Readings


Required:


Additional resources:


Announcements

  • Assignment 4 due tonight - submit by pushing to your class GitHub repo

  • No class next Tuesday (February break)

  • We’re half way through the course! We will send out a link to a mid-term evaluation form (we’ll use our own form because the official CALS version won’t be ready in time to work with our schedule). We would appreciate your candid feedback so we can make the most of our remaining time together. All responses are completely anonymous.

  • Your GitHub PAT (personal access token) may expire soon (if you had set it to 30 days). We’ll review how to renew it at the end of class



Learning objectives

So far, we’ve only worked with data that were already formatted for efficient processing with tidyverse functions. In this session we’ll learn some tools to help get data into that format - make it tidy and more coder-friendly.

By the end of today’s class, you should be able to:

  • Describe the concept of tidy data
  • Determine whether a dataset is in tidy format
  • Use tidyr::pivot_wider() and tidyr::pivot_longer() to reshape data frames
  • Use tidyr::unite() and tidyr::separate() to merge or separate information from different columns


Acknowledgements

Todays lesson integrates material from multiple sources, including the excellent R for Excel users course by Julia Stewart Lowndes and Allison Horst and several other sources specified below.



Set-up for today’s exercises

Create a new R script and load packages

  • Open the R Project associated with your personal class GitHub repository.

  • PULL to make sure your project is up to date

  • Create a new R script file and save it as my_tidying.Rmd

  • Load the tidyverse package


# Load packages
library(tidyverse)



What is tidy data?

“Tidy” might sound like a generic way to describe non-messy looking data, but it actually refers to a specific data structure.

A data set is tidy if:

  • Each column is a variable;
  • Each row is an observation;
  • Each cell is a value.

See: Ch. 12 in R for Data Science by Grolemund & Wickham.



An implication of this definition is that each value belongs to exactly one variable and one observation. This also means that tidy data is relative, as it depends on how you define your observational unit and variables.

A key idea here is that instead of building your analyses around whatever (likely weird) format your data are in, take deliberate steps to make your data tidy. When your data are tidy, you can use a growing assortment of powerful analytical and visualization tools instead of inventing home-grown ways to accommodate your data. This will save you time since you aren’t reinventing the wheel, and will make your work more clear and understandable to your collaborators (most importantly, Future You).

Note that to effectively use ggplot() your data must be in tidy format. It also makes it easier to take advantage of R’s vectorized nature (most built-in R functions work with vectors of values)

Review of the beautiful slides by Julia Lowndes and Allison Horst for a clear overview of the motivation for working with tidy data.



Let’s go through some examples to get a better understanding of what tidy data look like.


Let’s first compare the four different representations of the same dataset shown in Chapter 12.2 in Grolemund and Wickham’s “R for Data Science” including the same values of four variables country, year, population, and cases.

Which of these representations are in tidy format?


Exercise

The datasets discussed in Chapter 12 of for Data Science come with the tidyverse package, so you can access them by just typing their names, e.g. table1, table2 etc. We computed the infection rate per year 10,000 people for each year and each country from table1 together using our now familiar dplyr wrangling tools.

Your task: Now calculate this same statistic from table2 and table4a + table4b. You will need to perform four operations:

  1. Extract the number of TB cases per country per year.
  2. Extract the matching population per country per year.
  3. Divide cases by population, and multiply by 10000.
  4. Store back in the appropriate place.

Which representation is easiest to work with? Which is hardest? Why?



If I had one thing to tell biologists learning bioinformatics, it would be “write code for humans, write data for computers”. — Vince Buffalo (@vsbuffalo)



Pivoting between long and wide data formats

Now that the motivation for wanting to work with data in tidy format hopefully is clear, let’s explore some powerful functions from the package tidyr for reshaping data. (tidyr comes bundled with the tidyverse, so we don’t have to install it separately).

Often, datasets will not be in tidy format because they are organized to facilitate some use other than analysis. For example, data is often organized to make entry or reading by humans as easy as possible.

