550 lines
24 KiB
Plaintext
550 lines
24 KiB
Plaintext
# Tidy data
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## Introduction
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> "Happy families are all alike; every unhappy family is unhappy in its
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> own way." --– Leo Tolstoy
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> "Tidy datasets are all alike, but every messy dataset is messy in its
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> own way." --– Hadley Wickham
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In this chapter, you will learn a consistent way to organise your data in R, a organisation called __tidy data__. Getting your data into this format requires some upfront work, but that work pays off in the long-term. Once you have tidy data and the tidy tools provided by packages in the tidyverse, you will spend much less time munging data from one representation to another, allowing you to spend more time on the analytic questions at hand.
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This chapter will give you a practical introduction to tidy data and the accompanying tools in the __tidyr__ package. If you'd like to learn more about the underlying theory, you might enjoy the *Tidy Data* paper published in the Journal of Statistical Software, <http://www.jstatsoft.org/v59/i10/paper>.
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### Prerequisites
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In this chapter we'll focus on tidyr, a package that provides a bundle of tools to help tidy messy datasets. We'll also need to use a little dplyr, as is common when tidying data.
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```{r setup}
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library(tidyr)
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library(dplyr)
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```
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## Tidy data
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You can represent the same underlying data in multiple ways. For example, the datasets below show the same data organized in four different ways. Each dataset shows the same values of four variables *country*, *year*, *population*, and *cases*, but each dataset organizes the values in different way.
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```{r}
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table1
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table2
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table3
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# Spread across two tibbles
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table4a # cases
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table4b # population
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```
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These are all representations of the same underlying data, but they are not equally easy to use. One dataset, the tidy dataset, will be much easier work with inside the tidyverse. There are three interrelated rules which make a dataset tidy:
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1. Each variable has its own column.
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1. Each observation has its own row.
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1. Each value has its own cell.
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```{r, echo = FALSE, out.width = "100%"}
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knitr::include_graphics("images/tidy-1.png")
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```
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These three rules are interrelated because it's impossible to only satisfy two of the three rules. That interrelationship leads to even simpler set of practical instructions:
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1. Put each dataset in a tibble.
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1. Put each variable in a column.
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The principles of tidy data seem so obvious that you might wonder if you'll ever encounter a dataset that isn't tidy. Unfortunately, while the principles are obvious in hindsight, it took Hadley over 5 years of struggling with many datasets to figure out these very simple principles. Most datasets that you will encounter in real life will not be tidy, either because the creator was not aware of the principles of tidy data, or because the data is stored to optimise
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Once you have your data in tidy form, it's easy to manipulate it with dplyr or visualise it with ggplot2:
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```{r}
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# Compute rate
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table1 %>%
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mutate(rate = cases / population * 10000)
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# Compute cases per year
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table1 %>%
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count(year, wt = cases)
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# Visualise changes over time
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library(ggplot2)
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ggplot(table1, aes(year, cases)) +
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geom_line(aes(group = country), colour = "grey50") +
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geom_point(aes(colour = country))
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```
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There are two advantages to tidy data:
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1. There's a general advantage to just picking one consistent way of storing
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data. If you have a consistent data structure, you can design tools that
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work with that data without having to translate it into different
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structures.
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1. There's a specific advantage to placing variables in columns because
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it allows R's vectorised nature to shine. As you learned in [useful
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creation functions] and [useful summary functions], most built-in R
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functions work with a vector of values. That makes transforming tidy
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data feel particularly natural.
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As you'll learn later, tidy data is also very well suited for modelling, and in fact, the way that R's modelling functions work was an inspiration for the tidy data format.
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### Exercises
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1. Using prose, describe how the variables and observations are organised in
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each of the sample tables.
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1. Compute the `rate` for `table2`, and `table4a` + `table4b`.
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You will need to perform four operations:
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1. Extract the number of TB cases per country per year.
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2. Extract the matching population per country per year.
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3. Divide cases by population, and multiply by 10000.
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5. Store back in the appropriate place.
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Which is easiest? Which is hardest?
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1. Recreate the plot showing change in cases over time using `table2`
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instead of `table1`. What do you need to do first?
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## Spreading and gathering
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Now that you understand the basic principles of tidy data, it's time to learn the tools that allow you to transform untidy datasets into tidy datasets.
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The first step to tidying any dataset is to study it and figure out what the variables are. Sometimes this is easy; other times you'll need to consult with the people who originally generated the data.
