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8 Save time, don’t repeat yourself: Using functionals

We will continue covering the “Workflow” block in Figure 8.1.

Section of the overall workflow we will be covering.

Figure 8.1: Section of the overall workflow we will be covering.

And your folder and file structure should look like (use fs::dir_tree(recurse = 2) if you want to check using R):

LearnR3
├── data/
│   └── README.md
├── data-raw/
│   ├── README.md
│   ├── mmash-data.zip
│   ├── mmash/
│   │  ├── user_1
│   │  ├── ...
│   │  └── user_22
│   └── mmash.R
├── doc/
│   ├── README.md
│   └── lesson.Rmd
├── R/
│   ├── functions.R
│   └── README.md
├── .gitignore
├── DESCRIPTION
├── LearnR3.Rproj
└── README.md
For instructors: Click for details.

Briefly go over the bigger picture (found in the introduction section) and remind everyone the ‘what’ and ‘why’ of what we are doing.

8.1 Learning objectives

  1. Learn about and apply functional programming, vectorization, and functionals within R.
  2. Review the split-apply-combine technique and understand the link with functional programming.
  3. Apply functional programming to summarizing data and for using the split-apply-combine technique.

8.2 Functional programming

Please take 15 min to read over this section before we continue. Unlike many other programming languages, R’s primary strength and approach to programming is in functional programming. So what is it? It is programming that:

  • Uses functions (like function())
  • Applies functions to vectors all at once (called vectorisation), rather than one at a time
    • Vectors are multiple items, like a sequence of numbers from 1 to 5, that are bundled together, for instance a column for body weight in a dataset is a vector of numbers
  • Can use functions as input to other functions to then output a vector (called a functional)

We’ve already covered functions. You’ve definitely already used vectorization since it is one of R’s big strengths. For instance, functions like mean(), sd(), sum() are vectorized in that you give them a vector of numbers and they do something to all the values in the vector at once. In vectorized functions, you can give the function an entire vector (e.g. c(1, 2, 3, 4)) and R will know what to do with it. Figure 8.2 shows how a function conceptually uses vectorization.

A function using vectorization. Modified from the [RStudio purrr cheatsheet][purrr-cheatsheet].

Figure 8.2: A function using vectorization. Modified from the RStudio purrr cheatsheet.

For example, in R, there is a vectorized function called sum() that takes the entire vector of values and outputs the total sum, without needing a for loop.

values <- 1:10
# Vectorized
sum(values)
#> [1] 55

As a comparison, in other programming languages, if you wanted to calculate the sum you would need a loop:

total_sum <- 0
# a vector
values <- 1:10
for (value in values) {
    total_sum <- value + total_sum
}
total_sum
#> [1] 55
For instructors: Click for details.

Emphasize this next paragraph.

Writing effective and proper for loops is actually quite tricky and difficult to easily explain. Because of this and because there are better and easier ways of writing R code to replace for loops, we will not be covering loops in this course.

A functional on the other hand is a function that can also use a function as one of its arguments. Figure 8.3 shows how the functional map() from the purrr package works by taking a vector (or list), applying a function to each of those items, and outputting the results from each function. The name map() doesn’t mean a geographic map, it is the mathematical meaning of map: To use a function on each item in a set of items.

A functional that uses a function to apply it to each item in a vector. Modified from the [RStudio purrr cheatsheet][purrr-cheatsheet].

Figure 8.3: A functional that uses a function to apply it to each item in a vector. Modified from the RStudio purrr cheatsheet.

Here’s a simple toy example to show how it works. We’ll use paste() on each item of 1:5.

library(purrr)
map(1:5, paste)
#> [[1]]
#> [1] "1"
#> 
#> [[2]]
#> [1] "2"
#> 
#> [[3]]
#> [1] "3"
#> 
#> [[4]]
#> [1] "4"
#> 
#> [[5]]
#> [1] "5"

You’ll notice that map() outputs a list, with all the [[1]] printed. map() will always output a list. Also notice that the paste() function is given without the () brackets. Without the brackets, the function can be used by the map() functional and treated like any other object in R.

