7  Lab 1 Checklist

What you should have when Get Started is done

Abstract

This short chapter closes Lab 1. It first sums up each Get Started chapter in three columns: what you learned, what you did (and whether you did it in your web browser or in RStudio), and what you will do when you come back with your own research data. It then lists what should exist on your computer and in your ELN, with a one-line way to check each item and a link back to the section that made it. Lab 1 is setup: you install R and RStudio, make your project, install the packages once, start a Quarto file, and learn the routine for opening and closing a session. You do not analyze data in RStudio until Lab 2.

Keywords

checklist, Lab 1, setup

7.1 Two kinds of checklist

This playbook has two kinds of checklist, and they answer two different questions.

• A Lab checklist, like this one, closes each lab and answers “am I done with this lab?” It lists what should exist on your computer and in your ELN after the lab’s chapters, each with a quick way to check it. There is one at the end of Lab 1, Lab 2, and Lab 3. Labs 4 and 5 depend on your research question, so their chapters carry their own Ref’s checks instead.
• A Your Turn checklist sits at the end of each analysis chapter and answers “is this part of my report done?” It is about your team’s data and your RD Report and Final Report, not about the lab.

Labs are not graded and are not submitted. Check anyway, because every chapter from Lab 2 on assumes that each item on this list is done. If one is not, your code in Lab 2 will fail with an error message about something else, such as there is no package called 'readxl' or path does not exist, and nothing in that message will point back to the missing step. Ref’s call at the bottom of this page lists the three most common cases.

7.2 What each chapter asked of you

From Lab 2 on, most chapters have three parts with the same three names:

• The Play: you read. The chapter walks through the code with an example dataset. You do not retype it.
• The Lab: you practice, in RStudio on your own computer, with the lab dataset everyone shares. Ref shows the answer you should get.
• Your Turn: you run the same play on your team’s data, for your RD Report and Final Report. There is no Ref, only a checklist.

The Get Started chapters are setup chapters, so they do not have those three headings yet. The same three questions still apply, and the table below answers them for each chapter. The Where column answers the question students ask most: was I supposed to be coding in RStudio?

• Read: there was nothing to run.
• Browser: you ran R code in the webpage of the playbook itself. You did not use RStudio and nothing was saved.
• RStudio, setup: you used RStudio on your own computer, but to set things up, not to analyze data.

Chapter	What you learned	What you did	Where	Your Turn: with your data
Reproducible Reports	Why the code and the writing live in one file, and what a finished Quarto report looks like	Opened and skimmed example reports	Read	Your RD Report and Final Report will be reports like these
Coding a Plot	What an object and a function are, what <- and |> do, and that a plot is built with layers	Ran the code in the Try it boxes, changed one thing at a time, and found the two fouls	Browser	Return to Come Back Later to pick your team’s theme and colors when you make the plots for your report
R Software	What R and RStudio are, the four panes, and why a project sets the working directory	Installed R and RStudio, created the Lastname_FRI project, and made the data folder	RStudio, setup	Your team’s .cleandata data file goes in that data folder, and you always open RStudio through the project
R Packages	The two rules: install.packages() once per computer, library() every session	Created install.R and ran it one time	RStudio, setup	The load-library chunk is the first chunk of every report; install.packages() never appears in one
Start a Report	What a .qmd is, the short YAML header, what a code chunk is and why it gets a label, and Render	Made a practice .qmd, added the load-library chunk, and clicked Render	RStudio, setup (a practice file, no data)	In Lab 6, Start My Report adds the report’s file name, the full YAML header, and the five required parts of every chunk
Find the Ref	Ref’s kickoff and final whistle: the routine for opening and closing every session	Walked through the routine once and made the R Labs folder in your ELN	RStudio, setup	The same routine, every session, for your labs and your reports

ImportantImportant: you have not analyzed data in RStudio yet, and you were not supposed to

Nothing in Lab 1 asks you to analyze data in RStudio. Coding a Plot runs its code in your web browser. The four chapters after it put the software on your computer and set up your project, your packages, a practice Quarto file, and your routine. There is no Lastname_lab1.qmd; your first lab file is Lastname_lab2.qmd, made at the start of Lab 2.

The first time you write and run code on data in your own RStudio is The Lab in Import Data Once, in Lab 2. That chapter’s Play is still for reading; the coding starts at its heading The Lab, in a new file named Lastname_lab2.qmd. If you reach that Lab and the list below is not all checked, do this list first.

7.3 What you should have

Go down the list in RStudio. Every row has a check you can do in under a minute.

☐	What	How to check	Where it came from
☐	R and RStudio installed	RStudio opens; the Console shows a line beginning R version 4.	RStudio Software, Downloading R and RStudio
☐	A project called Lastname_FRI (your last name, no spaces)	Double-clicking Lastname_FRI.Rproj opens RStudio with Lastname_FRI in the top-right corner	RStudio Software, RStudio Projects and the Working Directory
☐	A data folder inside the project	list.files() in the Console shows data; it is empty for now	RStudio Software, Go: how to move a data file into your project folder
☐	install.R in the project folder, run once	The Files tab shows install.R next to Lastname_FRI.Rproj; library(tidyverse) in the Console runs with no there is no package error	Install and Load Packages, Creating install.R file
☐	You can tell a package from a library	You can say in one sentence why install.packages() never goes in a report and library() always does	Install and Load Packages, The two rules
☐	You have made and rendered a Quarto file	You created a .qmd with a YAML header and a code chunk, clicked Render, and an .html appeared next to it. (There is no required file for Lab 1; the first lab file is Lastname_lab2.qmd, which you will make at the start of Lab 2.)	Start a Report, Create a Quarto Markdown Document and Render Your Report
☐	You know the file names for the labs	Lastname_lab2.qmd … Lastname_lab5.qmd, one per lab, no file for Lab 1 (the report’s name comes in Lab 6)	Start a Report, Name the file
☐	Every chunk you write has a label	#| label: on the first line, lowercase with hyphens, saying what the chunk does (load-library, import-alldata)	Start a Report, Code Chunks
☐	You can run Ref’s routine from memory	Kickoff: Open Project → Open .qmd → Run load-library chunk → Run All Chunks Above → code. Final whistle: Save → Render → Back up to ELN → Quit, Don’t Save workspace	Find the Ref, Ref’s Quick Checklist
☐	An R Labs folder in your ELN	Your Google Drive has a folder where your lab .qmd files will be backed up after every session	Find the Ref, Important: Your ELN is your backup
☐	The DataCamp course is done	Introduction to the Tidyverse shows as complete in your DataCamp account, so the pipe, filter(), mutate(), and ggplot() are not new when they appear in Lab 2	Syllabus, pre-lab preparation

Caution Ref’s call: the three gaps that break Lab 2

• there is no package called 'readxl' (or tidyverse, psych) in Lab 2 → install.R was never sourced, or was sourced before the package was added. Open install.R and click Source.
• path does not exist when importing in Lab 2 → either there is no data folder in the project, or RStudio is not open in the project. Check the top-right corner for Lastname_FRI.
• Your .qmd is saved on the Desktop or in Downloads → it is outside the project, so relative paths like data/… will not work. Move it into the Lastname_FRI folder (Important: Save your Quarto documents in the project folder).

7.4 What Lab 2 will add

In Lab 2 you create Lastname_lab2.qmd, put the lab dataset and lab_prep.R from the class Google Drive into place, and import, clean, and transform data in RStudio for the first time. Lab 2 Checklist is the matching list for that lab.