This means for most real analyses, you’ll need to do some tidying. The first step is always to figure out what the variables and observations are. Sometimes this is easy; other times you’ll need to consult with the people who originally generated the data. The second step is to resolve one of two common problems:

  • One variable might be spread across multiple columns.

  • One observation might be scattered across multiple rows.


Typically a dataset will only suffer from one of these problems; it’ll only suffer from both if you’re really unlucky! To fix these problems, you’ll need the two most important functions in tidyr: pivot_longer() and pivot_wider().

We’ll walk through an illustration of how to use these by following Chapter 12.3 Pivoting in Grolemund and Wickham’s “R for Data Science”.

That overview uses a simple example with a small number of variables, so we can easily list them individually when we use pivot_longer(). For datasets with more variables, we can use more automated ways to index columns, the same helper functions we used for the select() function (you can refresh your memory here). See examples of this in the useful tidyr vignette on pivoting.


After reviewing the pivot functions, let’s continue on to also take a look at Chapter 12.4 in R for Data Science on separate() and unite() - two simple functions for splitting and combining information from different columns.



Application to a different dataset: LOTR

To explore tidy data in a different context, let’s work through a tutorial developed by Jenny Bryan using data on the Lord of the Rings movies. This nicely illustrates the concepts of lengtening and widening datasets. It uses outdated functions for pivoting the dataframes, however, so we’ll work through updated code here (i.e. only look at the 01-intro.md file, not the 02-gather.md and 03-spread.md - we’ll work through those steps here).

First let’s read the intro (01-intro.md) here

Then let’s work through reshaping the data.


1. Import untidy Lord of the Rings data

First, we bring the data into data frames or tibbles, one per film, and do some inspection.

fship <- read_csv("https://raw.githubusercontent.com/jennybc/lotr-tidy/master/data/The_Fellowship_Of_The_Ring.csv")

ttow <- read_csv("https://raw.githubusercontent.com/jennybc/lotr-tidy/master/data/The_Two_Towers.csv")

rking <- read_csv("https://raw.githubusercontent.com/jennybc/lotr-tidy/master/data/The_Return_Of_The_King.csv")


2. Collect untidy Lord of the Rings data into a single data frame

We now have one data frame per film, each with a common set of 4 variables. Step one in tidying this data is to glue them together into one data frame, stacking them up row wise. This is called row binding and we use dplyr::bind_rows().

lotr_untidy <- bind_rows(fship, ttow, rking)

lotr_untidy
## # A tibble: 9 × 4
##   Film                       Race   Female  Male
##   <chr>                      <chr>   <dbl> <dbl>
## 1 The Fellowship Of The Ring Elf      1229   971
## 2 The Fellowship Of The Ring Hobbit     14  3644
## 3 The Fellowship Of The Ring Man         0  1995
## 4 The Two Towers             Elf       331   513
## 5 The Two Towers             Hobbit      0  2463
## 6 The Two Towers             Man       401  3589
## 7 The Return Of The King     Elf       183   510
## 8 The Return Of The King     Hobbit      2  2673
## 9 The Return Of The King     Man       268  2459


3. Tidy the untidy Lord of the Rings data

We are still violating one of the fundamental principles of tidy data. “Word count” is a fundamental variable in our dataset and it’s currently spread out over two variables, Female and Male. Conceptually, we need to gather up the word counts into a single variable and create a new variable, Gender, to track whether each count refers to females or males. We use the pivot_longer() function from the tidyr package to do this.

lotr_tidy <-
  pivot_longer(lotr_untidy, c(Male, Female), names_to = 'Gender', values_to = 'Words')