Let’s say we wanted to paste together the number with the sentence “seconds have passed”. Normally it would look like:

paste(1, "seconds have passed")
#> [1] "1 seconds have passed"
paste(2, "seconds have passed")
#> [1] "2 seconds have passed"
paste(3, "seconds have passed")
#> [1] "3 seconds have passed"
paste(4, "seconds have passed")
#> [1] "4 seconds have passed"
paste(5, "seconds have passed")
#> [1] "5 seconds have passed"

Or as a loop:

for (num in 1:5) {
    sec_passed <- paste(num, "seconds have passed")
    print(sec_passed)
}
#> [1] "1 seconds have passed"
#> [1] "2 seconds have passed"
#> [1] "3 seconds have passed"
#> [1] "4 seconds have passed"
#> [1] "5 seconds have passed"

With map(), we’d do this a bit differently. purrr allows us to create anonymous functions (functions that are used once and disappear after usage) to extend its capabilities. Anonymous functions are created by writing function(x) followed by the function definition inside of map(). Using map() with an anonymous function allows us to do more things to the input vector (e.g. 1:5). Here is an example:

map(1:5, function(x) paste(x, "seconds have passed"))
#> [[1]]
#> [1] "1 seconds have passed"
#> 
#> [[2]]
#> [1] "2 seconds have passed"
#> 
#> [[3]]
#> [1] "3 seconds have passed"
#> 
#> [[4]]
#> [1] "4 seconds have passed"
#> 
#> [[5]]
#> [1] "5 seconds have passed"

As this is quite verbose, purrr supports the use of a syntax shortcut to write anonymous functions. This shortcut is using ~ (tilde) to start the function and .x as the replacement for the vector item. .x is used instead of x in order to avoid potential name collisions in functions where x is an function argument (for example in ggplot2::aes(), where x can be used to define the x-axis mapping for a graph). Here is the same example as above, now using the ~ shortcut:

map(1:5, ~paste(.x, "seconds have passed"))
#> [[1]]
#> [1] "1 seconds have passed"
#> 
#> [[2]]
#> [1] "2 seconds have passed"
#> 
#> [[3]]
#> [1] "3 seconds have passed"
#> 
#> [[4]]
#> [1] "4 seconds have passed"
#> 
#> [[5]]
#> [1] "5 seconds have passed"

This is the basics of using functionals. Functions, vectorization, and functionals provide expressive and powerful approaches to a simple task: Doing an action on each item in a set of items. And while technically using a for loop lets you “not repeat yourself”, they tend to be more error prone and harder to write and read compared to these other tools. For some alternative explanations of this, see Section D.1. Ok, stop reading and we’ll go over this again before continuing with the coding.

For instructors: Click for details.

Go over this section briefly by reinforcing what they read. Make sure they understand the concept of applying something to many things at once. Doing the code-along should also help reinforce this concept.

Also highlight that the resources appendix has some links for continued learning for this and that the RStudio purrr cheatsheet is an amazing resource to use.

But what does functionals have to do with what we are doing now? Well, our import_user_info() function only takes in one data file. But we have 22 files that we could load all at once if we used functionals.

The first thing we have to do is add library(purrr) to the setup code chunk in the doc/lesson.Rmd document. Then we need to add the package dependency by going to the Console and running:

usethis::use_package("purrr")

Then, the next step for using the map() functional is to get a vector or list of all the dataset files available to us. We will return to using the fs package, which has a function called dir_ls() that finds files of a certain pattern. In our case, the pattern is user_info.csv. So, let’s add library(fs) to the setup code chunk. Then, go to the bottom of the doc/lesson.Rmd document, create a new header called ## Using map, and create a code chunk below that.

The dir_ls() function takes the path that we want to search (data-raw/mmash/), uses the argument regexp (short for regular expression or also regex) to find the pattern, and recurse to look in all subfolders. We’ll cover regular expressions more in the next session.

user_info_files <- dir_ls(here("data-raw/mmash/"), 
                          regexp = "user_info.csv", 
                          recurse = TRUE)

Then let’s see what the output looks like. For the website, we are only showing the first 3 files. Your output will look slightly different from this.

user_info_files
#> data-raw/mmash/user_1/user_info.csv  data-raw/mmash/user_10/user_info.csv 
#> data-raw/mmash/user_11/user_info.csv

Alright, we now have all the files ready to give to map(). So let’s try it!

user_info_list <- map(user_info_files, import_user_info)

Remember, that map() always outputs a list, so when we look into this object, it will give us 22 tibbles (data.frames). Here we’ll only show the first one:

user_info_list[[1]]
#> # A tibble: 1 × 4
#>   gender weight height   age
#>   <chr>   <dbl>  <dbl> <dbl>
#> 1 M          65    169    29

This is great because with one line of code we imported all these datasets! But we’re missing an important bit of information: The user ID. A powerful feature of the purrr package is that it has other functions to make working with functionals easier. We know map() always outputs a list. What if you want to output a character vector instead? If we check the help:

?map
For instructors: Click for details.

