24  Reshaping Data

24.1 Objectives

Broadly, your objective while reading this chapter is to be able to identify datasets which have “messy” formats and determine a sequence of operations to transition the data into “tidy” format. To do this, you should be master the following concepts:

• Determine what data format is necessary to generate a desired plot or statistical model
• Understand the differences between “wide” and “long” format data and how to transition between the two structures

24.2 Tidy and Messy Data

24.2.1 Motivating Example

Consider the spreadsheet screenshot in Figure 24.1.

Figure 24.1: Spreadsheet intended for human consumption, from [1] (Chapter 3)

This spreadsheet shows New Zealand High School certificate achievement levels for a boys-only school. Typically, students would get level 1 in year 11, level 2 in year 12, and level 3 in year 13, but it is possible for students to gain multiple levels in a single year. This data is organized to show the number of students gaining each type of certification (broken out by gender) across each of the 3 years. There are many blank cells that provide ample space to see the data, and all of the necessary variables are represented: there are essentially three 2x3 tables showing the number of students attaining each NCEA level in each year of school. If all of the information is present in this table, is there really a problem? Perhaps not if the goal is just to display the data, but analyzing this data effectively, or plotting it in a way that is useful, requires some restructuring. Figure 24.2 shows a restructured version of this data in a more compact rectangular format.

Figure 24.2: Spreadsheet reorganized for data analysis

In Figure 24.2, each column contains one variable: Year, gender, level, and total number of students. Each row contains one observation. We still have 18 data points, but this format is optimized for statistical analysis, rather than to display for (human) visual consumption. We will refer to this restructured data as “tidy” data: it has a single column for each variable and a single row for each observation.

24.2.2 Defining Tidy data

The illustrations below are lifted from an excellent blog post [2] about tidy data; they’re reproduced here because

1. they’re beautiful and licensed as CCA-4.0-by, and
2. they might be more memorable than the equivalent paragraphs of text without illustration.

Most of the time, data does not come in a format suitable for analysis. Spreadsheets are generally optimized for data entry or viewing, rather than for statistical analysis:

• Tables may be laid out for easy data entry, so that there are multiple observations in a single row
• It may be visually preferable to arrange columns of data to show multiple times or categories on the same row for easy comparison

When we analyze data, however, we care much more about the fundamental structure of observations: discrete units of data collection. Each observation may have several corresponding variables that may be measured simultaneously, but fundamentally each discrete data point is what we are interested in analyzing.

The structure of tidy data reflects this preference for keeping the data in a fundamental form: each observation is in its own row, any observed variables are in single columns. This format is inherently rectangular, which is also important for statistical analysis - our methods are typically designed to work with matrices of data.

Figure 24.3: Tidy data format, illustrated.

An illustration of the principle that every messy dataset is messy in its own way.

The preference for tidy data has several practical implications: it is easier to reuse code on tidy data, allowing for analysis using a standardized set of tools (rather than having to build a custom tool for each data analysis job).

Tidy data is easier to manage because the same tools and approaches apply to multiple datasets.

In addition, standardized tools for data analysis means that it is easier to collaborate with others: if everyone starts with the same set of assumptions about the data set, you can borrow methods and tools from a collaborator’s analysis and easily apply them to your own data set.

Collaboration with tidy data.

Tidy data enables standardized workflows.

Figure 24.4: Tidy data makes it easier to collaborate with others and analyze new data using standardized workflows.

Examples: Messy Data

These datasets all display the same data: TB cases documented by the WHO in Afghanistan, Brazil, and China, between 1999 and 2000. There are 4 variables: country, year, cases, and population, but each table has a different layout.

Table 1

Table 1

country	year	cases	population
Afghanistan	1999	745	19987071
Afghanistan	2000	2666	20595360
Brazil	1999	37737	172006362
Brazil	2000	80488	174504898
China	1999	212258	1272915272
China	2000	213766	1280428583

Here, each observation is a single row, each variable is a column, and everything is nicely arranged for e.g. regression or statistical analysis. We can easily compute another measure, such as cases per 100,000 population, by taking cases/population * 100000 (this would define a new column).

2

Table 2

country	year	type	count
Afghanistan	1999	cases	745
Afghanistan	1999	population	19987071
Afghanistan	2000	cases	2666
Afghanistan	2000	population	20595360
Brazil	1999	cases	37737
Brazil	1999	population	172006362
Brazil	2000	cases	80488
Brazil	2000	population	174504898
China	1999	cases	212258
China	1999	population	1272915272
China	2000	cases	213766
China	2000	population	1280428583

Here, we have 4 columns again, but we now have 12 rows: one of the columns is an indicator of which of two numerical observations is recorded in that row; a second column stores the value. This form of the data is more easily plotted in e.g. ggplot2, if we want to show lines for both cases and population, but computing per capita cases would be much more difficult in this form than in the arrangement in table 1.

