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8 Analytically reproducible documents
Session objectives:
- Learn what a reproducible document is, how R Markdown/Quarto helps with reproducibility, and why it can save you time and effort.
- Write and use R code within a document, so that it will automatically insert the R output into the final document.
- Learn about and use Markdown formatting and syntax for writing documents.
- Learn about and create different document types like HTML or Word from an R Markdown/Quarto document.
8.1 Why try to be reproducible?
Reading task: ~5 minutes
Both reproducibility and replicability are cornerstones for doing rigorous and sound science. As we’ve learned, reproducibility in science is lacking, which this course aims to address. However, being reproducible isn’t just about doing better science. It can also mean that:
- You are much more efficient and productive, as less time is spent between coding and transferring your results to a document. No need to copy and paste!
- You can be confident in your results, since what you report and show as figures or tables will be exactly what you get from your analysis. Again, no copying and pasting required!
Hopefully by the end of this session, you’ll want to start using R Markdown files for writing your manuscripts and other technical documents. Believe us, you can save so much time and make your work more reproducible once you learn how to incorporate text with R code. Plus, you can create some very aesthetically appealing reports, which are way easier to produce than if you had done it in Word.
8.2 What is R Markdown and Quarto?
8.3 Creating an R Markdown / Quarto file
Now, we will create and save a Quarto file. We’ll use the Command Palette by typing Ctrl-Shift-P and then typing “quarto” and select the one that says “Create a new Quarto document”. You can also use the menu, by going to File -> New File -> Quarto Document ..., and a dialog box will then appear. Enter”Reproducible documents” in the title field and your name in the author field. HTML should be automatically selected as the output format. There’s also the option to use the “visual mode”. This mode is great if you are used to working with Word and you can test it out on your own later. For this course, we will focus on using the normal mode.
After clicking “Create”, the new file will open in RStudio. You will see some text that gives a brief overview of how to use the Quarto file. For now, let’s ignore the text. At the top of the file you will see something that looks a bit like this:
---
title: "Reproducible documents"
author: "Your Name"
format: html
---This section is called the YAML header and it contains the metadata about the document and the settings for how to process it into another document. Most Markdown documents have this YAML header at the top of the document and they are always surrounded by --- on the top and bottom of the section. YAML is a data format that has the form of a key: value pairing to store data. The keys in this case are title, author, and format. The values are those that follow the key (e.g. “Your Name” for author). In the case of Quarto, these key data are used to store the settings that Quarto will use to create the format output document. The keys listed above are some of many settings that R Markdown has available to use.
In the case of this YAML header, the Quarto document will generate an HTML file because of the format: html setting. You can also create a word document by changing this to format: docx. You can also create PDF documents, though this requires installing LaTeX through the R package tinytex, which can sometimes be complicated to install. We will only cover HTML and Word documents in this course. Before continuing, let’s save this file as learning.qmd in the doc/ folder.
So, how do we create a HTML (or Word) document from the this document? We do that by “rendering” it. At the top of the pane near the “Save” button, there is a button with the word “Render” (if it’s R Markdown, it will be called “Knit” with a yarn symbol beside it). To render, you either click that button or use the shortcut Ctrl-Shift-K anywhere in the R Markdown document.
When you click the “Render” button, a bunch of processing messages should appear in a new pane beside the Console, followed by a new window popping up with the newly created document. Alternatively, the HTML document may pop up in the “Viewer” pane.
You’ve now created a HTML document! Let’s try making a Word document. Change the YAML value in the key format: from html to docx. Then render the document again with the “Render” button or Ctrl-Shift-K for “Knit” (or using the Command Palette with Ctrl-Shift-P, then type “render”). A Word document should open up. This is the basic approach to creating documents from R Markdown or Quarto. Before continuing, let’s add and commit the newly created file into the Git history (Ctrl-Shift-P, then type “commit”).
8.4 Inserting R code into your document
Being able to insert R code directly into a document is one of the most powerful features of R Markdown. This frees you from having to switch between programs when simultaneously writing text and running R code to derive output that you’d then put into your manuscript.