Go through this help documentation and talk a bit about it.

We see that there are other functions, including a function called map_chr() that seems to output a character vector. There are several others that give an output based on the ending of map_, such as:

  • map_int() outputs an integer.
  • map_dbl() outputs a numeric value, called a “double” in programming.
  • map_dfr() outputs a data frame, combining the list items by row (r).
  • map_dfc() outputs a data frame, combining the list items by column (c).

The map_dfr() looks like the one we want, since we want all these datasets together as one. If we look at the help for it, we see that it has an argument .id, which we can use to create a new column that sets the user ID, or in this case, the file path to the dataset, which has the user ID information in it. So, let’s use it and create a new column called file_path_id.

user_info_df <- map_dfr(user_info_files, import_user_info,
                        .id = "file_path_id")

Your file_path_id variable will look different. Don’t worry, we’re going to tidy up the file_path_id variable later.

user_info_df
#> # A tibble: 22 × 5
#>    file_path_id                         gender weight height   age
#>    <chr>                                <chr>   <dbl>  <dbl> <dbl>
#>  1 data-raw/mmash/user_1/user_info.csv  M          65    169    29
#>  2 data-raw/mmash/user_10/user_info.csv M          85    180    27
#>  3 data-raw/mmash/user_11/user_info.csv M         115    186    27
#>  4 data-raw/mmash/user_12/user_info.csv M          67    170    27
#>  5 data-raw/mmash/user_13/user_info.csv M          74    180    25
#>  6 data-raw/mmash/user_14/user_info.csv M          64    171    27
#>  7 data-raw/mmash/user_15/user_info.csv M          80    180    24
#>  8 data-raw/mmash/user_16/user_info.csv M          67    176    27
#>  9 data-raw/mmash/user_17/user_info.csv M          60    175    24
#> 10 data-raw/mmash/user_18/user_info.csv M          80    180     0
#> # … with 12 more rows

Now that we have this working, let’s add and commit the changes to the Git history.

8.3 Exercise: Brainstorm and discuss how you’d use functionals in your work

Time: 10 min

As a group, discuss if you’ve ever used for loops or functionals like map() and your experiences with either. Discuss any advantages to using for loops over functionals and vice versa. Then, brainstorm and discuss as many ways as you can for how you might incorporate functionals like map(), or replace for loops with them, into your own work. Afterwards, groups will briefly share some of what they thought of before we move on to the next exercise.

8.4 Exercise: Make a function for importing other datasets with functionals

Time: 25 min

We need to do basically the exact same thing for the saliva.csv, RR.csv, and Actigraph.csv datasets, following this format:

user_info_files <- dir_ls(here("data-raw/mmash/"), 
                          regexp = "user_info.csv", 
                          recurse = TRUE)
user_info_df <- map_dfr(user_info_files, import_user_info,
                        .id = "file_path_id")

For importing the other datasets, we have to modify the code in two locations to get this code to import the other datasets: at the regexp = argument and at import_user_info. This is the perfect chance to make a function that you can use for other purposes and that is itself a functional (since it takes a function as an input). So inside doc/lesson.Rmd, convert this bit of code into a function that works to import the other three datasets.

  1. Create a new header ## Exercise: Map on the other datasets at the bottom of the document.
  2. Create a new code chunk below it.
  3. Repeat the steps you’ve taken previously to create a new function:
    • Wrap the code with function() { ... }
    • Name the function import_multiple_files
    • Within function(), set two new arguments called file_pattern and import_function.
    • Within the code, replace and re-write "user_info.csv" with file_pattern (this is without quotes around it) and import_user_info with import_function (also without quotes).
    • Create generic intermediate objects (instead of user_info_files and user_info_df). So, replace and re-write user_info_file with data_files and user_info_df with combined_data.
    • Use return(combined_data) at the end of the function to output the imported data frame.
    • Create and write Roxygen documentation to describe the new function
    • Append packagename:: to the individual functions (there are three packages used: fs, here, and purrr)
    • Run it and check that it works on saliva.csv
  4. After it works, cut and paste the function into the R/functions.R file. Then restart the R session, run the line with source(here("R/functions.R")), and test the code out in the Console.
  5. Once done, add the changes you’ve made and commit them to the Git history.

