Package ‘dslabs’

October 15, 2018

Title Data Science Labs
Version 0.5.1
Description Datasets and functions that can be used for data analysis practice, home-
work and projects in data science courses and workshops.
Author Rafael A. Irizarry
Maintainer Rafael A. Irizarry <rafa@jimmy.harvard.edu>
Depends R (>= 3.1.2)
Imports ggplot2
License Artistic-2.0
Encoding UTF-8
LazyData true
RoxygenNote 6.1.0
NeedsCompilation no
Repository CRAN
Date/Publication 2018-10-15 18:20:10 UTC

R topics documented:
admissions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
divorce_margarine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
ds_theme_set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
gapminder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
heights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
mnist_27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
movielens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
murders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
na_example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
olive . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
outlier_example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
polls_2008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
polls_us_election_2016 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

1
2 admissions

read_mnist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
reported_heights . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
research_funding_rates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
rfalling_object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
take_poll . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
tissue_gene_expression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
trump_tweets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
us_contagious_diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Index 19

admissions Gender bias among graduate school admissions to UC Berkeley.

Description
The admission data for six majors for the fall of 1973; often used as an example of Simpson’s
paradox

Usage
data(admissions)

Format
An object of class "data.frame".

Details
• major. The major or university department.
• gender. Men or women.
• admitted. Percent of students admitted.
• applicants. Total number of applicants.

Source
PJ Bickel, EA Hammel, and JW O’Connell. Science (1975)

Examples
data(admissions)
admissions
divorce_margarine 3

divorce_margarine Divorce rate and margarine consumption data

Description
Divorce rates in Maine and per capita consumption of margarine in US data

Usage
data(divorce_margarine)

Format
An object of class "data.frame".

Details
• divorce_rate_maine. Divorce per 1000 in Maine.
• margarine_consumption_per_capita. US per capita consumption of margarine in pounds.
• year. Year.

Source
Spurious Correlations

Examples
data(divorce_margarine)
with(divorce_margarine, plot(margarine_consumption_per_capita, divorce_rate_maine))

ds_theme_set dslabs theme set

Description
This function sets a ggplot2 theme used throughout the data science labs. It can be called without
arguments.

Usage
ds_theme_set(new = "theme_bw", args = NULL, base_size = 11,
bold_title = TRUE, ...)
4 gapminder

Arguments
new a prebuilt ggplot2 theme. Defaults to "theme_minimal"
args the arguments to be passed along to the ggplot2 theme function. Defaults to
"NULL".
base_size if "args" is "NULL", base_size is one of the arguments passed to the theme
function. It defaults to 11.
bold_title if TRUE, sets titles to be bold
... additional arguments to be used by theme

Value
None

Examples
library(ggplot2)
ds_theme_set()
qplot(hp, mpg, data=mtcars, color=am, facets=gear~cyl,
main="Scatterplots of MPG vs. Horsepower",
xlab="Horsepower", ylab="Miles per Gallon")

gapminder Gapminder Data

Description
Health and income outcomes for 184 countries from 1960 to 2016. Also includes two character
vectors, oecd and opec, with the names of OECD and OPEC countries from 2016.

Usage
data(gapminder)

Format
An object of class "data.frame".

Details
• country.
• year.
• infant_mortality. Infant deaths per 1000.
• life_expectancy. Life expectancy in years.
• fertility. Average number of children per woman.
heights 5

• population. Country population.

• gpd. GDP according to World Bankdev.
• continent.
• region. Geographical region.

Examples

data(gapminder)
head(gapminder)
print(oecd)
print(opec)

heights Self-Reported Heights

Description

Self-reported heights in inches for males and females.

Usage

data(heights)

Format

An object of class "data.frame".

Details

• sex. Male or Female.

• height. Height in inches.

Examples

data(heights)
head(heights)
6 mnist_27

mnist_27 Useful example for illustrating machine learning algorithms based on

MNIST data

Description

We only include a randomly selected set of 2s and 7s along with the two predictors based on the
proportion of dark pixels in the upper left and lower right quadrants respectively. The dataset is
divided into training and test sets.

Usage

data(mnist_27)

Format

An object of class list.

Details

• train. A data frame containing training data: labels and predictors.