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One of the most messy-data common problems is that you'll find some variables are not in the columns. One variable might be spread across multiple columns, or you might find that a set of variables is spread over the rows. To fix these problems, you'll need the two most important functions in tidyr: `gather()` and `spread()`. But before we can describe how they work, you need to understand the idea of the key-value pair.
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### Key-value
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A key-value pair is a simple way to record information. A pair contains two parts: a *key* that explains what the information describes, and a *value* that contains the actual information. So, for example, this would be a key-value pair:
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Password: 0123456789
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`0123456789` is the value, and it is associated with the key `Password`.
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Data values form natural key-value pairs. The value is the value of the pair and the variable that the value describes is the key. So for example, you could decompose `table1` into a group of key-value pairs, like this:
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Country: Afghanistan
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Country: Brazil
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Country: China
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Year: 1999
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Year: 2000
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Year: 2001
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Population: 19987071
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Population: 20595360
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Population: 172006362
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Population: 174504898
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Population: 1272915272
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Population: 1280428583
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Cases: 745
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Cases: 2666
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Cases: 37737
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Cases: 80488
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Cases: 212258
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Cases: 213766
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However, the key-value pairs would cease to be a useful dataset because you no longer know which values belong to the same observation.
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Every cell in a table of data contains one half of a key-value pair, as does every column name. In tidy data, each cell will contain a value and each column name will contain a key, but this doesn't need to be the case for untidy data. Consider `table2`.
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```{r}
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table2
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```
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In `table2`, the `key` column contains only keys (and not just because the column is labeled `key`). Conveniently, the `value` column contains the values associated with those keys.
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You can use the `spread()` function to tidy this layout.
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### Spreading
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`spread()` turns a pair of key:value columns into a set of tidy columns. To use `spread()`, pass a data frame, and the pair of key-value columns. This is particularly easy `table2` because the columns are already called key and value!
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```{r}
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spread(table2, key = key, value = value)
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```
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You can see that `spread()` maintains each of the relationships expressed in the original dataset. The output contains the four original variables, *country*, *year*, *population*, and *cases*, and the values of these variables are grouped according to the original observations.
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```{r, echo = FALSE, out.width = "100%"}
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knitr::include_graphics("images/tidy-8.png")
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```
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In general, you'll use `spread()` when you have a column that contains variable names, the `key` column, and a column that contains the values of that variable, the `value` column. Here's another simple example:
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```{r}
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weather <- frame_data(
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~ day, ~measurement, ~record,
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"Jan 1", "temp", 31,
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"Jan 1", "precip", 0,
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"Jan 2", "temp", 35,
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"Jan 2", "precip", 5
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)
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weather %>%
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spread(key = measurement, value = record)
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```
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The result of `spread()` without the `key` and `value` columns that you specified. Instead, it will have one new variable for each unique value in the `key` column.
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### Gathering
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`gather()` is the opposite of `spread()`. `gather()` collects a set of column names and places them into a single "key" column. It also collects the values associated with those columns and places them into a single value column. Let's use `gather()` to tidy `table4`.
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```{r}
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table4a
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```
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`gather()` takes a data frame, the names of the new key and value variables to create, and set a columns to gather:
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```{r}
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table4a %>% gather(key = "year", value = "cases", `1999`:`2000`)
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```
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Here, the column names (`key`) represent the years, and the cell values (`value`) represents the number of cases. We specify the columns to gather with `dplyr::select()` style notation: use all columns from "1999" to "2000". (Note that these are non-syntactic names so we have to surround in backticks.) To refresh your memory of the other ways you can select columns, see [select](#select).
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`gather()` returns a copy of the data frame with the specified columns removed, and two new columns: a "key" column that contains the former column names of the removed columns, and a value column that contains the former values of the removed columns. `gather()` repeats each of the former column names (as well as each of the original columns) to maintain each combination of values that appeared in the original dataset.
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```{r, echo = FALSE, out.width = "100%"}
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knitr::include_graphics("images/tidy-9.png")
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```
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Just like `spread()`, gather maintains each of the relationships in the original dataset. This time `table4` only contained three variables, *country*, *year* and *cases*. Each of these appears in the output of `gather()` in a tidy fashion. `gather()` also maintains each of the observations in the original dataset, organizing them in a tidy fashion.
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We can use `gather()` to tidy `table4b` in a similar fashion. The only difference is the variable stored in the cell values:
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```{r}
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table4b %>% gather(key = "year", value = "population", `1999`:`2000`)
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```
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It's easy to combine the `table4a` and `table4b` into a single single data frame because the new versions are both tidy. We'll use `dplyr::left_join()`, which you'll learn about in [relational data].
