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10 Analytically reproducible documents

When in RStudio, quickly jump to this page using r3::open_reproducible_documents().

Session objectives:

Learn what a reproducible document is, how R Markdown achieves being reproducible, 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 document.

10.1 Why try to be reproducible?

Take about 5 min to read over this section.

Both reproducibility and replicability are cornerstones for doing rigorous and sound science. As we’ve learned, reproducibility in science is fairly lacking, which this course aims to fill. But being reproducible isn’t just about doing better science, it can also:

Make you much more efficient and productive, as less time is spent between coding and putting your results in a document (e.g. no need to copy and paste).
Make you more 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 try to start using R Markdown files for writing your manuscripts and other technical documents. Believe us, after you’ve learned how to incorporate text with R code, it can save so much time in the end, and make your analysis and work more reproducible. Plus you can create some very aesthetically appealing reports, way more easily than you could if you did it in Word.

$Have a more reproducible workflow by using R Markdown. Artwork by [\@allison_horst](https://github.com/allisonhorst/stats-illustrations).$

Figure 10.1: Have a more reproducible workflow by using R Markdown. Artwork by @allison_horst.

10.2 Creating an R Markdown file

Take about 5 min to read over the next few paragraphs.

R Markdown is a file format (a plain text format like R scripts or .csv files) that allows you to be more reproducible in your analysis and to be more productive in general in your work. R Markdown is an extension of Markdown that integrates R code with written text (as Markdown formatting).

So what is Markdown? It is a markup syntax and formatting tool, like HTML, that allows you write a document in plain text that can then be converted into a vast range of other document types, e.g. HTML, PDF, Word documents, slides, posters, or websites. In fact, this website is built from R and Markdown! (Plus other things like HTML.) The Markdown used in R Markdown is based on pandoc (“pan” means all and “doc” means document, so “all documents”). Pandoc is a very powerful, popular, and well-maintained software tool for document conversion. You can use R Markdown in conjunction with other packages (e.g., bookdown) to do any number of things. Here are some examples:

Blogging (e.g., Yihui Xie’s blog, creator of many commonly-used R packages like rmarkdown) with the blogdown package.
Writing your thesis (e.g., Tyson Barrett’s experience of using pure R Markdown versus Ed Cherry’s experience of using R Markdown with the bookdown package).
Writing and formatting journal articles (e.g., a reproducibility project).
Writing book chapters (including the guide to bookdown).

For now, we’re going to focus on the main reason to use it: to incorporate R code and output into a document. By using R code in a document, you can have a seamless integration between document writing and doing your analysis.

Why would you use this? There are many reasons, some of them being:

There is less time between exploring a new dataset or analysis and sharing your findings with collaborators, because the writing and documenting is woven in with your R analysis code.
If you finish an analysis and produce a report, but later find out there are problems with the data or you get new data, updating your report is as easy as clicking a button to regenerate it.
How you got and present your results is based on the exact sequence of steps given in your R Markdown document, so showing others how the analysis is done is easy because the how is explicitly shown in the document.
Likewise, by reading others’ R Markdown documents, it is easier to learn what was done in their analysis because the logic and sequence is shown in the document itself.

Let’s go over this together.

Ok, let’s create and save an R Markdown file. Go to File -> New File -> R Markdown, and a dialog box will then pop up. Type in “Reproducible documents” in the title section and your name in the author section. Choose HTML as the output format. Then save this file as rmarkdown-session.Rmd in the doc/ folder.

We now have an R Markdown file. Inside the file, there is some text that gives a brief overview of how to use it. For now, let’s ignore the text.

At the top of the R Markdown file, you will see something that looks a bit like this:

---
title: "Reproducible documents"
author: "Your Name"
date: "6/18/2020"
output: html_document
---

This section is called the YAML header and it contains commands and metadata about the 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, date, and output. The values are those that follow the key (e.g. “Your Name” for author). In the case of R Markdown, these key data are used to store the settings that R Markdown will use to create the 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 R Markdown document will generate an HTML file because of the output: html_document setting. You can also create a word document with output: word_document. While PDF documents are also able to be created, they require installing LaTeX through the R package tinytex, which can sometimes be complicated to install. So we will only cover HTML and Word documents in this course.