Running and including R code in R Markdown is done using “R code chunks”. You insert these chunks into the document by placing the cursor at the location where you want the chunk to be, then using the shortcut Ctrl-Alt-I for “Insert” or the menu item Code -> Insert Chunk to insert a new code chunk. Like with everything else, you can also use the Command Palette with Ctrl-Shift-P, then type “chunk”). Before we do that, let’s delete all the text in your document, with exception of the YAML header (including the dashes surrounding it). Make sure that the YAML key format: is set to html.
Then, place your cursor two lines below the YAML header and insert a code chunk (Ctrl-Alt-I for “Insert” or Ctrl-Shift-P, then type “chunk”). The code chunk should look something like this:
```{r}
```In the code chunk, type out 2 + 2, so it looks like:
```{r}
2 + 2
```You can run R code inside the code chunk the same way as you would write it in an R script. Typing Ctrl-Enter on the line will send the code 2 + 2 to the console, with the output appearing directly below the code chunk in the document. Note that this output is temporary.
To ensure that the output is inserted into the HTML document, render (Ctrl-Shift-K or Ctrl-Shift-P, then type “render”) the document and see what happens in the resulting HTML document. The output 4 should appear below the code chunk in the HTML document, something like this:
This is a very simple example of how code chunks work. Things are usually more complicated than this though. Normally, we have to load R packages to use for our subsequent code, and this is no different in an R Markdown document. We will set this up together now.
Create a new code chunk (Ctrl-Alt-I for “Insert” or Ctrl-Shift-P, then type “chunk”) and then type setup right after the r. It should look like:
```{r setup}
```This area that you just typed ‘setup’ in is for code chunk labels. In this case, we labelled the code chunk with the name setup. Code chunk labels should be named without _, spaces, or . and instead should be one word or be separated by -. An error may not necessarily occur if you don’t follow this rule, but there can be unintended side effects that you may not realize and R will likely not tell you about it, probably causing you quite a bit of annoyance and frustration. Note, you can’t use duplicate code chunk labels in your document.
Tip
A nifty thing about using chunk labels is that you can get an overview of your code chunks using the “Document Outline” (found using Ctrl-Shift-O), but only if you have this option set up in: Tools -> Global Options -> R Markdown -> Show in document outline. These settings can also be found with the Command Palette (Ctrl-Shift-P) followed by typing “document outline”.
The name setup also has a special meaning for R Markdown. When you run other code chunks in the document, R Markdown will know to first look for and run the code in the setup chunk. Therefore, this is a good place to put your library() calls or other setup functions. Let’s enter some code to load the packages and the dataset we have been using to the setup chunk:
```{r setup}
library(tidyverse)
library(NHANES)
nhanes_small <- read_csv(here::here("data/nhanes_small.csv"))
```Let’s insert another code chunk below this one (Ctrl-Alt-I for “Insert” or Ctrl-Shift-P, then type “chunk”), and simply put nhanes_small in the chunk:
```{r}
nhanes_small
```#> # A tibble: 10,000 × 8
#> age sex bmi diabetes phys_active bp_sys_ave bp_dia_ave
#> <dbl> <chr> <dbl> <chr> <chr> <dbl> <dbl>
#> 1 34 male 32.2 No No 113 85
#> 2 34 male 32.2 No No 113 85
#> 3 34 male 32.2 No No 113 85
#> 4 4 male 15.3 No <NA> NA NA
#> 5 49 female 30.6 No No 112 75
#> 6 9 male 16.8 No <NA> 86 47
#> 7 8 male 20.6 No <NA> 107 37
#> 8 45 female 27.2 No Yes 118 64
#> 9 45 female 27.2 No Yes 118 64
#> 10 45 female 27.2 No Yes 118 64
#> # ℹ 9,990 more rows
#> # ℹ 1 more variable: education <chr>Let’s run this code as we normally would in a script file, by placing the cursor over the code and using the shortcut Ctrl-Enter. We can also render (Ctrl-Shift-K for “Knit” or Ctrl-Shift-P, then type “render”) the document and see what it looks like. When the HTML document opens, you should see some text below the setup chunk that might look something like this:
── Attaching packages ──────────────────────── tidyverse 1.3.2 ──
✔ ggplot2 3.4.0 ✔ purrr 1.0.0
✔ tibble 3.1.8 ✔ dplyr 1.0.10
✔ tidyr 1.2.1 ✔ stringr 1.5.0
✔ readr 2.1.3 ✔ forcats 0.5.2
── Conflicts ─────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()You probably don’t want this text in your generated document, so we will add a chunk option to remove this message. Chunk options are used to change how code chunks work. When adding them inside the code chunk, they always need to start with #|. If you want to run the code but not show those messages and warnings, you can add the options #| message: false and #| warning: false:
```{r setup}
#| message: false
#| warning: false
library(tidyverse)
library(NHANES)
nhanes_small <- read_csv(here::here("data/nhanes_small.csv"))
```If you want to hide the code, messages, warnings, and output, but still run the code, you can use the option #| include: false.