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```{r}
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tidy4a <- table4a %>% gather("year", "cases", `1999`:`2000`)
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tidy4b <- table4b %>% gather("year", "population", `1999`:`2000`)
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left_join(tidy4a, tidy4b)
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```
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### Exercises
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1. Why are `gather()` and `spread()` not perfectly symmetrical?
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Carefully consider the following example:
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```{r, eval = FALSE}
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stocks <- data_frame(
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year = c(2015, 2015, 2016, 2016),
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half = c( 1, 2, 1, 2),
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return = c(1.88, 0.59, 0.92, 0.17)
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)
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stocks %>%
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spread(year, return) %>%
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gather("year", "return", `2015`:`2016`)
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```
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1. Both `spread()` and `gather()` have a `convert` argument. What does it
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do?
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1. Why does spreading this tibble fail?
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```{r}
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people <- frame_data(
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~name, ~key, ~value,
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"Phillip Woods", "age", 45,
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"Phillip Woods", "height", 186,
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"Phillip Woods", "age", 50,
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"Jessica Cordero", "age", 37,
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"Jessica Cordero", "height", 156
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)
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```
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1. Tidy the simple tibble below. Do you need to spread or gather it?
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What are the variables?
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```{r}
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preg <- frame_data(
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~pregnant, ~male, ~female,
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"yes", NA, 10,
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"no", 20, 12
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)
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```
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## Separating and uniting
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You may have noticed that we skipped `table3` in the last section. `table3` has a different problem: we have one column (`rate`) that contains two variables (`cases` and `population`). To fix this problem, we'll need the `separate()` function. In this section, we'll discuss the inverse of `separate()`: `unite()`, which you use if a single variable is spread across multiple columns.
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### Separate
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`separate()` pulls apart one column into multiple variables, by separating wherever a separator character appears.
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We need to use `separate()` to tidy `table3`, which combines values of *cases* and *population* in the same column. `separate()` take a data frame, the name of the column to separate, and the names of the columns to seperate into:
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```{r}
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table3
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table3 %>%
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separate(rate, into = c("cases", "population"))
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```
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By default, `separate()` will split values wherever it sees a non-alphanumeric character (i.e. a character that isn't a number or letter). For example, in the code above, `separate()` split the values of `rate` at the forward slash characters. If you wish to use a specific character to separate a column, you can pass the character to the `sep` argument of `separate()`. For example, we could rewrite the code above as:
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```{r eval=FALSE}
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table3 %>%
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separate(rate, into = c("cases", "population"), sep = "/")
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```
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Look carefully at the column types: you'll notice that `case` and `population` are character columns. This is the default behaviour in `separate()`: it leaves the type of the column as is. Here, however, it's not very useful those really are numbers. We can ask `separate()` to try and convert to better types using `convert = TRUE`:
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```{r}
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table3 %>%
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separate(rate, into = c("cases", "population"), convert = TRUE)
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```
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You can also pass an integer or vector of integers to `sep`. `separate()` will interpret the integers as positions to split at. Positive values start at 1 on the far-left of the strings; negative value start at -1 on the far-right of the strings. When using integers to separate strings, the length of `sep` should be one less than the number of names in `into`. You can use this arrangement to separate the last two digits of each year.
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```{r}
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table3 %>%
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separate(year, into = c("century", "year"), sep = 2)
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```
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### Unite
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`unite()` does the opposite of `separate()`: it combines multiple columns into a single column. You'll need it much less frequently that `separate()`, but it's still a useful tool to have in your back pocket.
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We can use `unite()` to rejoin the *century* and *year* columns that we created in the last example. That data is saved as `tidyr::table5`. `unite()` takes a data frame, the name of the new variable to create, and a set of columns to combine, again specified in `dplyr::select()` style:
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```{r}
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table5
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table5 %>%
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unite(new, century, year)
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```
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In this case we also need to use the `sep` arguent. The default is will place an underscore (`_`) between values from separate columns. Here we don't want any separate so we use `""`:
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```{r}
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table5 %>%
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unite(new, century, year, sep = "")
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```
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`unite()` returns a copy of the data frame that includes the new column, but not the columns used to build the new column.
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### Exercises
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1. What do the `extra` and `fill` arguments do in `separate()`?
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Experiment with the various options for the following two toy datasets.
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```{r, eval = FALSE}
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tibble::tibble(x = c("a,b,c", "d,e,f,g", "h,i,j")) %>%
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separate(x, c("one", "two", "three"))
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tibble::tibble(x = c("a,b,c", "d,e", "f,g,i")) %>%
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separate(x, c("one", "two", "three"))
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```
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1. Both `unite()` and `separate()` have a `remove` argument. What does it
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do? When would you set it to `FALSE`?