3

Table 3

country	year	rate
Afghanistan	1999	745/19987071
Afghanistan	2000	2666/20595360
Brazil	1999	37737/172006362
Brazil	2000	80488/174504898
China	1999	212258/1272915272
China	2000	213766/1280428583

This form has only 3 columns, because the rate variable (which is a character) stores both the case count and the population. We can’t do anything with this format as it stands, because we can’t do math on data stored as characters. However, this form might be easier to read and record for a human being.

4

Table 4a

country	1999	2000
Afghanistan	745	2666
Brazil	37737	80488
China	212258	213766

Table 4b

country	1999	2000
Afghanistan	19987071	20595360
Brazil	172006362	174504898
China	1272915272	1280428583

In this form, we have two tables - one for population, and one for cases. Each year’s observations are in a separate column. This format is often found in separate sheets of an excel workbook. To work with this data, we’ll need to transform each table so that there is a column indicating which year an observation is from, and then merge the two tables together by country and year.

5

Table 5

country	century	year	rate
Afghanistan	19	99	745/19987071
Afghanistan	20	00	2666/20595360
Brazil	19	99	37737/172006362
Brazil	20	00	80488/174504898
China	19	99	212258/1272915272
China	20	00	213766/1280428583

Table 5 is very similar to table 3, but the year has been separated into two columns - century, and year. This is more common with year, month, and day in separate columns (or date and time in separate columns), often to deal with the fact that spreadsheets don’t always handle dates the way you’d hope they would.

Try it out: Classifying Messy Data

Problem

For each of the datasets in the previous example, determine whether each table is tidy. If it is not, identify which rule or rules it violates.

What would you have to do in order to compute a standardized TB infection rate per 100,000 people?

Table 1

Table 1

country	year	cases	population
Afghanistan	1999	745	19987071
Afghanistan	2000	2666	20595360
Brazil	1999	37737	172006362
Brazil	2000	80488	174504898
China	1999	212258	1272915272
China	2000	213766	1280428583

This is tidy data. Computing a standardized infection rate is as simple as creating the variable rate = cases/population*100,000.

2

Table 2

country	year	type	count
Afghanistan	1999	cases	745
Afghanistan	1999	population	19987071
Afghanistan	2000	cases	2666
Afghanistan	2000	population	20595360
Brazil	1999	cases	37737
Brazil	1999	population	172006362
Brazil	2000	cases	80488
Brazil	2000	population	174504898
China	1999	cases	212258
China	1999	population	1272915272
China	2000	cases	213766
China	2000	population	1280428583

Each variable does not have its own column (so a single year’s observation of one country actually has 2 rows). Computing a standardized infection rate requires moving cases and population so that each variable has its own column, and then you can proceed using the process in 1.

3

Table 3

country	year	rate
Afghanistan	1999	745/19987071
Afghanistan	2000	2666/20595360
Brazil	1999	37737/172006362
Brazil	2000	80488/174504898
China	1999	212258/1272915272
China	2000	213766/1280428583

Each value does not have its own cell (and each variable does not have its own column). In Table 3, you’d have to separate the numerator and denominator of each cell, convert each to a numeric variable, and then you could proceed as in 1.

4

Table 4a

country	1999	2000
Afghanistan	745	2666
Brazil	37737	80488
China	212258	213766

Table 4b

country	1999	2000
Afghanistan	19987071	20595360
Brazil	172006362	174504898
China	1272915272	1280428583

There are multiple observations in each row because there is not a column for year. To compute the rate, you’d need to “stack” the two columns in each table into a single column, add a year column that is 1999, 1999, 1999, 2000, 2000, 2000, and then merge the two tables. Then you could proceed as in 1.

5

Table 5

country	century	year	rate
Afghanistan	19	99	745/19987071
Afghanistan	20	00	2666/20595360
Brazil	19	99	37737/172006362
Brazil	20	00	80488/174504898
China	19	99	212258/1272915272
China	20	00	213766/1280428583

Each variable does not have its own column (there are two columns for year, in addition to the issues noted in table3). Computing the rate would be similar to table 3; the year issues aren’t actually a huge deal unless you plot them, at which point 99 will seem to be bigger than 00 (so you’d need to combine the two year columns together first).

