create("./data")
dir.create("./scripts")
dir.create("./results")
  1. Please download the following files before the workshop, and place them in your data folder. You can download the files from the URLs below and move the files the same way that you would for downloading and moving any other kind of data.

Alternatively, you can copy and paste the following into the R console to download the data.

setwd("~/Desktop/experimental_design")
download.file("https://raw.githubusercontent.com/smcclatchy/dals-inference/gh-pages/data/bodyWeights.csv", "./data/bodyWeights.csv")
download.file("https://raw.githubusercontent.com/smcclatchy/dals-inference/gh-pages/data/CGDpheno3.csv", "./data/CGDpheno3.csv")