Use this code as a guide to help complete this exercise:

___ <- ___(___, ___) {
    ___ <- ___dir_ls(___here("data-raw/mmash/"),
                     regexp = ___,
                     recurse = TRUE)
    
    ___ <- ___map_dfr(___, ___, 
                      .id = "file_path_id")
    ___(___)
}
Click for the (possible) solution. Click only if you are really struggling or you are out of time for the exercise.

#' Import multiple MMASH data files and merge into one data frame.
#'
#' @param file_pattern Pattern for which data file to import.
#' @param import_function Function to import the data file.
#'
#' @return A single data frame/tibble.
#'
import_multiple_files <- function(file_pattern, import_function) {
    data_files <- fs::dir_ls(here::here("data-raw/mmash/"),
                             regexp = file_pattern,
                             recurse = TRUE)
    
    combined_data <- purrr::map_dfr(data_files, import_function,
                                    .id = "file_path_id")
    return(combined_data)
}

# Test on saliva in the Console
import_multiple_files("saliva.csv", import_saliva)

8.5 Adding to the processing script and clean up R Markdown document

We’ll do this together. We’ve now made a function that imports multiple data files based on the type of data file, we can start using this function directly, like we did in the exercise above for the saliva data. We’ve already imported the user_info_df previously, but now we should do some tidying up of our R Markdown file and to start updating the data-raw/mmash.R script. Why are we doing that? Because the R Markdown file is only a sandbox to test code out and in the end we want a script that takes the raw data, processes it, and creates a working dataset we can use for analysis.

First thing we will do is delete everything below the setup code chunk that contains the library() and source() code. Why do we delete everything? Because it keeps things cleaner and makes it easier to look through the file. And because we use Git, nothing is truly gone so you can always go back to the text later. Next, we restart the R session (Ctrl-Shift-F10). Then we’ll create a new code chunk below the setup chunk where we will use the import_multiple_files() function to import the user info and saliva data.

user_info_df <- import_multiple_files("user_info.csv", import_user_info)
saliva_df <- import_multiple_files("saliva.csv", import_saliva)

To test that things work, we’ll “Knit” our R Markdown document into HTML by using the “Knit” button at the top of the pane or with Ctrl-Shift-K. Once it creates the file, it should either pop up or open in the Viewer pane on the side. If it works, then we can move on and open up the data-raw/mmash.R script. Inside the script, copy and paste these two lines of code to the bottom of the script. Afterwards, go the top of the script and right below the library(here) code, add these two lines of code, so it looks like this:

library(here)
library(tidyverse)
source(here("R/functions.R"))

Save the files, then add and commit the changes to the Git history.

8.6 Split-apply-combine technique and functionals

For instructors: Click for details.

Verbally cover this section before moving on to the summarizing. Let them know they can read more about this in this section.

We’re taking a quick detour to briefly talk about a concept that perfectly illustrates how vectorization and functionals fit into doing data analysis. The concept is called the split-apply-combine technique, which we covered in the beginner R course. The method is:

  1. Split the data into groups (e.g. diabetes status).
  2. Apply some analysis or statistics to each group (e.g. finding the mean of age).
  3. Combine the results to present them together (e.g. into a data frame that you can use to make a plot or table).

So when you split data into multiple groups, you make a vector that you can than apply (i.e. the map functional) some statistical technique to each group through vectorization. This technique works really well for a range of tasks, including for our task of summarizing some of the MMASH data so we can merge it all into one dataset.

8.7 Exercise: What is the pipe?

Time: 5 min

For instructors: Click for details.

Before starting this exercise, ask how many have used the pipe before. If everyone has, then move on to the next section. If some haven’t, let the others in the group explain, but do not use much time or even demonstrate it. If they don’t know what it is, they can look it up after. We covered this in the introduction course, so we should not cover it again here.