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1. Compare and contrast `separate()` and `extract()`. Why are there
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three variations of separation, but only one unite?
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## Missing values
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Changing the representation of a dataset brings up an important fact about missing values. There are two types of missing values:
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* __Explicit__ missing values are flagged with `NA`.
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* __Implicit__ missing values are simply not present in the data.
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Let's illustrate this idea with a very simple data set:
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```{r}
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stocks <- data_frame(
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year = c(2015, 2015, 2015, 2015, 2016, 2016, 2016),
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qtr = c( 1, 2, 3, 4, 2, 3, 4),
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return = c(1.88, 0.59, 0.35, NA, 0.92, 0.17, 2.66)
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)
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```
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There are two missing values in this dataset:
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* The return for the fourth quarter of 2015 is explicitly missing, because
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the cell where its value should be instead contains `NA`.
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* The return for the first quarter of 2016 is implicitly missing, because it
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simply does not appear in the dataset.
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One way to think about the difference is this Zen-like koan: An implicit missing value is the presence of an absence; an explicit missing value is the absence of a presence.
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The way that a dataset is represented can make implicit values explicit. For exmaple, we can make the implicit missing value explicit putting years in the columns:
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```{r}
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stocks %>%
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spread(year, return)
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```
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Because these explicit missing values may not be important in other representations of the data, you can set `na.rm = TRUE` in `gather()` to turn explicit missing values implicit:
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```{r}
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stocks %>%
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spread(year, return) %>%
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gather(year, return, `2015`:`2016`, na.rm = TRUE)
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```
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An important tool to making missing values explicit in tidy data is `complete()`:
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```{r}
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stocks %>%
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complete(year, qtr)
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```
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`complete()` takes a set of columns, and finds all unique combinations. It then ensures the original dataset contains all those values, filling in explicit `NA`s where necessary.
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There's one other important tool that you should know for working with missing values. Sometimes when a data source has primarily been used for data entry, missing values indicate the the previous value should be carried forward:
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```{r}
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treatment <- frame_data(
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~ person, ~ treatment, ~response,
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"Derrick Whitmore", 1, 7,
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NA, 2, 10,
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NA, 3, 9,
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"Katherine Burke", 1, 4
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)
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```
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You can fill in these missing values with `fill()`. It takes a set of columns where you want missing values to be replaced by the most recent non-missing value (sometimese called last observation carried forward).
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```{r}
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treatment %>%
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fill(person)
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```
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### Exercises
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1. Compare and contrast the `fill` arguments to `spread()` and `complete()`.
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1. What does the direction argument to `fill()` do?
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## Case Study
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The `who` dataset in tidyr contains cases of tuberculosis (TB) reported between 1995 and 2013 sorted by country, age, and gender. The data comes in the *2014 World Health Organization Global Tuberculosis Report*, available for download at <www.who.int/tb/country/data/download/en/>. The data provides a wealth of epidemiological information, but it's challenging to work with the data in the form that it's provided:
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```{r}
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who
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```
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This is a very typical example of data you are likely to encounter in real life. It contains redundant columns, odd variable codes, and many missing values. In short, `who` is messy. The most unique feature of `who` is its coding system. Columns five through sixty encode four separate pieces of information in their column names:
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1. The first three letters of each column denote whether the column
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contains new or old cases of TB. In this dataset, each column contains
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new cases.
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1. The next two letters describe the type of case being counted. We will
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treat each of these as a separate variable.
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* `rel` stands for cases of relapse
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* `ep` stands for cases of extrapulmonary TB
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* `sn` stands for cases of pulmonary TB that could not be diagnosed by
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a pulmonary smear (smear negative)
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* `sp` stands for cases of pulmonary TB that could be diagnosed be
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a pulmonary smear (smear positive)
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3. The sixth letter describes the sex of TB patients. The dataset groups
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cases by males (`m`) and females (`f`).
