BIOL 327: Homework FAQ

How do I set up the BIOL327 project in my Posit Cloud account?

NOTE: You only need to do the next steps once!!

To set up the BIOL327 project in Posit Cloud, click this link. You might need to log in to your Posit Cloud account if you are not already. Once you are logged in and the “Deploying Project” completes, you should see a screen somewhat like this:

Note the bright blinking red “TEMPORARY COPY” text at the top! Click the “Save a Permanent Copy” button to the right.

Once you have clicked the button, the project will save to your account and reload without the shiny red text at the top.

To make sure it worked, click on the “Your Workspace” button in the left panel.

You should see the following, showing that the project is now saved in your workspace.

How do I set up the BIOL327 project in RStudio on my laptop?

NOTE: You only need to do the next steps once!!

1. Follow the steps for setting up the BIOL327 project in Posit Cloud.

2. Click on “Your Workspace” in the left panel of Posit Cloud.

3. Click on the down arrow to export the project to your computer.

Posit Cloud will prepare your project for export and then show a message letting you know the project is ready for download. Click the “Download” button.

4. On a Mac, it will ask you what you want to name the file (e.g. BIOL327) and where you would like it downloaded. On a PC, it might automatically download. The file will be a ZIP file.

5. Find out, based on your operating system, how to unzip a ZIP File and then unzip/extract it. It should create a folder with a numeric name (see picture below for what it looks like after unzipping on a Mac).

Feel free to rename the folder to, e.g., BIOL327. If you are on a PC, please make sure you work with the extracted version.

6. Click in to the folder and you should see files and folders matching the Files pane in Posit Cloud (see below). Single-click or double-click on the project.Rproj file to load the project in RStudio. You are now ready to work on your Homework!

How do I create a new Quarto file for each Homework assignment?

The best way is to copy the Homework2.qmd file located within the Assignments folder of the BIOL327 project.

1. Go to the Assignments folder in the Files pane.

2. Check the box next to Homework2.qmd.

3. Click the “More” button.

4. Click “Copy To”.

5. Choose an appropriate name based on the Homework assignment.

Delete all of your work for Homework #2 except for (1) the YAML at the top (between the ---s) and (2) the first R-chunk labeled setup. You should have something like the following:

---
title: "Homework2"
author: "Steve Steverson"
date: September 21, 2025
format:
  html:
    toc: true
    toc_depth: 3
  docx:
    toc: true
    number-sections: true
---

```{r setup}
#| echo: FALSE
#| warning: FALSE
#| message: FALSE
library(here)
library(tidyverse)
```

Another option would be to create an empty new Quarto document and copy-and-paste the text above into the empty document. From within your BIOL327 project in RStudio, in the menu (upper left), choose File -> New File -> Quarto Document. Click “Create Empty Document”.

Finally, copy-and-paste the above text (the YAML and setup R-chunk) into the empty document.

How do I load a dataset for a Homework problem?

When you are ready to answer a homework question using R code, most times the first step is to load the data into R.

Step 1. Make sure the here and tidyverse packages are loaded in the Console.

Note: This will only need to be done once at the beginning of working on your homework.

Scroll to the top of your Homework document, find the setup R chunk, and click the green play button in the upper right of the R chunk.

Step 2. From within the Console, type the following:

finchData <- read.csv(here(""))

Replace finchData with a name that matches the context of the problem you are working on. Make sure the cursor is between the two double quotes. Click the <tab> key, which should bring up a menu. Choose the Data folder.

Step 3. Choose the folder for the chapter you are working on.

The command in the console should now look like this:

finchData <- read.csv(here("Data/"))

Note that Data/ was added. The cursor should be after the / character. Press the <tab> key again, which should bring up another menu showing the folders for the chapters. Choose the chapter you want.

Step 4. Choose the dataset.

Assuming you chose chapter03, the command in the console should now look like this:

finchData <- read.csv(here("Data/chapter03/"))

Finally, choose the dataset you want.

Step 5. Run the resulting command.

Assuming you chose chap03q04KenyaFinches.csv, the command in the console should now look like this:

finchData <- read.csv(here("Data/chapter03/chap03q04KenyaFinches.csv"))

Press enter in the console to load the data.

Step 6. Copy-and-paste the command into an R chunk in your Quarto document.

The previous command will load the data in the console, but now you need the command in your Quarto document. Place the cursor in the Quarto document where you want to load the data and insert an R-chunk.

This will add the following to your Quarto document:

```{r}

```

Copy-and-paste the R code from the Console into the R chunk. It should look something like this:

```{r}
finchData <- read.csv(here("Data/chapter03/chap03q04KenyaFinches.csv"))
```

Click the green play button in the upper right of the chunk to run the code in the console again. This is just a double check to make sure the code still works.

Finally, click the render button to make sure the code works in the rendered Quarto document.

Note #1: I will usually add a str command in the same R chunk after loading the data to see what the data contains. So, for example, you might have

```{r}
finchData <- read.csv(here("Data/chapter03/chap03q04KenyaFinches.csv"))
str(finchData)
```

Note #2: When navigating the subfolders to get to the dataset, instead of clicking on the Data directory or the chapter folders, and then hitting <tab> again, you can put the cursor over the choice you want and just hit <tab> directly. This changes the flow to:

1. Press <tab> when cursor is between the double quotes;
2. Hover the cursor over the Data folder and press <tab>;
3. Hover the cursor over the chapter03 folder and press <tab>;
4. Hover the cursor over the dataset and press <tab>, click, or <enter>.

How do I render to a Microsoft Word document for submission?

Click on the down caret icon next to the Render button and choose “Render MS Word”. That should render it to a Word document and prompt you to download the resulting file to your computer.