We haven’t used the %>% pipe from the magrittr package yet, but it is used extensively in many R packages and is the foundation of tidyverse packages. The function fundamentally changed how people write R code so much that in version 4.1 a similar function, |>, was added to base R. To make sure everyone is aware of what the pipe is, in your groups please do either task:

  • If one or more person in the group doesn’t know what the pipe is, take some time to talk about and explain it (if you know).
  • If no one in the group knows, please read the section on it from the beginner course.

8.8 Summarising data through functionals

Functionals and vectorization are an integral component of how R works and they appear throughout many of R’s functions and packages. They are particularly used throughout the tidyverse packages like dplyr. Let’s get into some more advanced features of dplyr functions that work as functionals. Before we continue, re-run the code for getting user_info_df since you had restarted the R session previously.

There are many “verbs” in dplyr, like select(), rename(), mutate(), summarise(), and group_by() (covered in more detail in the Data Management and Wrangling session of the beginner course). The common usage of these verbs is through acting on and directly using the column names (e.g. without " quotes around the column name). For instance, to select only the age column, you would type out:

user_info_df %>% 
    select(age)
#> # A tibble: 22 × 1
#>      age
#>    <dbl>
#>  1    29
#>  2    27
#>  3    27
#>  4    27
#>  5    25
#>  6    27
#>  7    24
#>  8    27
#>  9    24
#> 10     0
#> # … with 12 more rows

But many dplyr verbs can also take functions as input. When you combine select() with the where() function, you can select different variables. The where() function is a tidyselect helper, a set of functions that make it easier to select variables. Some additional helper functions include:

Table 8.1: Common tidyselect helper functions and some of their use cases.
What it selects Example Function
Select variables where a function returns TRUE Select variables that have data as character (is.character) where()
Select all variables Select all variables in user_info_df everything()
Select variables that contain the matching string Select variables that contain the string "user_info" contains()
Select variables that ends with string Select all variables that end with "date" ends_with()

Let’s select columns that are numeric:

user_info_df %>% 
    select(where(is.numeric))
#> # A tibble: 22 × 3
#>    weight height   age
#>     <dbl>  <dbl> <dbl>
#>  1     65    169    29
#>  2     85    180    27
#>  3    115    186    27
#>  4     67    170    27
#>  5     74    180    25
#>  6     64    171    27
#>  7     80    180    24
#>  8     67    176    27
#>  9     60    175    24
#> 10     80    180     0
#> # … with 12 more rows

Or, only character columns:

user_info_df %>% 
    select(where(is.character))
#> # A tibble: 22 × 2
#>    file_path_id                         gender
#>    <chr>                                <chr> 
#>  1 data-raw/mmash/user_1/user_info.csv  M     
#>  2 data-raw/mmash/user_10/user_info.csv M     
#>  3 data-raw/mmash/user_11/user_info.csv M     
#>  4 data-raw/mmash/user_12/user_info.csv M     
#>  5 data-raw/mmash/user_13/user_info.csv M     
#>  6 data-raw/mmash/user_14/user_info.csv M     
#>  7 data-raw/mmash/user_15/user_info.csv M     
#>  8 data-raw/mmash/user_16/user_info.csv M     
#>  9 data-raw/mmash/user_17/user_info.csv M     
#> 10 data-raw/mmash/user_18/user_info.csv M     
#> # … with 12 more rows

Likewise, with functions like summarise(), if you want to for example calculate the mean of cortisol in the saliva dataset, you would usually type out:

saliva_df %>% 
    summarise(cortisol_mean = mean(cortisol_norm))
#> # A tibble: 1 × 1
#>   cortisol_mean
#>           <dbl>
#> 1        0.0490

If you want to calculate the mean of multiple columns, you might think you’d have to do something like:

saliva_df %>% 
    summarise(cortisol_mean = mean(cortisol_norm),
              melatonin_mean = mean(melatonin_norm))
#> # A tibble: 1 × 2
#>   cortisol_mean melatonin_mean
#>           <dbl>          <dbl>
#> 1        0.0490  0.00000000765

But instead, there is the across() function that works like map() and allows you to calculate the mean across which ever columns you want. In many ways, across() is a duplicate of map(), particularly in the arguments you give it.