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4. The remaining numbers describe the age group of TB patients. The dataset
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groups cases into seven age groups:
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* `014` = 0 -- 14 years old
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* `1524` = 15 -- 24 years old
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* `2534` = 25 -- 34 years old
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* `3544` = 35 -- 44 years old
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* `4554` = 45 -- 54 years old
|
||
* `5564` = 55 -- 64 years old
|
||
* `65` = 65 or older
|
||
|
||
The `who` dataset is untidy in multiple ways, so we'll need multiple steps to tidy it. Like dplyr, tidyr is designed so that each function does one thing well. That means in real-life situations you'll typically need to string together multiple verbs.
|
||
|
||
Let's start by gathering the columns that are not variables. This is almost always the best place to start when tidying a new dataset. Here we'll use `na.rm` just so we can focus on the values that are present, not the many missing values.
|
||
|
||
```{r}
|
||
who1 <- who %>% gather(code, value, new_sp_m014:newrel_f65, na.rm = TRUE)
|
||
who1
|
||
```
|
||
|
||
We need to make a minor fix to the format of the column names: unfortunately the names are inconsistent because instead of `new_rel_` we have `newrel` (it's hard to spot this here but if you don't fix it we'll get errors in subsequent steps). You'll learn about `str_replace()` in [strings], but the basic idea is pretty simple: replace the string "newrel" with "new_rel". This makes all variable names consistent.
|
||
|
||
```{r}
|
||
who2 <- who1 %>% mutate(code = stringr::str_replace(code, "newrel", "new_rel"))
|
||
who2
|
||
```
|
||
|
||
We can separate the values in each code with two passes of `separate()`. The first pass will split the codes at each underscore.
|
||
|
||
```{r}
|
||
who3 <- who2 %>% separate(code, c("new", "type", "sexage"), sep = "_")
|
||
who3
|
||
```
|
||
|
||
Then we might as well drop the `new` colum because it's consistent in this dataset:
|
||
|
||
```{r}
|
||
who3 %>% count(new)
|
||
who4 <- who3 %>% select(-new)
|
||
```
|
||
|
||
The second pass will split `sexage` after the first character to create two columns, a sex column and an age column.
|
||
|
||
```{r}
|
||
who5 <- who4 %>% separate(sexage, c("sex", "age"), sep = 1)
|
||
who5
|
||
```
|
||
|
||
The `rel`, `ep`, `sn`, and `sp` keys are all contained in the same column. We can now move the keys into their own column names with `spread()`.
|
||
|
||
```{r}
|
||
who6 <- who5 %>% spread(type, value)
|
||
who6
|
||
```
|
||
|
||
The `who` dataset is now tidy. It is far from clean (for example, it contains several redundant columns and many missing values), but it will now be much easier to work with in R.
|
||
|
||
Typically you wouldn't assign each step to a new variable. Instead you'd join everything together in one big pipeline:
|
||
|
||
```{r}
|
||
who %>%
|
||
gather(code, value, new_sp_m014:newrel_f65, na.rm = TRUE) %>%
|
||
mutate(code = stringr::str_replace(code, "newrel", "new_rel")) %>%
|
||
separate(code, c("new", "var", "sexage")) %>%
|
||
select(-new) %>%
|
||
separate(sexage, c("sex", "age"), sep = 1) %>%
|
||
spread(var, value)
|
||
```
|
||
|
||
### Exercises
|
||
|
||
1. In this case study I set `na.rm = TRUE` just to make it easier to
|
||
check that we had the correct values. Is this reasonable? Think about
|
||
how missing values are represented in this dataset. What's the difference
|
||
between an `NA` and zero? Do you think we should use `fill = 0` in
|
||
the final `spread()` step?
|
||
|
||
1. What happens if you neglect the `mutate()` step? How might you use the
|
||
`fill` argument to `gather()`?
|
||
|
||
1. Compute the total number of cases of tb across all four diagnoses methods.
|
||
You can perform the computation either before or after the final
|
||
`spread()`. What are the advantages and disadvantages of each location?
|
||
|
||
## Non-tidy data
|
||
|
||
Before you go on further, it's worth talking a little bit about non-tidy data. Early in the chapter, I used the perjorative term "messy" to refer to non-tidy data. But that is an oversimplification: there are lots of useful and well founded data structures that are not tidy data.
|
||
|
||
There are two mains reasons to use other data structures:
|
||
|
||
* Alternative, non-tidy, representations maybe have substantial performance
|
||
or memory advantages.
|
||
|
||
* Specialised fields have evolved their own conventions for storing data
|
||
that may be quite different to the conventions of tidy data.
|
||
|
||
Generally, however, these reason will require the usage of something other than a tibble or a data frame. If you data does fit naturally into a rectangular structure composed of observations and variables, I think tidy data should be your default choice. But there are good reasons to other structures; tidy data is not the only way.
|
||
|
||
If you'd like to learn more about non-tidy data, I'd highly recommend this thoughtful blog post by Jeff Leek: <http://simplystatistics.org/2016/02/17/non-tidy-data/>
|