It is actually impossible to have a table that violates only one of the rules of tidy data - you have to violate at least two. So a simpler way to state the rules might be:

1. Each data set goes into its own table (or tibble, if you are using R)
2. Each variable gets its own column

24.3 Additional reading

[3] - IBM SPSS ad that talks about the perils of spreadsheets

[4] - assembled news stories involving spreadsheet mishaps

You have learned some of the skills to tidy data in Chapter 23, and you’ll learn more in Chapter 25, but by the end of this chapter you will have many of the skills needed to wrangle the most common “messy” data sets into “tidy” form.

24.4 Pivot operations

It’s fairly common for data to come in forms which are convenient for either human viewing or data entry. Unfortunately, these forms aren’t necessarily the most friendly for analysis.

Wide and Long format data. Source

The two operations we’ll learn here are wide -> long and long -> wide.

Pivoting from wide to long (and back) Source

This animation uses the R functions pivot_wider() and pivot_longer() Animation source, but the concept is the same in both R and python.

24.4.1 Longer

In many cases, the data come in what we might call “wide” form - some of the column names are not names of variables, but instead, are themselves values of another variable.

Picture the Operation

Tables 4a and 4b are good examples of data which is in “wide” form and should be in long(er) form: the years, which are variables, are column names, and the values are cases and population respectively.

table4a
## # A tibble: 3 × 3
##   country     `1999` `2000`
##   <chr>        <dbl>  <dbl>
## 1 Afghanistan    745   2666
## 2 Brazil       37737  80488
## 3 China       212258 213766
table4b
## # A tibble: 3 × 3
##   country         `1999`     `2000`
##   <chr>            <dbl>      <dbl>
## 1 Afghanistan   19987071   20595360
## 2 Brazil       172006362  174504898
## 3 China       1272915272 1280428583

The solution to this is to rearrange the data into “long form”: to take the columns which contain values and “stack” them, adding a variable to indicate which column each value came from. To do this, we have to duplicate the values in any column which isn’t being stacked (e.g. country, in both the example above and the image below).

A visual representation of what the pivot_longer operation looks like in practice.

Once our data are in long form, we can (if necessary) separate values that once served as column labels into actual variables, and we’ll have tidy(er) data.

R

tba <- table4a %>% 
  pivot_longer(-country, names_to = "year", values_to = "cases")
tbb <- table4b %>% 
  pivot_longer(-country, names_to = "year", values_to = "population")

# To get the tidy data, we join the two together (see Table joins below)
left_join(tba, tbb, by = c("country", "year")) %>%
  # make year numeric b/c it's dumb not to
  mutate(year = as.numeric(year))
## # A tibble: 6 × 4
##   country      year  cases population
##   <chr>       <dbl>  <dbl>      <dbl>
## 1 Afghanistan  1999    745   19987071
## 2 Afghanistan  2000   2666   20595360
## 3 Brazil       1999  37737  172006362
## 4 Brazil       2000  80488  174504898
## 5 China        1999 212258 1272915272
## 6 China        2000 213766 1280428583

The columns are moved to a variable with the name passed to the argument “names_to” (hopefully, that is easy to remember), and the values are moved to a variable with the name passed to the argument “values_to” (again, hopefully easy to remember).

We identify ID variables (variables which we don’t want to pivot) by not including them in the pivot statement. We can do this in one of two ways:

• select only variables we want to pivot: pivot_longer(table4a, cols =1999:2000, names_to = "year", values_to = "cases")
• select variables we don’t want to pivot, using - to remove them. (see above, where -country excludes country from the pivot operation)

Which option is easier depends how many things you’re pivoting (and how the columns are structured).

If we wanted to avoid the table join, we could do this process another way: first, we would add a column to each tibble called id with values “cases” and “population” respectively. Then, we could bind the two tables together by row (so stack them on top of each other). We could then do a wide-to-long pivot, followed by a long-to-wide pivot to get our data into tidy form.