Take 2 min and read through this list. When you look in ?across, there are two main arguments and two optional ones:

  1. .cols argument: Columns you want to use.
  2. .fns: The function to use on the .cols.
    • A bare function (mean) applies it to each column and returns the output, with the column name unchanged.
    • A list with bare functions (list(mean, sd)) applies each function to each column and returns the output with the column name appended with a number (e.g. cortisol_norm_1).
    • A named list with bare functions (list(average = mean, stddev = sd)) does the same as above but instead returns an output with the column names appended with the name given to the function in the list (e.g. cortisol_norm_average).
    • A function passed with ~ and .x, like in map(). For instance, across(c(age, weight), ~ mean(.x, na.rm = TRUE)) is used to say “put age and weight, one after the other, in place of where .x is located” to calculate the mean for age and the mean for weight.
  3. ... argument: Arguments to give to the functions in .fns. For instance, across(age, mean, na.rm = TRUE) passes the argument to remove missingness na.rm into the mean() function.
  4. .names argument: Customize the output of the column names. We won’t cover this argument.

Ok, stop reading and we’ll cover this together.

For instructors: Click for details.

Go over the first two arguments again, reinforcing what they read.

Let’s try out some examples. To calculate the mean of cortisol_norm like we did above, we’d do:

saliva_df %>% 
    summarise(across(cortisol_norm, mean))
#> # A tibble: 1 × 1
#>   cortisol_norm
#>           <dbl>
#> 1        0.0490

To calculate the mean of another column:

saliva_df %>% 
    summarise(across(c(cortisol_norm, melatonin_norm), mean))
#> # A tibble: 1 × 2
#>   cortisol_norm melatonin_norm
#>           <dbl>          <dbl>
#> 1        0.0490  0.00000000765

This is nice, but changing the column names so that the function name is added would make reading what the column contents are clearer. That’s when we would use “named lists”, which are lists that look like:

list(item_one_name = ..., item_two_name = ...)

So, for having a named list with mean inside across(), it would look like:

list(mean = mean)
# or
list(average = mean)
# or
list(ave = mean)

You can confirm that it is a list by using the function names():

names(list(mean = mean))
#> [1] "mean"
names(list(average = mean))
#> [1] "average"
names(list(ave = mean))
#> [1] "ave"

Let’s stick with list(mean = mean):

saliva_df %>% 
    summarise(across(cortisol_norm, list(mean = mean)))
#> # A tibble: 1 × 1
#>   cortisol_norm_mean
#>                <dbl>
#> 1             0.0490

If we wanted to do that for all numeric columns and also calculate sd():

saliva_df %>% 
    summarise(across(where(is.numeric), list(mean = mean, sd = sd)))
#> # A tibble: 1 × 4
#>   cortisol_norm_mean cortisol_norm_sd melatonin_norm_mean melatonin_norm_sd
#>                <dbl>            <dbl>               <dbl>             <dbl>
#> 1             0.0490           0.0478       0.00000000765     0.00000000651

We can use these concepts and code to process the other longer datasets, like RR.csv, in a way that makes it more meaningful to eventually merge (also called “join”) them with the smaller datasets like user_info.csv or saliva.csv. Let’s work with the RR.csv dataset to eventually join it with the others.

8.9 Summarizing long data like the RR dataset

With the RR dataset, each participant had almost 100,000 data points recorded over two days of collection. So if we want to join with the other datasets, we need to calculate summary measures by at least file_path_id and also preferably by day as well. In this case, we need to group_by() these two variables before summarising that lets us use the split-apply-combine technique. Let’s first summarise by taking the mean of ibi_s (which is the inter-beat interval in seconds):

rr_df <- import_multiple_files("RR.csv", import_rr)
rr_df %>% 
    group_by(file_path_id, day) %>% 
    summarise(across(ibi_s, list(mean = mean)))
#> # A tibble: 44 × 3
#> # Groups:   file_path_id [22]
#>    file_path_id                    day ibi_s_mean
#>    <chr>                         <dbl>      <dbl>
#>  1 data-raw/mmash/user_1/RR.csv      1      0.666
#>  2 data-raw/mmash/user_1/RR.csv      2      0.793
#>  3 data-raw/mmash/user_10/RR.csv     1      0.820
#>  4 data-raw/mmash/user_10/RR.csv     2      0.856
#>  5 data-raw/mmash/user_11/RR.csv     1      0.818
#>  6 data-raw/mmash/user_11/RR.csv     2      0.923
#>  7 data-raw/mmash/user_12/RR.csv     1      0.779
#>  8 data-raw/mmash/user_12/RR.csv     2      0.883
#>  9 data-raw/mmash/user_13/RR.csv     1      0.727
#> 10 data-raw/mmash/user_13/RR.csv     2      0.953
#> # … with 34 more rows