So how do we create an HTML (or Word) document from the R Markdown document? By “knitting” it! At the top of the pane near the save button, there is a button with the word “Knit” and a yarn beside it, as shown in Figure 10.2. To knit, you either click that button or by using Ctrl-Shift-K anywhere in the R Markdown document.

Figure 10.2: Location of the Knit button in RStudio.

When you click it, a bunch of commands should pop up in a new pane called “R Markdown”, followed by a new window popping up with the newly created document. Alternatively, the HTML document may pop up in the “Viewer” pane.

Cool, so now you’ve created an HTML document! Let’s try making a Word document. Change the YAML value in the key output: from html_document to word_document. Then knit the document again (with the “Knit” button or with Ctrl-Shift-K). Now, a Word document should open up. This is the basic approach to creating documents from R Markdown. Before doing the exercise, add and commit the newly created R Markdown file into the Git history.

10.3 Exercise: Create another R Markdown document.

Time: 7 min

Create another R Markdown document using RStudio’s interface.
- Write the title as “Trying out R Markdown”.
- Choose “HTML” as the document type.
Save the document in the doc/ folder and name it another-one.Rmd.
Knit the document with either Ctrl-Shift-K or with the RStudio “Knit” button.
Look at the output document, then change the YAML value for the output: key from html_document to word_document. Knit again.
Open the Word file if it hasn’t been opened already.
Finally, add and commit only the .Rmd file to the Git history and push to your GitHub repository.

10.4 Inserting R code into your document

Being able to insert R code directly into a document is one of the most powerful characteristics of using R Markdown. This frees you from having to switch between programs when writing text and when running R code in order to obtain an output that you’d then put into the document.

Running and including R code in R Markdown is done through “R code chunks”. You insert these chunks into the document by either typing Ctrl-Alt-I or using the menu item Code -> Insert Chunk, with the cursor at the location you want the chunk to be. Before we do that, delete all the text in your R Markdown document (the rmarkdown-session.Rmd file), excluding the YAML header. Make sure that the YAML key output: is set to html_document.

Then, place your cursor two lines below the YAML header and insert a code chunk (Ctrl-Alt-I or Code -> Insert 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 as you would when in an R script. Typing Ctrl-Enter on the line will send the code 2 + 2 to the Console, putting the output directly below the code chunk in the R Markdown document. This output though is temporary.

To get it inserted into the HTML document, knit (Ctrl-Shift-K) the document and see what happens in the created HTML document. The output 4 should appear below the code chunk in the HTML document. Something like this:

2 + 2
#> [1] 4

This is a very simple example of how code chunks work. Normally, things are more complicated than this though. Usually we have to load R packages to use for running R, and this is no different in an R Markdown document. Create a new code chunk and then type setup right after the r. It should look like:

```{r setup}

```

This area that you typed 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.

A nifty thing about using chunk labels is that you can see the name when using “Document Outline” (found using Ctrl-Shift-O), but only if you have the option set in the Tools -> Global Options -> R Markdown -> Show in document outline.

The name setup is also a special name for R Markdown. When you run other code chunks in the document, if the document was just opened up, R Markdown will first run the code in the setup chunk. This is a good place to put your library() calls or, in our case, the function source() to load all the packages. Let’s add the code to load the packages and the dataset to the chunk:

```{r setup}
source(here::here("R/package-loading.R"))
load(here::here("data/nhanes_small.rda"))
```

Let’s insert another code chunk below this one, and this time simply put nhanes_small in it:

```{r}
nhanes_small
```

You can run this code normally, with the cursor over the code and typing Ctrl-Enter. Or we can knit (Ctrl-Shift-K) 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:

Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      
── Attaching packages ─────────────────────────────────────────── tidyverse 1.3.0 ──
✓ ggplot2 3.3.2          ✓ purrr   0.3.4     
✓ tibble  3.0.1          ✓ dplyr   1.0.0.9000
✓ tidyr   1.1.0          ✓ stringr 1.4.0     
✓ readr   1.3.1          ✓ forcats 0.5.0

You probably don’t want this text in your generated document. You can change how code chunks work by using chunk options. They are available either by clicking on the gear in the top right corner of the chunk (shown in Figure 10.3) or by typing in the area after the chunk label section.