lotr_tidy
## # A tibble: 18 × 4
##    Film                       Race   Gender Words
##    <chr>                      <chr>  <chr>  <dbl>
##  1 The Fellowship Of The Ring Elf    Male     971
##  2 The Fellowship Of The Ring Elf    Female  1229
##  3 The Fellowship Of The Ring Hobbit Male    3644
##  4 The Fellowship Of The Ring Hobbit Female    14
##  5 The Fellowship Of The Ring Man    Male    1995
##  6 The Fellowship Of The Ring Man    Female     0
##  7 The Two Towers             Elf    Male     513
##  8 The Two Towers             Elf    Female   331
##  9 The Two Towers             Hobbit Male    2463
## 10 The Two Towers             Hobbit Female     0
## 11 The Two Towers             Man    Male    3589
## 12 The Two Towers             Man    Female   401
## 13 The Return Of The King     Elf    Male     510
## 14 The Return Of The King     Elf    Female   183
## 15 The Return Of The King     Hobbit Male    2673
## 16 The Return Of The King     Hobbit Female     2
## 17 The Return Of The King     Man    Male    2459
## 18 The Return Of The King     Man    Female   268

Tidy data… mission accomplished!

To explain our call to pivot_longer() above, let’s read it from right to left: we took the variables Female and Male and gathered their values into a single new variable Words. This forced the creation of a companion variable Gender, which tells whether a specific value of Words came from Female or Male. All other variables, such as Film, remain unchanged and are simply replicated as needed.


4. OPTIONAL: Write the tidy data to a delimited file

Now we write this multi-film, tidy dataset to file for use in various downstream scripts for further analysis and visualization.

write_csv(lotr_tidy, file = "datasets/lotr_tidy.csv")


Your turn

  1. After tidying the data and completing your analysis, you may want to output a table that has each race in its own column. Let’s use the pivot_wider() function to make such a table and save it as “lotr_wide”

  2. OPTIONAL: Use the pivot_longer() function to transform you lotr_wide back to tidy format.


click to see our approach 
# let's get one variable per Race
lotr_tidy %>% 
  pivot_wider(names_from = Race, values_from = Words)
## # A tibble: 6 × 5
##   Film                       Gender   Elf Hobbit   Man
##   <chr>                      <chr>  <dbl>  <dbl> <dbl>
## 1 The Fellowship Of The Ring Male     971   3644  1995
## 2 The Fellowship Of The Ring Female  1229     14     0
## 3 The Two Towers             Male     513   2463  3589
## 4 The Two Towers             Female   331      0   401
## 5 The Return Of The King     Male     510   2673  2459
## 6 The Return Of The King     Female   183      2   268
# let's get one variable per Gender
lotr_tidy %>% 
  pivot_wider(names_from = Gender, values_from = Words)
## # A tibble: 9 × 4
##   Film                       Race    Male Female
##   <chr>                      <chr>  <dbl>  <dbl>
## 1 The Fellowship Of The Ring Elf      971   1229
## 2 The Fellowship Of The Ring Hobbit  3644     14
## 3 The Fellowship Of The Ring Man     1995      0
## 4 The Two Towers             Elf      513    331
## 5 The Two Towers             Hobbit  2463      0
## 6 The Two Towers             Man     3589    401
## 7 The Return Of The King     Elf      510    183
## 8 The Return Of The King     Hobbit  2673      2
## 9 The Return Of The King     Man     2459    268
# let's get one variable per combo of Race and Gender
lotr_tidy %>% 
  unite(Race_Gender, Race, Gender) %>% 
  pivot_wider(names_from = Race_Gender, values_from = Words)
## # A tibble: 3 × 7
##   Film                       Elf_Male Elf_Female Hobbi…¹ Hobbi…² Man_M…³ Man_F…⁴
##   <chr>                         <dbl>      <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
## 1 The Fellowship Of The Ring      971       1229    3644      14    1995       0
## 2 The Two Towers                  513        331    2463       0    3589     401
## 3 The Return Of The King          510        183    2673       2    2459     268
## # … with abbreviated variable names ¹​Hobbit_Male, ²​Hobbit_Female, ³​Man_Male,
## #   ⁴​Man_Female


More exercises on the LOTR data (you can do these on your own later)

The word count data is given in two untidy and gender-specific files available at these URLs:

https://raw.githubusercontent.com/jennybc/lotr-tidy/master/data/Female.csv
https://raw.githubusercontent.com/jennybc/lotr-tidy/master/data/Male.csv

Write an R script that reads them in and writes a single tidy data frame to file. Literally, reproduce the lotr_tidy data frame and the lotr_tidy.csv data file from above.