• test. A data frame containing test data: labels and predictors.
• index_train. The index of the original mnist training data used for the training set.
• index_test. The index of the original mnist test data used for the test set.
• true_p. A data.frame containing the two predictors x_1 and x_2 and the conditional proba-
bility of being a 7 for x_1, x_2.

Source

http://yann.lecun.com/exdb/mnist/

Examples

data(mnist_27)
with(mnist_27$train, plot(x_1, x_2, col = as.numeric(y)))
movielens 7

movielens Movie ratings

Description

MovieLens Latest Dataset (Small)

Usage

data(movielens)

Format

Two object of class data.frame.

Details

• movieId. Unique ID for the movie.

• title. Movie title (not unique).
• year. Year the movie was released.
• genres. Genres associated with the movie.
• userId. Unique ID for the user.
• rating. A rating between 0 and 5 for the movie.
• timestamp. Date and time the rating was given.

Source

http://files.grouplens.org/datasets/movielens/ml-latest-small.zip

References

F. Maxwell Harper and Joseph A. Konstan. 2015. The MovieLens Datasets: History and Context.
ACM Transactions on Interactive Intelligent Systems (TiiS) 5, 4, Article 19 (December 2015), 19
pages. DOI=http://dx.doi.org/10.1145/2827872

Examples
data(movielens)
head(movielens)
8 na_example

murders US gun murders by state for 2010

Description
Gun murder data from FBI reports. Also contains the population of each state.

Usage
data(murders)

Format
An object of class "data.frame".

Details
• state. US state
• abb. Abbreviation of US state
• region. Geographical US region
• population. State population (2010)
• total. Number of gun murders in state (2010)

Source
Wikipedia

Examples
data(murders)
print(murders)

na_example Count data with some missing values

Description
This dataset was randomly generated.

Usage
data(na_example)

Format
An object of class "integer".
olive 9

Examples
data(na_example)
print(sum(is.na(na_example)))

olive Italian olive

Description
Composition in percentage of eight fatty acids found in the lipid fraction of 572 Italian olive oils

Usage
data(olive)

Format
An object of class "data.frame".

Details
• region. General region of Italy.
• area. Area of Italy.
• palmitic. Percent palmitic acid of sample.
• palmitoleic. Percent palmitoleic of sample.
• stearic. Percent stearic acid of sample.
• oleic. Percent oleic acid of sample.
• linoleic. Percent linoleic acid of sample.
• linolenic. Percent linolenic acid of sample.
• arachidic. Percent arachidic acid of sample.
• eicosenoic. Percent eicosenoic acid of sample.

Source
J. Zupan, and J. Gasteiger. Neural Networks in Chemistry and Drug Design.

Examples
data(olive)
head(olive)
10 polls_2008

outlier_example Adult male heights in feet with outliers

Description
This dataset was randomly generated with a normal distribution (average: 5 feet 9 inches, standard
deviation: 3 inches). One value was changed to be mistakenly reported in centimeters rather than
feet.

Usage
data(outlier_example)

Format
An object of class "numeric".

Examples
data(outlier_example)
mean(outlier_example)
median(outlier_example)

polls_2008 Poll data for popular vote in 2008 presidential election

Description
Data from different pollsters for the popular vote between Obama and McCain in the 2008 presi-
dential election.

Usage
data(polls_2008)

Format
An object of class data.frame.

Details
• day. Days until election day. Negative numbers are reported so that days can increase up to 0,
which is election day.
• margin. Average difference between Obama and McCain for that day.
polls_us_election_2016 11

Source
https://web.archive.org/web/20161108190914/http://www.pollster.com/08USPresGEMvO-2.html

Examples
data(polls_2008)
with(polls_2008, plot(day, margin))

polls_us_election_2016
Fivethirtyeight 2016 Poll Data

Description
Poll results from US 2016 presidential elections aggregated from HuffPost Pollster, RealClearPoli-
tics, polling firms and news reports. The original csv file is here: http://projects.fivethirtyeight.
com/general-model/president_general_polls_2016.csv. The dataset also includes election
results (popular vote) and electoral college votes in results_us_election_2016.

Usage
data(polls_us_election_2016)

Format
An object of class "data.frame".