While there are no missing values here, let’s add the argument na.rm = TRUE just in case.

rr_df %>% 
    group_by(file_path_id, day) %>% 
    summarise(across(ibi_s, list(mean = mean), na.rm = TRUE))
#> # A tibble: 44 × 3
#> # Groups:   file_path_id [22]
#>    file_path_id                    day ibi_s_mean
#>    <chr>                         <dbl>      <dbl>
#>  1 data-raw/mmash/user_1/RR.csv      1      0.666
#>  2 data-raw/mmash/user_1/RR.csv      2      0.793
#>  3 data-raw/mmash/user_10/RR.csv     1      0.820
#>  4 data-raw/mmash/user_10/RR.csv     2      0.856
#>  5 data-raw/mmash/user_11/RR.csv     1      0.818
#>  6 data-raw/mmash/user_11/RR.csv     2      0.923
#>  7 data-raw/mmash/user_12/RR.csv     1      0.779
#>  8 data-raw/mmash/user_12/RR.csv     2      0.883
#>  9 data-raw/mmash/user_13/RR.csv     1      0.727
#> 10 data-raw/mmash/user_13/RR.csv     2      0.953
#> # … with 34 more rows

You might notice a message (depending on the version of dplyr you have):

`summarise()` regrouping output by 'file_path_id' (override with `.groups` argument)

Take 5 min to read this section over before we continue. This message talks about regrouping, and overriding based on the .groups argument. If we look in the help ?summarise, at the .groups argument, we see that this argument is currently “experimental”. At the bottom there is a message about:

In addition, a message informs you of that choice, unless the option “dplyr.summarise.inform” is set to FALSE, or when summarise() is called from a function in a package.

So how would be go about removing this message? By putting the “dplyr.summarise.inform” in the options() function. So, go to the setup code chunk at the top of the document and add this code to the top:

options(dplyr.summarise.inform = FALSE)

You will now no longer get the message. Please stop reading and we will continue together.

Let’s also add standard deviation as another measure from the RR datasets:

summarised_rr_df <- rr_df %>% 
    group_by(file_path_id, day) %>% 
    summarise(across(ibi_s, list(mean = mean, sd = sd), na.rm = TRUE))
summarised_rr_df
#> # A tibble: 44 × 4
#> # Groups:   file_path_id [22]
#>    file_path_id                    day ibi_s_mean ibi_s_sd
#>    <chr>                         <dbl>      <dbl>    <dbl>
#>  1 data-raw/mmash/user_1/RR.csv      1      0.666   0.164 
#>  2 data-raw/mmash/user_1/RR.csv      2      0.793   0.194 
#>  3 data-raw/mmash/user_10/RR.csv     1      0.820   0.225 
#>  4 data-raw/mmash/user_10/RR.csv     2      0.856   0.397 
#>  5 data-raw/mmash/user_11/RR.csv     1      0.818   0.137 
#>  6 data-raw/mmash/user_11/RR.csv     2      0.923   0.182 
#>  7 data-raw/mmash/user_12/RR.csv     1      0.779   0.0941
#>  8 data-raw/mmash/user_12/RR.csv     2      0.883   0.258 
#>  9 data-raw/mmash/user_13/RR.csv     1      0.727   0.147 
#> 10 data-raw/mmash/user_13/RR.csv     2      0.953   0.151 
#> # … with 34 more rows