```{r setup}
#| include: false
library(tidyverse)
library(NHANES)
nhanes_small <- read_csv(here::here("data/nhanes_small.csv"))
```Other common options are:
-
echo: To show the code. Default value istrue. Usefalseto hide. -
results: To show the output. Default ismarkup. Usehideto hide orasisas regular text (not inside a code block). -
eval: To evaluate (run) the R code in the chunk. Default value istrue, whilefalsedoes not run the code.
These options all work on the individual code chunk. If you want to set an option to all the code chunks (e.g. to hide all the code but keep the output), you can use Quarto’s execute options. These options are added to the YAML header and will apply the settings to everything in the document. We won’t do this in this session, but here is what it looks like:
---
title: "Reproducible documents"
author: "Your Name"
format: html
execute:
echo: false
warning: false
message: false
---8.5 Creating tables of results
Let’s try running some R code to get Quarto to create a table. First, create a new header1 ## Table of results and a new code chunk with the label mean-age-bmi-table. Second, copy the code we worked on from the Data Wrangling session, in Section 7.15, which is shown below for you to copy from. Instead of using phys_active, let’s change that to education.
1 A “header” is something like a Chapter in books, or section titles in manuscripts like “Introduction” or “Results”.
```{r mean-age-bmi-table}
nhanes_small %>%
filter(!is.na(diabetes)) %>%
group_by(diabetes, education) %>%
summarise(
mean_age = mean(age, na.rm = TRUE),
mean_bmi = mean(bmi, na.rm = TRUE)
) %>%
ungroup()
```#> # A tibble: 12 × 4
#> diabetes education mean_age mean_bmi
#> <chr> <chr> <dbl> <dbl>
#> 1 No 8th Grade 51.8 28.8
#> 2 No 9 - 11th Grade 46.3 28.6
#> 3 No College Grad 46.0 27.3
#> 4 No High School 46.1 28.9
#> 5 No Some College 43.8 28.7
#> 6 No <NA> 10.1 20.5
#> 7 Yes 8th Grade 63 32.0
#> 8 Yes 9 - 11th Grade 61.4 33.1
#> 9 Yes College Grad 60.6 31.3
#> 10 Yes High School 59.6 33.8
#> 11 Yes Some College 58.9 33.0
#> 12 Yes <NA> 16.7 26.1Putting the cursor somewhere in the code, use the shortcut Ctrl-Enter to run the code and see what it looks like. This output is almost in a table format. We have the columns that would be the table headers and rows that would be meaningful table rows. Ideally, we would want this to be report-ready. The first thing we should remove are the NA education rows, just like we did with diabetes. Then, we’ll convert it into a more elegant table in the R Markdown HTML output document, we use the kable() function from the knitr package. Because we don’t want to load all of the knitr functions, we’ll use knitr::kable() instead:
nhanes_small %>%
filter(!is.na(diabetes), !is.na(education)) %>%
group_by(diabetes, education) %>%
summarise(
mean_age = mean(age, na.rm = TRUE),
mean_bmi = mean(bmi, na.rm = TRUE)
) %>%
ungroup() %>%
knitr::kable(caption = "Mean values of Age and BMI for each education and diabetes status.")| diabetes | education | mean_age | mean_bmi |
|---|---|---|---|
| No | 8th Grade | 51.8 | 28.8 |
| No | 9 - 11th Grade | 46.3 | 28.6 |
| No | College Grad | 46.0 | 27.3 |
| No | High School | 46.1 | 28.9 |
| No | Some College | 43.8 | 28.7 |
| Yes | 8th Grade | 63.0 | 32.0 |
| Yes | 9 - 11th Grade | 61.4 | 33.1 |
| Yes | College Grad | 60.6 | 31.3 |
| Yes | High School | 59.6 | 33.8 |
| Yes | Some College | 58.9 | 33.0 |
Now, render (Ctrl-Shift-K for “Knit” or Ctrl-Shift-P, then type “render”) and view the output in the HTML document. Pretty eh! Before continuing, let’s run styler (Ctrl-Shift-P, then type “style file”) and then add and commit these changes into the Git history (Ctrl-Shift-P, then type “commit”).