Details
• state. State in which poll was taken. ‘U.S‘ is for national polls.
• startdate. Poll’s start date.
• enddate. Poll’s end date.
• pollster. Pollster conducting the poll.
• grade. Grade assigned by fivethirtyeight to pollster.
• samplesize. Sample size.
• population. Type of population being polled.
• rawpoll_clinton. Percentage for Hillary Clinton.
• rawpoll_trump. Percentage for Donald Trump
• rawpoll_johnson. Percentage for Gary Johnson
• rawpoll_mcmullin. Percentage for Evan McMullin.
• adjpoll_clinton. Fivethirtyeight adjusted percentage for Hillary Clinton.
• ajdpoll_trump. Fivethirtyeight adjusted percentage for Donald Trump
• adjpoll_johnson. Fivethirtyeight adjusted percentage for Gary Johnson
• adjpoll_mcmullin. Fivethirtyeight adjusted percentage for Evan McMullin.
12 read_mnist

Source

Ballotpedia

Examples
data(polls_us_election_2016)
head(polls_us_election_2016)

read_mnist Download and read the mnist dataset

Description

This function downloads the mnist training and test data from http://yann.lecun.com/exdb/mnist/

Usage

read_mnist()

Value

A list with two components: train and test. Each of these is a list with two components: images and
labels. The images component is a matrix with each column representing one of the 28*28 = 784
pixels. The values are integers between 0 and 255 representing grey scale. The labels components
is a vector representing the digit shown in the image.
Note that the data is over 200MB, so the download may take several seconds depending on internet
speed.

Author(s)

Samuela Pollack, <spollack@jimmy.harvard.edu>

Source

http://yann.lecun.com/exdb/mnist/

References

Y. LeCun, L. Bottou, Y. Bengio, and P. Haffner. "Gradient-based learning applied to document

recognition." Proceedings of the IEEE, 86(11):2278-2324, November 1998.
reported_heights 13

Examples
# this can take several seconds, depending on internet speed.
## Not run:
mnist <- read_mnist()
i <- 5
image(1:28, 1:28, matrix(mnist$test$images[i,], nrow=28)[ , 28:1],
col = gray(seq(0, 1, 0.05)), xlab = "", ylab="")
## the labels for this image is:
mnist$test$labels[i]

## End(Not run)

reported_heights Self-reported Heights

Description

Students were asked to report their height (in inches) and sex in an online form. This table includes
the results from four courses.

Usage

data(reported_heights)

Format

An object of class "data.frame".

Details

• time_stamp. Time and date of the entry.

• sex. Sex of the student.
• height. Height as reported by student by filling in a text free box.

Examples
data(reported_heights)
head(reported_heights)
14 research_funding_rates

research_funding_rates
Gender bias in research funding in the Netherlands

Description
Table S1 from paper title "Gender contributes to personal research funding success in The Nether-
lands"

Usage
data(research_funding_rates)

Format
An object of class "data.frame".

Details
• discipline. Research area discipline.
• applications_total. Total applications.
• applications_men. Total applications by men.
• applications_women. Total applications by women.
• awards_total. Total awards.
• awards_men. Total awards received by men.
• awards_women. Total awards received by women.
• success_rates_total. Overall success rate.
• success_rates_men. Success rate for men.
• success_rates_women. Success rate for women.

Source
van der Lee and Ellemers (2015) PNAS http://www.pnas.org/content/112/40/12349.abstract

Examples
data(research_funding_rates)
research_funding_rates
# The raw data for this table is available from
data(raw_data_research_funding_rates)
rfalling_object 15

rfalling_object Simulate falling object data

Description

The function simulates a falling object’s position. Default parameters are for dropping a weight
from the tower of Pisa.

Usage

rfalling_object(n = 14, d_0 = 55.86, v_0 = 0, g = -9.8,

scale = 1, time = seq(0, 3.25, length.out = n),
error_distribution = c("rnorm", "rt"), df = 3)

Arguments

n Sample size
d_0 Height from which object will fall in meters.
v_0 Initial velocity with which object will fall in meters per second.
g Gravitational constant, 9.8 meters per second per seonnd
scale The measurement errors will be multiplied by this constant.
time Numeric vector of times, in seconds, at which measurements were taken.
error_distribution
Character. Either rnorm for normal or rt for t-distribution.
df If using t-distribution, the degrees of freedom.