# Create ID columns
table4a.x <- table4a %>% mutate(id = "cases")
table4b.x <- table4b %>% mutate(id = "population")
# Create one table
table4 <- bind_rows(table4a.x, table4b.x)

table4_long <- table4 %>%
  # rearrange columns
  select(country, id, `1999`, `2000`) %>%
  # Don't pivot country or id
  pivot_longer(-c(country:id), names_to = "year", values_to = "count")

# Intermediate fully-long form
table4_long
## # A tibble: 12 × 4
##    country     id         year       count
##    <chr>       <chr>      <chr>      <dbl>
##  1 Afghanistan cases      1999         745
##  2 Afghanistan cases      2000        2666
##  3 Brazil      cases      1999       37737
##  4 Brazil      cases      2000       80488
##  5 China       cases      1999      212258
##  6 China       cases      2000      213766
##  7 Afghanistan population 1999    19987071
##  8 Afghanistan population 2000    20595360
##  9 Brazil      population 1999   172006362
## 10 Brazil      population 2000   174504898
## 11 China       population 1999  1272915272
## 12 China       population 2000  1280428583

# make wider, with case and population columns
table4_tidy <- table4_long %>%
  pivot_wider(names_from = id, values_from = count)

table4_tidy
## # A tibble: 6 × 4
##   country     year   cases population
##   <chr>       <chr>  <dbl>      <dbl>
## 1 Afghanistan 1999     745   19987071
## 2 Afghanistan 2000    2666   20595360
## 3 Brazil      1999   37737  172006362
## 4 Brazil      2000   80488  174504898
## 5 China       1999  212258 1272915272
## 6 China       2000  213766 1280428583

Python

In Pandas, pandas.melt(...) takes id_vars, value_vars, var_name, and value_name. Otherwise, it functions nearly exactly the same as pivot_longer; the biggest difference is that column selection works differently in python than it does in the tidyverse.

As in R, we can choose to either do a melt/pivot_longer operation on each table and then join the tables together, or we can concatenate the rows and do a melt/pivot_longer operation followed by a pivot/pivot_wider operation.

import pandas as pd

# Get tables from R
table4a = r.table4a
table4b = r.table4b

tba = pd.melt(table4a, id_vars = ['country'], value_vars = ['1999', '2000'], var_name = 'year', value_name = 'cases')
tbb = pd.melt(table4b, id_vars = ['country'], value_vars = ['1999', '2000'], var_name = 'year', value_name = 'population')

# To get the tidy data, we join the two together (see Table joins below)
table4_tidy = pd.merge(tba, tbb, on = ["country", "year"], how = 'left')

Here’s the melt/pivot_longer + pivot/pivot_wider version:

import pandas as pd

# Get tables from R
table4a = r.table4a
table4b = r.table4b

table4a['id'] = "cases"
table4b['id'] = "population"

table4 = pd.concat([table4a, table4b])

# Fully long form
table4_long = pd.melt(table4, id_vars = ['country', 'id'], value_vars = ['1999', '2000'], var_name = 'year', value_name = 'count')

# Tidy form - case and population columns
table4_tidy2 = pd.pivot(table4_long, index = ['country', 'year'], columns = ['id'], values = 'count')
# reset_index() gets rid of the grouped index
table4_tidy2.reset_index()
## id      country  year     cases    population
## 0   Afghanistan  1999     745.0  1.998707e+07
## 1   Afghanistan  2000    2666.0  2.059536e+07
## 2        Brazil  1999   37737.0  1.720064e+08
## 3        Brazil  2000   80488.0  1.745049e+08
## 4         China  1999  212258.0  1.272915e+09
## 5         China  2000  213766.0  1.280429e+09

24.4.2 Wider

While it’s very common to need to transform data into a longer format, it’s not that uncommon to need to do the reverse operation. When an observation is scattered across multiple rows, your data is too long and needs to be made wider again.

Picture the Operation

Table 2 is an example of a table that is in long format but needs to be converted to a wider layout to be “tidy” - there are separate rows for cases and population, which means that a single observation (one year, one country) has two rows.

A visual representation of what the pivot_wider operation looks like in practice.

R

table2 %>%
  pivot_wider(names_from = type, values_from = count)
## # A tibble: 6 × 4
##   country      year  cases population
##   <chr>       <dbl>  <dbl>      <dbl>
## 1 Afghanistan  1999    745   19987071
## 2 Afghanistan  2000   2666   20595360
## 3 Brazil       1999  37737  172006362
## 4 Brazil       2000  80488  174504898
## 5 China        1999 212258 1272915272
## 6 China        2000 213766 1280428583

Python

table2 = r.table2

pd.pivot(table2, index = ['country', 'year'], columns = ['type'], values = 'count').reset_index()
## type      country    year     cases    population
## 0     Afghanistan  1999.0     745.0  1.998707e+07
## 1     Afghanistan  2000.0    2666.0  2.059536e+07
## 2          Brazil  1999.0   37737.0  1.720064e+08
## 3          Brazil  2000.0   80488.0  1.745049e+08
## 4           China  1999.0  212258.0  1.272915e+09
## 5           China  2000.0  213766.0  1.280429e+09

Try it Out!