8.6 Exercise: Creating a table using R code
Time: ~20 minutes.
-
In the
doc/learning.qmdfile, create a new header called## Prettier tablealong with a code chunk and label itprettier-table. Copy the code below (that includes some code we wrote above) and paste the code into the new chunk. Add the option#| echo: falseto the code chunk.```{r prettier-table} nhanes_small %>% filter(!is.na(diabetes), !is.na(education)) %>% group_by(diabetes, education) %>% summarise( mean_age = mean(age, na.rm = TRUE), mean_bmi = mean(bmi, na.rm = TRUE) ) %>% ungroup() %>% mutate( # Task 2a. ___ = ___(mean_age, ___), ___ = ___(mean_bmi, ___), # Task 2b. ___ = ___(education) ) %>% rename( # Task 3. "___" = ___, "___" = ___, "___" = ___, "___" = ___ ) %>% knitr::kable(caption = "Mean values of Age and BMI for each education and diabetes status.") ``` -
Use
mutate()to perform the following wrangling tasks: Rename
diabetesto"Diabetes Status",educationtoEducation, andmean_ageandmean_bmito"Mean Age"and"Mean BMI", usingrename()function. Hint: You can rename columns to include spaces by using"around the new column name (e.g."Diabetes Status" = diabetes). Don’t forget, the renaming form isnew = old.Run the code chunk to make sure the code works, including the
knitr::kable()function at the end of the pipe, with a table caption of your choice. If you want you can keep the same caption as is provided in the starting point below.Run styler on the document (
Ctrl-Shift-P, then type “style file”).Render the document to HTML (
Ctrl-Shift-Kfor “Knit” orCtrl-Shift-P, then type “render”) and see what the table looks like.End the exercise by adding, committing, and pushing the files to your GitHub repository (
Ctrl-Shift-P, then type “commit”).
Click for the solution. Only click if you are struggling or are out of time.
nhanes_small %>%
filter(!is.na(diabetes)) %>%
group_by(diabetes, education) %>%
summarise(
mean_age = mean(age, na.rm = TRUE),
mean_bmi = mean(bmi, na.rm = TRUE)
) %>%
ungroup() %>%
# 2. Round the means to 1 digit and
# modify the `education` column so that male and female get capitalized.
mutate(
mean_age = round(mean_age, 1),
mean_bmi = round(mean_bmi, 1),
education = str_to_sentence(education)
) %>%
# 3. Rename `diabetes` to `"Diabetes Status"` and `education` to `Education`
rename(
"Diabetes Status" = diabetes,
"Education" = education,
"Mean Age" = mean_age,
"Mean BMI" = mean_bmi
) %>%
knitr::kable(caption = "Mean values of Age and BMI for each education and diabetes status.")8.7 Formatting text with Markdown syntax
Tip
For more details about other Markdown “syntax”, check out Appendix F as well as the R Markdown cheatsheet (
Tools -> Cheatsheets) and Quarto’s Markdown Basics page. Continue to the exercise below.