Whenever you are finished with a grouping effect, it’s good practice to end the group_by() with ungroup(). Let’s add it to the end:

summarised_rr_df <- rr_df %>% 
    group_by(file_path_id, day) %>% 
    summarise(across(ibi_s, list(mean = mean, sd = sd), na.rm = TRUE)) %>% 
    ungroup()
summarised_rr_df
#> # A tibble: 44 × 4
#>    file_path_id                    day ibi_s_mean ibi_s_sd
#>    <chr>                         <dbl>      <dbl>    <dbl>
#>  1 data-raw/mmash/user_1/RR.csv      1      0.666   0.164 
#>  2 data-raw/mmash/user_1/RR.csv      2      0.793   0.194 
#>  3 data-raw/mmash/user_10/RR.csv     1      0.820   0.225 
#>  4 data-raw/mmash/user_10/RR.csv     2      0.856   0.397 
#>  5 data-raw/mmash/user_11/RR.csv     1      0.818   0.137 
#>  6 data-raw/mmash/user_11/RR.csv     2      0.923   0.182 
#>  7 data-raw/mmash/user_12/RR.csv     1      0.779   0.0941
#>  8 data-raw/mmash/user_12/RR.csv     2      0.883   0.258 
#>  9 data-raw/mmash/user_13/RR.csv     1      0.727   0.147 
#> 10 data-raw/mmash/user_13/RR.csv     2      0.953   0.151 
#> # … with 34 more rows

Ungrouping the data with ungroup() does not provide any visual indication of what is happening. However, in the background, it removes certain metadata that the group_by() function added.

Before continuing, let’s knit the R Markdown document to confirm that everything runs as it should. If the knitting works, then switch to the Git interface and add and commit the changes so far.

8.10 Exercise: Summarise the Actigraph data

Time: 15 min

Like with the RR.csv dataset, let’s process the Actigraph.csv dataset so that it makes it easier to join with the other datasets later.

  1. Like usual, create a new Markdown header called e.g. ## Exercise: Summarise Actigraph and insert a new code chunk below that.
  2. Import all the Actigraph data files using the import_multiple_files() function you created previously. Name the new data frame actigraph_df.
  3. Look into the Data Description to find out what each column is for.
  4. Based on the documentation, which variables would you be most interested in analyzing more?
  5. Decide which summary measure(s) you think may be most interesting for you (e.g. median(), sd(), mean(), max(), min(), var()).
  6. Use group_by() of file_path_id and day, then use summarise() with across() to summarise the variables you are interested in (from item 4 above) with the summary functions you chose. Assign the newly summarised data frame to a new data frame and call it summarised_actigraph_df.
  7. End the grouping effect with ungroup().
  8. Knit the doc/lesson.Rmd document to make sure everything works.
  9. Add and commit the changes you’ve made into the Git history.
Click for the (possible) solution. Click only if you are really struggling or you are out of time for the exercise.

actigraph_df <- import_multiple_files("Actigraph.csv", import_actigraph)
summarised_actigraph_df <- actigraph_df %>% 
    group_by(file_path_id, day) %>% 
    # These statistics will probably be different for you
    summarise(across(hr, list(mean = mean, sd = sd), na.rm = TRUE)) %>% 
    ungroup()

8.11 Cleaning up and adding to the processing script

We’ll do this all together. We’ve tested out, imported, and processed two new datasets, the RR and the Actigraph datasets. First, in the R Markdown document, cut the code that we used to import and process the rr_df and actigraph_df data. Then open up the data-raw/mmash.R file and paste the cut code into the bottom of the script. It should look something like this:

user_info_df <- import_multiple_files("user_info.csv", import_user_info)
saliva_df <- import_multiple_files("saliva.csv", import_saliva)
rr_df <- import_multiple_files("RR.csv", import_rr)
actigraph_df <- import_multiple_files("Actigraph.csv", import_actigraph)

summarised_rr_df <- rr_df %>% 
    group_by(file_path_id, day) %>% 
    summarise(across(ibi_s, list(mean = mean, sd = sd), na.rm = TRUE)) %>% 
    ungroup()

# Code pasted here that was made from the above exercise

Next, go to the R Markdown document and again delete everything below the setup code chunk. After it has been deleted, add and commit the changes to the Git history.

8.12 Summary

For instructors: Click for details.

Quickly cover this before finishing the session and when starting the next session.

  • R is a functional programming language:
    • It uses functions that take an input, do an action, and give an output
    • It uses vectorisation that apply a function to multiple items (in a vector) all at once rather than using loops
    • It uses functionals that allow functions to use other functions as input
  • Use the purrr package and its function map() when you want to repeat a function on multiple items at once
  • Use group_by(), summarise(), and across() followed by ungroup() to use the split-apply-combine technique when needing to do an action on groups within the data (e.g. calculate the mean age between education groups)