In the next section, we’ll be using the WHO surveillance of disease incidence data (link). I originally wrote this using data from 2020, but the WHO has since migrated to a new system and now provides their data in a much tidier long form (link). For demonstration purposes, I’ll continue using the messier 2020 data, but the link is no longer available on the WHO’s site.

It will require some preprocessing before it’s suitable for a demonstration. I’ll do some of it, but in this section, you’re going to do the rest.

Preprocessing

You don’t have to understand what this code is doing just yet.

library(readxl)
library(purrr) # This uses the map() function as a replacement for for loops. 
# It's pretty sweet
library(tibble)
library(dplyr)

download.file("https://github.com/srvanderplas/datasets/raw/main/raw/2020_WHO_incidence_series.xls", "../data/2020_WHO_incidence_series.xls")
sheets <- excel_sheets("../data/2020_WHO_incidence_series.xls")
sheets <- sheets[-c(1, length(sheets))] # get rid of 1st and last sheet name

# This command says "for each sheet, read in the excel file with that sheet name"
# map_df means paste them all together into a single data frame
disease_incidence <- map_df(sheets, ~read_xls(path ="../data/2020_WHO_incidence_series.xls", sheet = .))

# Alternately, we could write a loop:
disease_incidence2 <- tibble() # Blank data frame
for (i in 1:length(sheets)) {
  disease_incidence2 <- bind_rows(
    disease_incidence2, 
    read_xls(path = "../data/2020_WHO_incidence_series.xls", sheet = sheets[i])
  )
}

# export for Python (and R, if you want)
readr::write_csv(disease_incidence, file = "../data/2020_who_disease_incidence.csv")

Problem

Download the exported data here and import it into Python and R. Transform it into long format, so that there is a year column. You should end up with a table that has dimensions of approximately 6 columns and 83,000 rows (or something close to that).

Can you make a line plot of cases of measles in Bangladesh over time?

head(disease_incidence)
## # A tibble: 6 × 43
##   WHO_REGION ISO_code Cname    Disease `2018` `2017` `2016` `2015` `2014` `2013`
##   <chr>      <chr>    <chr>    <chr>    <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
## 1 EMR        AFG      Afghani… CRS         NA     NA     NA      0      0      0
## 2 EUR        ALB      Albania  CRS          0      0     NA     NA     NA      0
## 3 AFR        DZA      Algeria  CRS         NA     NA      0      0     NA     NA
## 4 EUR        AND      Andorra  CRS          0      0      0     NA     NA      0
## 5 AFR        AGO      Angola   CRS         NA     NA     NA     NA     NA     NA
## 6 AMR        ATG      Antigua… CRS          0      0      0      0      0      0
## # ℹ 33 more variables: `2012` <dbl>, `2011` <dbl>, `2010` <dbl>, `2009` <dbl>,
## #   `2008` <dbl>, `2007` <dbl>, `2006` <dbl>, `2005` <dbl>, `2004` <dbl>,
## #   `2003` <dbl>, `2002` <dbl>, `2001` <dbl>, `2000` <dbl>, `1999` <dbl>,
## #   `1998` <dbl>, `1997` <dbl>, `1996` <dbl>, `1995` <dbl>, `1994` <dbl>,
## #   `1993` <dbl>, `1992` <dbl>, `1991` <dbl>, `1990` <dbl>, `1989` <dbl>,
## #   `1988` <dbl>, `1987` <dbl>, `1986` <dbl>, `1985` <dbl>, `1984` <dbl>,
## #   `1983` <dbl>, `1982` <dbl>, `1981` <dbl>, `1980` <dbl>

R solution

library(ggplot2)
library(readr)
library(tidyr)
library(stringr)
who_disease <- read_csv("../data/2020_who_disease_incidence.csv", na = ".")

who_disease_long <- who_disease %>%
  pivot_longer(matches("\\d{4}"), names_to = "year", values_to = "cases") %>%
  rename(Country = Cname) %>%
  mutate(Disease = str_replace(Disease, "CRS", "Congenital Rubella"),
         year = as.numeric(year),
         cases = as.numeric(cases))

filter(who_disease_long, Country == "Bangladesh", Disease == "measles") %>%
  ggplot(aes(x = year, y = cases)) + geom_line()

Python solution

import pandas as pd
from plotnine import *

who_disease = pd.read_csv("../data/2020_who_disease_incidence.csv", na_values = ['NA', 'NaN'])
who_disease_long = pd.melt(who_disease, id_vars = ['WHO_REGION', 'ISO_code', 'Cname', 'Disease'], var_name = 'year', value_name = 'cases')
# Rename cname to country
who_disease_long = who_disease_long.rename(columns={"Cname": "Country"})
who_disease_long.replace("CRS", "Congenital Rubella")
who_disease_long['year'] = pd.to_numeric(who_disease_long['year'])

tmp = who_disease_long.query("Country=='Bangladesh' & Disease == 'measles'")
ggplot(tmp, aes(x = "year", y = "cases")) + geom_line()

24.5 Example: Gas Prices Data

The US Energy Information Administration tracks gasoline prices, with data available on a weekly level since late 1994. You can go to this site to see a nice graph of gas prices, along with a corresponding table.