8.8 Exercise: Practice using Markdown for writing text
Time: ~5 minutes.
Get some practice writing Markdown by completing these tasks in the doc/learning.qmd file.
- Right under the YAML header, insert a list (either numbered or unnumbered) with your name and affiliation(s)/institution(s).
- Create three level 1 headers (
#), called “Intro”, “Methods and Results”, and “Discussion”. - Create a level 2 header (
##) under “Methods and Results” called “Analysis”. - Write one random short sentence under each header. Bold (
**word**) one word in each and italicize (*word*) another. - Insert a code chunk to make a simple calculation (e.g.
2 + 2). - Finally, add and commit these changes into the Git history (
Ctrl-Shift-P, then type “commit”).
8.9 Inserting figures as files or from R code
Reading task: ~5 minutes
Aside from tables, figures are the most common form of output inserted into documents. Like tables, you can insert figures into the document either with Markdown or R code chunks. We’ll do it with Markdown in this session and with R code in the next session. First, we need an image to use. Open a browser and search for a picture to use (we’re using a kitten, because they’re cute). Download the image, create a folder in doc/ called images, and save the image in that folder. Then, in your R Markdown document, use the Markdown syntax for images: . The image can be in png, jpeg, or pdf formats. If you download an image and intend to use it in an official document, you will need to add text on the source and author of the image for copyright purposes.
Gives…
You can include a link to a picture instead of downloading the image, though this may only work in HTML documents and only if you have internet access. Quarto has amazing image capabilities, which they show in the Figures guide.
Warning
Image files are always relative to the .qmd file.
Render the document again (Ctrl-Shift-K) and view the HTML document with the new picture. We can, if we want to, change the width and height of the image as well as its alignment. We do this by adding a {} to the end of the Markdown image tag and put options inside there.
-
fig-align: To align the figure, either in"center","left", or"right". -
widthandheight: To set the image width and height for external images (not created by R). You can use percent to set the size as well, e.g."75%". -
#fig-LABEL: Use this to add a label so you can cross-reference it by typing inline@fig-LABEL.
For this image, we will change the width and height to "50%", and change the caption to something like "Kittens attacking flowers!", and add a label and reference:
Cute kitten in @fig-kitten-attack!
{#fig-kitten-attack width="50%" height="50%"}
Now in Figure 8.1, we see a kitten! Render again (Ctrl-Shift-K for “Knit” or Ctrl-Shift-P, then type “render”) to see how the image changes.
8.10 Other R Markdown features
8.11 Exercise: Adding figures and changing the theme
Time: 20 minutes.
Complete these tasks in the doc/learning.qmd file.
- Search online for a picture that you like and want to put into the R Markdown file. Download it and save the image in
doc/. - In the R Markdown file, insert the image somewhere (e.g. under
# Results) and give it an appropriate caption. - Render the document (
Ctrl-Shift-Kfor “Knit” orCtrl-Shift-P, then type “render”) to make sure the image gets inserted. - Go to Quarto’s HTML Theming page and look through the different themes that are available for the HTML output. Find a theme you like by changing the
themeoption in the YAML header and re-render the document (Ctrl-Shift-Kfor “Knit” orCtrl-Shift-P, then type “render”). - Finally, add and commit the changes you’ve made to the document (
Ctrl-Shift-P, then type “commit”). For now, don’t add and commit the HTML output file.
8.12 Summary
- Making your research reproducible not only improves the scientific quality of your work, but also makes you more efficient, productive, and have more confidence in your results.
- Use R Markdown to construct files that can easily be turned into a variety of file types such as HTML or Word.
- Insert R code chucks in R Markdown and automatically include the results in the final document.
- Make tables by using
knitr::kable() - Use headers (
# Header 1), text formatting (**bold**) and lists (-) in the R Markdown file. - Insert pictures directly into the R Markdown file with
. - For HTML, choose different themes to personalize the appearance of your R Markdown output document.