Value

A data.frame with the time, the distance travelled, and the observed distance.

Examples

dat <- rfalling_object()

with(dat, plot(time, observed_distance))
with(dat, lines(time, distance, col = "blue"))
16 tissue_gene_expression

take_poll Models results from taking a poll

Description
The function shows a plot of a random sample drawn from an urn with blue and red beads. The
sample is taken with replacement. The proportion of blue beads is not shown so that students can
try to estimate it.

Usage
take_poll(n, ...)

Arguments
n Sample size
... additional arguments to be used by the function sample.

Value
None

Examples
take_poll(25)

tissue_gene_expression
Gene expression profiles for 189 biological samples taken from seven
different tissue types.

Description
This is a subset of the data provided by the tissuesGeneExpression package available from the
genomicsclass GitHub repository. The predictors are gene expression measurements from 500
genes that are a random subset of the original 22,215.

Usage
data(tissue_gene_expression)

Format
An object of class list.
trump_tweets 17

Details
The example dataset is recommended for illustrating clustering and machine learning techniques.

• x. The predictors composed of 500 genes. Each row is a gene expression profile and each
column is different gene. The column names are the gene symbols.
• y. The outcomes. A character vector representing the tissue. One of seven tissue types.

Source
https://github.com/genomicsclass/tissuesGeneExpression

Examples
data(tissue_gene_expression)
table(tissue_gene_expression$y)
dim(tissue_gene_expression$x)

trump_tweets Trump Tweets from2009 to 2017

Description
All tweets from Donald Trump’s twitter account from 2009 to 2017

Usage
data(trump_tweets)

Format
An object of class "data.frame".

Details
• source. Device or service used to compose tweet.
• id_str. Tweet ID.
• text. Tweet.
• created_at. Data and time tweet was tweeted.
• retweet_count. How many times tweet had been retweeted at time dataset was created.
• in_reply_to_user_id_str. If a reply, the user id of person being replied to.
• favorite_count. Number of times tweet had been favored at time dataset was created.
• is_retweet. A logical telling us if it is a retweet or not.

Source
The Trump Twitter Archive: http://www.trumptwitterarchive.com
18 us_contagious_diseases

Examples
data(trump_tweets)
head(trump_tweets)

us_contagious_diseases
Contagious disease data for US states

Description
Yearly counts for Hepatitis A, Measles, Mumps, Pertussis, Polio, Rubella, and Smallpox for US
states. Original data courtesy of Tycho Project (http://www.tycho.pitt.edu/).

Usage
data(us_contagious_diseases)

Format
An object of class "data.frame".

Details
• disease. A factor containing disease names.
• state. A factor containing state names.
• year.
• weeks_reporting. Number of weeks counts were reported that year.
• count. Total number of reported cases.
• population. State population, interpolated for non-census years.

Source
Tycho Project

Examples
data(us_contagious_diseases)
head(us_contagious_diseases)
Index

∗Topic datasets raw_data_research_funding_rates

admissions, 2 (research_funding_rates), 14
divorce_margarine, 3 read_mnist, 12
gapminder, 4 reported_heights, 13
heights, 5 research_funding_rates, 14
mnist_27, 6 results_us_election_2016
movielens, 7 (polls_us_election_2016), 11
murders, 8 rfalling_object, 15
na_example, 8
olive, 9 take_poll, 16
outlier_example, 10 tissue_gene_expression, 16
polls_2008, 10 trump_tweets, 17
polls_us_election_2016, 11
reported_heights, 13 us_contagious_diseases, 18
research_funding_rates, 14
tissue_gene_expression, 16
trump_tweets, 17
us_contagious_diseases, 18

admissions, 2

divorce_margarine, 3
ds_theme_set, 3

gapminder, 4

heights, 5

mnist_27, 6
movielens, 7
murders, 8

na_example, 8

oecd (gapminder), 4
olive, 9
opec (gapminder), 4
outlier_example, 10

polls_2008, 10
polls_us_election_2016, 11

19