Gas prices at US EIA site

The data in the table is structured in a fairly easy to read form: each row is a month; each week in the month is a set of two columns: one for the date, one for the average gas price. While this data is definitely not tidy, it is readable.

But looking at the chart at the top of the page, it’s not clear how we might get that chart from the data in the format it’s presented here: to get a chart like that, we would need a table where each row was a single date, and there were columns for date and price. That would be tidy form data, and so we have to get from the wide, human-readable form into the long, tidier form that we can graph.

24.5.1 Setup: Gas Price Data Cleaning

For the next example, we’ll read the data in from the HTML table online and work to make it something we could e.g. plot. Before we can start cleaning, we have to read in the data:

R

library(rvest) # scrape data from the web
library(xml2) # parse xml data
url <- "https://www.eia.gov/dnav/pet/hist/LeafHandler.ashx?n=pet&s=emm_epm0u_pte_nus_dpg&f=w"

htmldoc <- read_html(url)
gas_prices_html <- html_table(htmldoc, fill = T, trim = T)[[5]][,1:11]

First 6 rows of gas prices data as read into R

Year-Month	Week 1	Week 1	Week 2	Week 2	Week 3	Week 3	Week 4	Week 4	Week 5	Week 5
Year-Month	End Date	Value	End Date	Value	End Date	Value	End Date	Value	End Date	Value
1994-Nov							11/28	1.175
1994-Dec	12/05	1.143	12/12	1.118	12/19	1.099	12/26	1.088
1995-Jan	01/02	1.104	01/09	1.111	01/16	1.102	01/23	1.110	01/30	1.109
1995-Feb	02/06	1.103	02/13	1.099	02/20	1.093	02/27	1.101

Python

import pandas as pd
gas_prices_html = pd.read_html("https://www.eia.gov/dnav/pet/hist/LeafHandler.ashx?n=pet&s=emm_epm0u_pte_nus_dpg&f=w")[4]
## ImportError: Missing optional dependency 'lxml'.  Use pip or conda to install lxml.

NameError: name ‘gas_prices_html’ is not defined

Try it out: Manual Formatting in Excel

Problem

An excel spreadsheet of the data as downloaded in January 2023 is available here. Can you manually format the data (or even just the first year or two of data) into a long, skinny format?

What steps are involved?

Solution

1. Copy the year-month column, creating one vertical copy for every set of columns

2. Move each block of two columns down to the corresponding vertical copy

3. Delete empty rows

4. Format dates

5. Delete empty columns

Video

Figure 24.5: Here is a video of me doing most of the cleaning steps - I skipped out on cleaning up the dates because Excel is miserable for working with dates.

Try it out: Formatting with Pivot Operations

Problem

Can you format the data in a long-skinny format for plotting using pivot operations without any database merges?

Write out a list of steps, and for each step, sketch out what the data frame should look like.

How do your steps compare to the steps you used for the manual approach?

Sketch

Steps to work through the gas prices data cleaning process

R solution

library(tidyverse)
library(magrittr) # pipe friendly operations

# Function to clean up column names
# Written as an extra function because it makes the code a lot cleaner
fix_gas_names <- function(x) {
  # Add extra header row information
  paste(x, c("", rep(c("Date", "Value"), times = 5))) %>%
    # trim leading/trailing spaces
    str_trim() %>%
    # replace characters in names that aren't ok for variables in R
    make.names()
}