Write R code to compute the total number of words spoken by each race across the entire trilogy. Do it two ways:

  • Using film-specific or gender-specific, untidy data frames as the input data.
  • Using the lotr_tidy data frame (that we generated above) as input.

Reflect on the process of writing this code and on the code itself. Which is easier to write? Easier to read?

Write R code to compute the total number of words spoken in each film. Do this by copying and modifying your own code for totalling words by race. Which approach is easier to modify and repurpose – the one based on multiple, untidy data frames or the tidy data?



Application to our coronavirus dataset

Let’s now return to our Coronavirus dataset. Let’s remind ourselves of it’s structure

coronavirus <- read_csv('https://raw.githubusercontent.com/RamiKrispin/coronavirus/master/csv/coronavirus.csv')

coronavirus
## # A tibble: 919,308 × 15
##    date       province country   lat  long type    cases   uid iso2  iso3  code3
##    <date>     <chr>    <chr>   <dbl> <dbl> <chr>   <dbl> <dbl> <chr> <chr> <dbl>
##  1 2020-01-22 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  2 2020-01-23 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  3 2020-01-24 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  4 2020-01-25 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  5 2020-01-26 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  6 2020-01-27 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  7 2020-01-28 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  8 2020-01-29 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
##  9 2020-01-30 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
## 10 2020-01-31 Alberta  Canada   53.9 -117. confir…     0 12401 CA    CAN     124
## # … with 919,298 more rows, and 4 more variables: combined_key <chr>,
## #   population <dbl>, continent_name <chr>, continent_code <chr>


QUESTION: Is this in tidy format?


Similar to what we did in the last class, we could visualize the global sums for the different types of case counts by date (note that in August 2021, the dataset stopped tracking recoveries)

coronavirus %>%
  filter(cases > 0) %>% 
  group_by(date, type) %>%
  summarize(cases = sum(cases)) %>%
  ggplot() +
  geom_col(aes(x = date, y = cases, fill = type))


Let’s see how we would do that if the data had been in a wider format.


Your turn

Convert the coronavirus dataset to a wider format where the confirmed cases, deaths and recovered cases are shown in separate columns.


click to see our approach 
# Let's just select a few key columns so we better can follow what happens to the data structure
corona_wide <- coronavirus %>% 
  select(date, country, province, type, cases) %>% 
  pivot_wider(names_from = type, values_from = cases)


Now how do we reproduce the barchart of total cases per day broken down by type?

And how would we plot the daily counts of different case types within a country?

With the long format this is easy:

coronavirus %>% 
  filter(cases > 0, country == "US") %>% 
  ggplot() +
  geom_line(aes(x = date, y = cases, color = type))


How would we do this with the coronavirus_wide format? That would be much more difficult.


As mentioned above, however, there are plot types where the wide format provides the best input. In an earlier class, for example, I showed the example of plotting the total death count per country against the total count of confirmed cases. It would be cumbersome to pull these out of the long format because in ggplot we are mapping variables to aesthetics and now we want to map different levels of a variable to different aesthetics. So let’s make those different levels separate variables by widening the data.

coronavirus_ttd <- coronavirus %>% 
  group_by(country, type) %>%
  summarize(total_cases = sum(cases)) %>%
  pivot_wider(names_from = type, values_from = total_cases)

# Now we can plot this easily
ggplot(coronavirus_ttd) +
  geom_label(mapping = aes(x = confirmed, y = death, label = country))

This case highlights how the definition of what a variable and an observation is context-dependent so different formats of the same data can be considered tidy based on how we are thinking about the data and we may need to switch back and forth between long and wide formats to explore different levels of a dataset.




Before we wrap up - Renew our GitHub access token

When we configured git to connect with our GitHub account through RStudio, many of you may have used a PAT (personal access token) that was only valid for 30 days. Let’s revisit how we can set up with a new token by working through the procedures described in Lesson 2.