Figure 10.3: Changing the settings for the code chunk actions.

So, 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}
source(here::here("R/package-loading.R"))
load(here::here("data/nhanes_small.rda"))
```

If you want to hide the code, the messages, the warnings, and the output, but still run the code, you use the option include=FALSE.

```{r setup, include=FALSE}
source(here::here("R/package-loading.R"))
load(here::here("data/nhanes_small.rda"))
```

Other common options are:

echo: To show the code. The default value to show is TRUE, to hide is FALSE.
results: To show the output results. The default is 'markup', to hide is 'hide'.
eval: To evaluate (to run) the R code in the chunk. The default value is TRUE and FALSE does not run the code.

These options all work on the individual code chunk. Note, that all the chunk options must be on one line, after the {r tag. If you want to set an option to all the code chunks, for instance to hide all the code but keep the output, you use the function knitr::opts_chunk$set(echo = FALSE). We won’t do this in this session, but here is what it looks like:

```{r setup}
source(here::here("R/package-loading.R"))
load(here::here("data/nhanes_small.rda"))
knitr::opts_chunk$set(echo = FALSE)
```

A common results output that is included in documents are tables. So let’s run some R code and get R Markdown to create one. First, create a new code chunk and name it mean-age-bmi-table. Then, let’s copy the code from the Data Wrangling session, from Section 9.17.

```{r mean-age-bmi-table}
nhanes_small %>%
    filter(!is.na(diabetes)) %>% 
    group_by(diabetes, sex) %>% 
    summarise(mean_age = mean(age, na.rm = TRUE),
              mean_bmi = mean(bmi, na.rm = TRUE)) %>% 
    ungroup()
```

#> # A tibble: 4 x 4
#>   diabetes sex    mean_age mean_bmi
#>   <fct>    <fct>     <dbl>    <dbl>
#> 1 No       female     36.5     26.2
#> 2 No       male       34.3     26.1
#> 3 Yes      female     59.9     33.7
#> 4 Yes      male       58.6     31.5

This output is almost in a table format. We have the columns that could be the table headers, and we have rows that would be meaningful table rows too. To convert it into a pretty 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.