# Clean up the table a bit
gas_prices_raw <- gas_prices_html %>%
  set_names(fix_gas_names(names(.))) %>%
  # remove first row that is really an extra header row
  filter(Year.Month != "Year-Month") %>%
  # get rid of empty rows
  filter(Year.Month != "")

head(gas_prices_raw)
## # A tibble: 6 × 11
##   Year.Month Week.1.Date Week.1.Value Week.2.Date Week.2.Value Week.3.Date
##   <chr>      <chr>       <chr>        <chr>       <chr>        <chr>      
## 1 1994-Nov   ""          ""           ""          ""           ""         
## 2 1994-Dec   "12/05"     "1.143"      "12/12"     "1.118"      "12/19"    
## 3 1995-Jan   "01/02"     "1.104"      "01/09"     "1.111"      "01/16"    
## 4 1995-Feb   "02/06"     "1.103"      "02/13"     "1.099"      "02/20"    
## 5 1995-Mar   "03/06"     "1.103"      "03/13"     "1.096"      "03/20"    
## 6 1995-Apr   "04/03"     "1.116"      "04/10"     "1.134"      "04/17"    
## # ℹ 5 more variables: Week.3.Value <chr>, Week.4.Date <chr>,
## #   Week.4.Value <chr>, Week.5.Date <chr>, Week.5.Value <chr>

# gas_prices_raw <- select(gas_prices_raw, -c(X, Date))
gas_prices_long <- pivot_longer(gas_prices_raw, -Year.Month,
                                names_to = "variable", values_to = "value")

head(gas_prices_long)
## # A tibble: 6 × 3
##   Year.Month variable     value
##   <chr>      <chr>        <chr>
## 1 1994-Nov   Week.1.Date  ""   
## 2 1994-Nov   Week.1.Value ""   
## 3 1994-Nov   Week.2.Date  ""   
## 4 1994-Nov   Week.2.Value ""   
## 5 1994-Nov   Week.3.Date  ""   
## 6 1994-Nov   Week.3.Value ""

gas_prices_sep <- separate(gas_prices_long, variable, into = c("extra", "week", "variable"), sep = "\\.") %>%
  select(-extra)
head(gas_prices_sep)
## # A tibble: 6 × 4
##   Year.Month week  variable value
##   <chr>      <chr> <chr>    <chr>
## 1 1994-Nov   1     Date     ""   
## 2 1994-Nov   1     Value    ""   
## 3 1994-Nov   2     Date     ""   
## 4 1994-Nov   2     Value    ""   
## 5 1994-Nov   3     Date     ""   
## 6 1994-Nov   3     Value    ""

gas_prices_wide <- pivot_wider(gas_prices_sep, id_cols = c("Year.Month", "week"), names_from = variable, values_from = value)
head(gas_prices_wide)
## # A tibble: 6 × 4
##   Year.Month week  Date    Value  
##   <chr>      <chr> <chr>   <chr>  
## 1 1994-Nov   1     ""      ""     
## 2 1994-Nov   2     ""      ""     
## 3 1994-Nov   3     ""      ""     
## 4 1994-Nov   4     "11/28" "1.175"
## 5 1994-Nov   5     ""      ""     
## 6 1994-Dec   1     "12/05" "1.143"

gas_prices_date <- gas_prices_wide %>%
  filter(nchar(Value) > 0) %>%
  separate(Year.Month, into = c("Year", "Month"), sep = "-") %>%
  mutate(Date = paste(Year, Date, sep = "/")) %>%
  select(-c(1:3))
  
head(gas_prices_date)
## # A tibble: 6 × 2
##   Date       Value
##   <chr>      <chr>
## 1 1994/11/28 1.175
## 2 1994/12/05 1.143
## 3 1994/12/12 1.118
## 4 1994/12/19 1.099
## 5 1994/12/26 1.088
## 6 1995/01/02 1.104

library(lubridate)
gas_prices <- gas_prices_date %>%
  mutate(Date = ymd(Date),
         Price.per.gallon = as.numeric(Value)) %>%
  select(-Value)
  
head(gas_prices)
## # A tibble: 6 × 2
##   Date       Price.per.gallon
##   <date>                <dbl>
## 1 1994-11-28             1.18
## 2 1994-12-05             1.14
## 3 1994-12-12             1.12
## 4 1994-12-19             1.10
## 5 1994-12-26             1.09
## 6 1995-01-02             1.10

Python solution

import numpy as np

def fix_gas_names(x):
  xx = pd.Series(x)
  # add extra stuff to x
  y = ["Date", "Value"]*5
  y = ["", *y, "", ""]
  names = xx + ' ' + y
  names = names.str.strip()
  names = names.str.replace(" ", ".")
  return list(names)


gas_prices_raw = gas_prices_html.copy()
## NameError: name 'gas_prices_html' is not defined

# What do column names look like?
gas_prices_raw.columns # Multi-Index 
## NameError: name 'gas_prices_raw' is not defined
# (https://stackoverflow.com/questions/25189575/pandas-dataframe-select-columns-in-multiindex)

colnames = fix_gas_names(gas_prices_raw.columns.get_level_values(0))
## NameError: name 'gas_prices_raw' is not defined
colnames
## NameError: name 'colnames' is not defined

