data wrangling with dplyr - nhs-r community€¦ · wrangling reshaping or transforming “raw”...

data wrangling with dplyr

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Andrew Jones | Strategy Unit

Wrangling

Reshaping or transforming “raw” data into a

format which is easier to work with.

(For later visualisation, computing of statistics,

and modelling.)

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The dplyr package

Dplyr is a language for data manipulation.

Most wrangling puzzles can be solved with

knowledge of just 5 dplyr verbs (5 functions).

These will be the subject of this session.

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Gap

min

der

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Gapminder

Data from gapminder.org

install.packages(“gapminder”)

library(gapminder)

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Q. How many variables here?Meaningful names?

What type?(more on this tomorrow)

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dplyr

5 verbs

Will help us gain a deeper understanding of our

data sets.

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arrange filter mutate summarisegroup_by

Newspaper puzzles

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18 ÷3 x7 −6 ÷3Level 2

Visualising instructions

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18 ÷3 x7 −6

Input

then then then

Output = new number

Visualising Instructions

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18 then

÷3 then

x7

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18 then

3 then

7

÷

x

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18 then

3 then

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divide by

multiply by

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18 then

by=3 then

by=7

divide

multiply

verbs

Rules (for each verb)

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18 then

by=3 then

by=7

divide( )

multiply( )

verbs

Rules (for each verb)

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18 %>%

by=3 %>%

by=7

divide( )

multiply( )

Input (number)

Output (new number)

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18 %>%

by=3 %>%

by=7

divide( )

multiply( )

Input (number)

What is the output at this step?

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18 %>%

by=3 %>%

by=7

divide( )

multiply( )

Input (number)

What is the output at this step?

The next step builds on the previous one

data_frame then

do_this(rules) then

do_this(rules)

Tidyverse syntax

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Input

dplyr verb

Output (new data frame)

data_frame %>%

do_this(rules) %>%

do_this(rules)

Tidyverse syntax

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Combine simple pieces to solve complex puzzles

data_frame %>%

do_this(rules) %>%

do_this(rules)

The tidyverse

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Gap

min

der

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Q1. How many years does this Gapminder excerpt

cover?

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1. arrangeReorder rows based on selected variable

gapminder %>%

arrange(year)

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“then”Input data frame

dplyr verb variable to arrange by

1. arrangeReorder rows based on selected variable

gapminder %>%

arrange(year)

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“then” – Ctrl + Shift + mInput data frame

dplyr verb variable to arrange by

1. arrangeIn descending order:

gapminder %>%

arrange(desc(year))

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1. arrangeIn descending order (easy way):

gapminder %>%

arrange(-year)

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“then” – Ctrl + Shift + m

Q2. Which 5 countries have the highest human

populations?(2007)

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gapminder %>%

arrange(desc(pop))

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2. filterpick observations by their value

gapminder %>%

filter( )

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“then”Input data frame

dplyr verb

2. filterpick observations by their value

gapminder %>%

filter(year == 2007)

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2. filterpick observations by their value

gapminder %>%

filter(year == 2007)

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We are testing equality so ==

Here we are choosing rows

where this expression is

TRUE

The expression inside brackets

should be TRUE or FALSE

2. filter

gapminder %>%

filter(year == 2007) %>%

arrange(desc(pop))

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“then”strings multiple

verbstogether

2. filter

gapminder %>%

filter(continent == “Africa”) %>%

arrange(desc(pop))

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Use quotes if referring to text

(character) strings

‘single’ or “double”as you wish

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Pre

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What is this not?

Q3. Which 5 countries* have the lowest GDP?

(2007)

*Not all countries represented in data

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Q3. Which 5 countries have the lowest GDP?

gapminder %>%

filter(year == 2007) %>%

arrange(gdpPercap)

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This is per capita GDP(but we can get what we need from existing variables)

3. mutate

create new variables from existing ones

gapminder %>%

mutate(gdp = pop * gdpPercap)

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3. mutate

gapminder %>%

mutate(gdp = pop*gdpPercap)

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NOT a test of equality, so =

new column name

Usually a function of existing variable(s)

3. mutate

gapminder %>%

mutate(gdp = pop*gdpPercap) %>%

arrange(gdp)

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We can refer to variables we’ve just created in the pipe chain

Q4. Which country has the highest population for each

year of data?

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5. summarisecollapse many values into a single summary value

gapminder %>%

summarise(pop_high = max(pop))

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(summary)function

new column name

Similar to mutate:

4. group_byFor each group…

… summarise (collapse into a single summary value)

gapminder %>%

group_by(year) %>%

summarise(pop_high = max(pop))

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4. group_byUseful if we desire breakdowns by variable(s)

gapminder %>%

group_by(year) %>%

summarise(pop_high = max(pop))

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4.group_by and 5.summarise

gapminder %>%

group_by(year) %>%

summarise(pop_high = max(pop))

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year pop_high

A column is created for each grouping variable

A column for the summary

4.group_by and 5.summarise

gapminder %>%

group_by(year) %>%

summarise(pop_high = max(pop))

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A row for each year group

year pop_high

1952

1957

4.group_by and 5.summarise

gapminder %>%

group_by(year, continent) %>%

summarise(mean_life = max(pop))

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A column is created for each

grouping variable

year continent pop_high

1952 Africa

1957 Africa

4.group_by and 5.summarise

gapminder %>%

group_by(year, continent) %>%

summarise(mean_life = max(pop))

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A row for each unique combo of

the grouping variables

year continent pop_high

1952 Africa

1957 Africa

Q5. How hasmean life expectancy

in Africachanged (1952–2007)?

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Q5. How hasmean life expectancy

in Africachanged (1952–2007)?

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A summary value…

Q5. How hasmean life expectancy

in Africachanged (1952–2007)?

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A summary value…

for each year…

Q5. How hasmean life expectancy

in Africachanged (1952–2007)?

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A summary value…

for each year…

but pick only the African continent

Q5. How hasmean life expectancy

in Africachanged (1952–2007)?

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A summary value…

for each year…

but pick only the African continent

Over to you:

Q. How many countries from each continent?

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Hint:

summarise(any_name = n())

Is a common pattern – it will count the number of rows in each group

Extension:

This work is licensed as

Creative Commons

Attribution-ShareAlike 4.0

International

To view a copy of this license, visit

https://creativecommons.org/licenses/by-sa/4.0/

For title photo:

https://creativecommons.org/licenses/by/2.0/

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End

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6. selectselect a subset of variables from existing data set

gapminder %>%

select(var1, var2)

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6. selectselect a subset of variables from existing data set

gapminder %>%

select(-var2)

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To remove a column

6. selectselect a subset of variables from existing data set

gapminder %>%

select(1:5)

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You can also refer to columns by number.

Here 1:5 saves having to type: 1,2,3,4,5

6. selectselect a subset of variables from existing data set

gapminder %>%

select(var6, everything())

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If you want this column at the start of your data frame