```{r mean-age-bmi-table}
nhanes_small %>%
    filter(!is.na(diabetes)) %>% 
    group_by(diabetes, sex) %>% 
    summarise(mean_age = mean(age, na.rm = TRUE),
              mean_bmi = mean(bmi, na.rm = TRUE)) %>% 
    ungroup() %>% 
    knitr::kable(caption = "Table caption. Mean values of Age and BMI for each sex and diabetes status.")
```

Table 10.1: Table caption. Mean values of Age and BMI for each sex and diabetes status.
diabetes	sex	mean_age	mean_bmi
No	female	36.46581	26.21885
No	male	34.34953	26.10141
Yes	female	59.90476	33.70212
Yes	male	58.64764	31.53878

Now, knit (Ctrl-Shift-K) and view the output in the HTML document. Pretty eh! Let’s add and commit these changes into the Git history.

10.5 Exercise: Creating a table using R code

Time: 12 min

In the doc/another-one.Rmd, create a new code chunk and call it setup. Include the source() function to load the packages and use load() with here::here() to load the nhanes_small dataset.
Create another code chunk and call it prettier-table. Copy the code from above that calculates the mean BMI and Age and paste the code into the new chunk. Add the option echo = FALSE to the code chunk.
Use mutate() to update:
- The mean_age and mean_bmi columns and applying the function round() on them, rounding the values to 1 digit (digits is the second argument of round()).
- The sex column so that male and female get capitalized by using str_to_sentence(sex) to capitalize the first letter of the word. This new function takes the values of sex and capitalizes the first letter (e.g. female to Female).
Rename diabetes to "Diabetes Status", sex to Sex, and mean_age and mean_bmi to "Mean Age" and "Mean BMI" by using rename(). 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 is new = old.
Run the code chunk to make sure the code works. Include the knitr::kable() function at the end of the pipe, with a table caption of your choice.
Knit the document and check the created table.
End the exercise by adding, committing, and pushing the files to your GitHub repository.

Click for the (possible) solution.

li lo  # nhanes_small               

r"># 1. Loading libraries brary(tidyverse) ad(here::here("data/nhanes_small.rda")) 2. Calculating mean BMI and Age %>% filter(!is.na(diabetes)) %>%  group_by(diabetes, sex) %>%  summarise(mean_age = mean(age, na.rm = TRUE), mean_bmi = mean(bmi, na.rm = TRUE)) %>%  ungroup() %>%  # 3. Round the means to 1 digit and # modify the `sex` column so that male and female get capitalized. mutate(mean_age = round(mean_age, 1), mean_bmi = round(mean_bmi, 1), sex = str_to_sentence(sex)) %>%  # 4. Rename `diabetes` to `"Diabetes Status"` and `sex` to `Sex` rename("Diabetes Status" = diabetes, Sex = sex, "Mean Age" = mean_age, "Mean BMI" = mean_bmi) %>%  # 5. Include the `knitr::kable()` function at the end of the pipe. knitr::kable(caption = "A prettier Table. Mean values of Age and BMI for each sex and diabetes status.")

10.6 Formatting text with Markdown syntax

Take about 8 min to read over the first few parts of this section, then move to the next exercise. You can also access a quick guide using the RStudio menu: Help -> Cheatsheets -> R Markdown Cheat Sheet. For learning more formatting features of Markdown, check out Appendix B.3.

Formatting text in Markdown is done using characters that are considered “special” and act like commands. So these special characters indicate what text is bolded, what is a header, what is a list, and so on. Almost every feature you need to write a scientific document is available in Markdown, though not all. If you can’t get Markdown to do what you want, our suggestion would be to try to fit your writing around Markdown, rather than force or fight with Markdown to do something it wasn’t designed to do. You might actually find that the simpler Markdown approach is easier than what you wanted or were thinking of doing, and that you can actually do quite a lot with Markdown’s capabilities.

10.6.1 Headers

Creating headers (like chapters or sections) is done by using one or more # at the beginning of a line and should always be preceded and followed by an empty line:

# Header 1

Paragraph.

## Header 2

Paragraph.

### Header 3

Paragraph.

10.6.2 Lists

Lists are created by adding either - or 1. to the beginning of a line and an empty line must be at the start and end of the list.

For unnumbered lists, it looks like:

- item 1
- item 2
- item 3

which gives…

item 1
item 2
item 3

And numbered lists look like:

1. item 1
2. item 2
3. item 3

which gives…

item 1
item 2
item 3

10.6.3 General text formatting

**bold** gives bold.
*italics* gives italics.
super^script^ gives super^script.
sub~script~ gives sub_script.

10.6.4 Inline R code

R Markdown also allows you to including numbers (or other output) directly into a paragraph. For instance, if you want to add a mean into some text, it would look like:

The mean of BMI is `r round(mean(nhanes_small$bmi, na.rm = TRUE), 2)`.

which gives…

The mean of BMI is 26.66.

But note that using inline R code can only insert a single number or character value, nothing more.

10.7 Exercise: Practice using Markdown for writing text

Time: 5 min

Go into the doc/another-one.Rmd file and complete these items:

Right under the YAML header, insert a list item with your name. Put your affiliations and your university or institution as items in a sub-list.
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).

10.8 Inserting figures, as files or from R code

Take about 7-10 mins to read over and work through the next few sections.

Aside from tables, figures are the other most common form of output inserted into documents. And like tables, you can insert figures into the document either with Markdown or with R code chunks. We’ll do it with Markdown in this session and next session will be with R code. 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: ![Caption text](path/to/image.png). The image can be png, jpeg, or pdf. 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.

![Image by Dimitri Houtteman from Pixabay.](images/kitten.jpg)

Which gives…

Image by Dimitri Houtteman from Pixabay

You can also directly 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.

Markdown syntax to control the image is limited. If you want to change the size of the image, it can be difficult. However, using R code chunks can simplify this!

First, let’s create a new code chunk (Ctrl-Alt-I), name the code chunk kitten-image, and add the function knitr::include_graphics(). To make it easier to find the image, use here::here() to point to the picture. It should look like this:

```{r kitten-image}
knitr::include_graphics(here::here("doc/images/kitten.jpg"))
```

Knit the document again (Ctrl-Shift-K) and view the HTML document with the new picture. Now, let’s change the width and height of the image, along with adding a figure caption. We do this with these code chunk options:

fig.cap: For writing the figure caption.
fig.align: To align the figure, either in "center", "left", or "right".
out.width and out.height: Sets the image width and height for external images (not created by R). Can use percent to set the size, e.g. "75%".

Change the width and height to "50%", along with adding a caption like "Kittens attacking flowers!":

```{r kitten-image, out.width="50%", out.height="50%", fig.cap="Kittens attacking flowers!"}
knitr::include_graphics(here::here("images/kitten.jpg"))
```

Figure 10.4: Kittens attacking flowers!

Knit again to see how the image changed. Great!

10.9 Other R Markdown features

Take 5 min to read these sections below before proceeding to the final exercise.

10.9.1 Making your report prettier

For HTML documents, customizing the appearance (e.g. fonts) is pretty easy, since settings to change the theme can be used directly in the YAML header. For instance, there’s a setting within html_document called theme. It would look like this:

---
title: "My report"
output:
    html_document:
        theme: sandstone
---

Notice the indentations. Indentation tells YAML what key is related to another key, i.e. if it is a sub-key. The key theme is a sub-key (an option) of html_document, which is a sub-key (an option) of output. Check out the R Markdown documentation to see other themes you can use. The themes are all Bootswatch themes, with most of them being available for use in HTML documents.

Modifying the theme and appearance of Word documents, on the other hand, is much more difficult. Since Word can’t easily be programmatically modified like HTML can, changing the appearance of the document itself requires that you manually create a Word template file first, manually modify the appearance, and then link to that template file with the reference_docx option in the YAML header (as a sub-key of word_document). More detail on this can be found in the documentation.

10.9.2 Collaborating on R Markdown documents

There are multiple ways in general of collaborating on a document:

One person has the primary task of writing up the report and then gets feedback from other collaborators through the use of “Track Changes” or by inserting comments in Word.
Multiple people are responsible for writing the report and probably use different documents that they will end up merging later on. Or they email back and forth (or use something like Dropbox or shared folders) and work on a single document.

The first workflow is not possible in an R Markdown document. Instead, you’d use a workflow that probably resembles how peer reviews are done, i.e. reading the document and making comments in a separate file to upload to the journal later. Or you’d use a workflow that revolves around GitHub and Git, an efficient workflow that has been tried and tested by tens of thousands of teams in tens of hundreds of companies globally. The goal of this course is to slowly move researchers more into the modern era, based on modern technology, tools, and workflows.

The second workflow is pretty similar. You might split up a document into sections that each collaborator may work on, and then later on merge them together. This last approach is what we will get you to do for the group project.

10.10 Exercise: Adding figures and change the theme

Time: 20 minutes

Go into the doc/another-one.Rmd and complete these tasks:

Search online for a picture that you like and that you will 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.
- For inserting the images, use the code-chunk with knitr::include_graphics()
- Use fig.cap to include a caption, center align with fig.align, and resize it to "75%" with out.width.
- Knit the document to make sure the image gets inserted.
Go to the R Markdown documentation site and look at the different available themes for the HTML output. Find a theme you like by changing the theme option in the YAML header and re-knitting the document.
Finally, add and commit the changes you’ve made to the doc/another-one.Rmd. For now, don’t add and commit the HTML output file.

10.11 Summary of session

Making your research reproducible not only improves your science, 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 files 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()
Apply headers ( # Header 1), text formatting (**bold**), lists (-), and links [Link](www) directly in the R Markdown file.
Insert pictures directly in R Markdown with ![Caption text](path/to/image.png) or knitr::include_graphics("path/to/image.png")) in a code chunk.
For HTML, choose different themes for appearance to personalise your R Markdown output document.