# Set new column names
gas_prices_raw.columns = colnames
## NameError: name 'colnames' is not defined

# Drop any rows with NaN in Year-Month
gas_prices_raw = gas_prices_raw.dropna(axis = 0, subset = ['Year-Month'])
## NameError: name 'gas_prices_raw' is not defined

# Drop extra columns on the end
gas_prices_raw = gas_prices_raw.iloc[:,0:11]
## NameError: name 'gas_prices_raw' is not defined
gas_prices_raw.head()
## NameError: name 'gas_prices_raw' is not defined

gas_prices_long = pd.melt(gas_prices_raw, id_vars = 'Year-Month', var_name = 'variable')
## NameError: name 'gas_prices_raw' is not defined
gas_prices_long.head()
## NameError: name 'gas_prices_long' is not defined

gas_prices_sep = gas_prices_long
## NameError: name 'gas_prices_long' is not defined
gas_prices_sep[["extra", "week", "variable"]] = gas_prices_sep.variable.str.split(r'\.', expand = True)
## NameError: name 'gas_prices_sep' is not defined
gas_prices_sep = gas_prices_sep.drop('extra', axis = 1)
## NameError: name 'gas_prices_sep' is not defined
gas_prices_sep.head()
## NameError: name 'gas_prices_sep' is not defined

gas_prices_wide = pd.pivot(gas_prices_sep, index=['Year-Month', 'week'], columns = 'variable', values = 'value')
## NameError: name 'gas_prices_sep' is not defined
gas_prices_wide.head()
## NameError: name 'gas_prices_wide' is not defined

gas_prices_date = gas_prices_wide.dropna(axis = 0, subset = ['Date', 'Value']).reset_index()
## NameError: name 'gas_prices_wide' is not defined
gas_prices_date[['Year', 'Month']] = gas_prices_date['Year-Month'].str.split(r'-', expand = True)
## NameError: name 'gas_prices_date' is not defined
gas_prices_date['Date'] = gas_prices_date.Year + '/' + gas_prices_date.Date
## NameError: name 'gas_prices_date' is not defined
gas_prices_date['Date'] = pd.to_datetime(gas_prices_date.Date)
## NameError: name 'gas_prices_date' is not defined

gas_prices_date.head()
## NameError: name 'gas_prices_date' is not defined

gas_prices = gas_prices_date.drop(["Year-Month", "Year", "Month", "week"], axis = 1)
## NameError: name 'gas_prices_date' is not defined
gas_prices['Price_per_gallon'] = gas_prices.Value
## NameError: name 'gas_prices' is not defined
gas_prices = gas_prices.drop("Value", axis = 1)
## NameError: name 'gas_prices' is not defined
gas_prices.head()
## NameError: name 'gas_prices' is not defined

We’ll return to this example in Section 25.5 to demonstrate how you can use pivot operations and database merges together to complete this operation in a slightly different way.

24.6 Other resources

[5] - very nice task-oriented chapter that’s below the level addressed in this course but still useful

24.7 References

[1]

Q. E. McCallum, Bad data handbook: Mapping the world of data problems, 1. ed. Beijing, Köln: O’Reilly, 2013.

[2]

J. Lowndes and A. Horst, “Tidy data for efficiency, reproducibility, and collaboration,” Openscapes. Oct. 2020 [Online]. Available: https://www.openscapes.org/blog/2020/10/12/tidy-data//. [Accessed: Jul. 21, 2022]

[3]

International Business Machines, “The risks of using spreadsheets for statistical analysis,” The risks of using spreadsheets for statistical analysis. Nov. 2018 [Online]. Available: https://web.archive.org/web/20240415181938/https://www.statwks.com/wp-content/uploads/2018/11/ytw03240-usen-03\_YTW03240USEN.pdf. [Accessed: Nov. 03, 2024]

[4]

P. O’Beirne, F. Hermans, T. Cheng, and M. P. Campbell, “Horror Stories,” European Spreadsheet Risks Interest Group Horror Stories. Oct. 2020 [Online]. Available: https://eusprig.org/research-info/horror-stories/. [Accessed: Nov. 03, 2024]

[5]

J. Dougherty and I. Ilyankou, “Clean Up Messy Data,” in Hands-On Data Visualization, 1st ed., O’Reilly Media, 2021, p. 480 [Online]. Available: https://handsondataviz.org/. [Accessed: Nov. 03, 2024]