Tag: tidyverse

R resources (free courses, books, tutorials, & cheat sheets)

R resources (free courses, books, tutorials, & cheat sheets)

Help yourself to these free books, tutorials, packages, cheat sheets, and many more materials for R programming. There’s a separate overview for handy R programming tricks. If you have additions, please comment below or contact me!


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LAST UPDATED: 2021-09-24


Table of Contents (clickable)

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Introductory R

Introductory Books

Online Courses

Style Guides

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Advanced R

Package Development

Non-standard Evaluation

Functional Programming

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Cheat Sheets

Many of the above cheat sheets are hosted in the official RStudio cheat sheet overview.


Data Manipulation


Data Visualization

Colors

Interactive / HTML / JavaScript widgets

ggplot2

ggplot2 extensions

Miscellaneous

  • coefplot – visualizes model statistics
  • circlize – circular visualizations for categorical data
  • clustree – visualize clustering analysis
  • quantmod – candlestick financial charts
  • dabestr– Data Analysis using Bootstrap-Coupled ESTimation
  • devoutsvg – an SVG graphics device (with pattern fills)
  • devoutpdf – an PDF graphics device
  • cartography – create and integrate maps in your R workflow
  • colorspace – HSL based color palettes
  • viridis – Matplotlib viridis color pallete for R
  • munsell – Munsell color palettes for R
  • Cairo – high-quality display output
  • igraph – Network Analysis and Visualization
  • graphlayouts – new layout algorithms for network visualization
  • lattice – Trellis graphics
  • tmap – thematic maps
  • trelliscopejs – interactive alternative for facet_wrap
  • rgl – interactive 3D plots
  • corrplot – graphical display of a correlation matrix
  • googleVis – Google Charts API
  • plotROC – interactive ROC plots
  • extrafont – fonts in R graphics
  • rvg – produces Vector Graphics that allow further editing in PowerPoint or Excel
  • showtext – text using system fonts
  • animation – animated graphics using ImageMagick.
  • misc3d – 3d plots, isosurfaces, etc.
  • xkcd – xkcd style graphics
  • imager – CImg library to work with images
  • ungeviz – tools for visualize uncertainty
  • waffle – square pie charts a.k.a. waffle charts
  • Creating spectograms in R with hht, warbleR, soundgen, signal, seewave, or phonTools

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Shiny, Dashboards, & Apps


Markdown & Other Output Formats

  • tidystats – automating updating of model statistics
  • papaja – preparing APA journal articles
  • blogdown – build websites with Markdown & Hugo
  • huxtable – create Excel, html, & LaTeX tables
  • xaringan – make slideshows via remark.js and markdown
  • summarytools – produces neat, quick data summary tables
  • citr – RStudio Addin to Insert Markdown Citations

Cloud, Server, & Database

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Statistical Modeling & Machine Learning

Books

Courses

Cheat sheets

Time series

Survival analysis

Bayesian

Miscellaneous

  • corrr – easier correlation matrix management and exploration

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Natural Language Processing & Text Mining

Regular Expressions

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Geographic & Spatial mapping


Bioinformatics & Computational Biology

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Integrated Development Environments (IDEs) &
Graphical User Inferfaces (GUIs)

Descriptions mostly taken from their own websites:

  • RStudio*** – Open source and enterprise ready professional software
  • Jupyter Notebook*** – open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text across dozens of programming languages.
  • Microsoft R tools for Visual Studio – turn Visual Studio into a powerful R IDE
  • R Plugins for Vim, Emax, and Atom editors
  • Rattle*** – GUI for data mining
  • equisse – RStudio add-in to interactively explore and visualize data
  • R Analytic Flow – data flow diagram-based IDE
  • RKWard – easy to use and easily extensible IDE and GUI
  • Eclipse StatET – Eclipse-based IDE
  • OpenAnalytics Architect – Eclipse-based IDE
  • TinnR – open source GUI and IDE
  • DisplayR – cloud-based GUI
  • BlueSkyStatistics – GUI designed to look like SPSS and SAS 
  • ducer – GUI for everyone
  • R commander (Rcmdr) – easy and intuitive GUI
  • JGR – Java-based GUI for R
  • jamovi & jmv – free and open statistical software to bridge the gap between researcher and statistician
  • Exploratory.io – cloud-based data science focused GUI
  • Stagraph – GUI for ggplot2 that allows you to visualize and connect to databases and/or basic file types
  • ggraptr – GUI for visualization (Rapid And Pretty Things in R)
  • ML Studio – interactive Shiny platform for data visualization, statistical modeling and machine learning

R & other software and languages

R & Excel

R & Python

R & SQL

  • sqldf – running SQL statements on R data frames

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R Help, Connect, & Inspiration


R Blogs


R Conferences, Events, & Meetups

R Jobs

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Harry Plotter: Celebrating the 20 year anniversary with tidytext and the tidyverse in R

Harry Plotter: Celebrating the 20 year anniversary with tidytext and the tidyverse in R

It has been twenty years since the first Harry Potter novel, the sorcerer’s/philosopher’s stone, was published. To honour the series, I started a text analysis and visualization project, which my other-half wittily dubbed Harry Plotter. In several blogs, I intend to demonstrate how Hadley Wickham’s tidyverse and packages that build on its principles, such as tidytext (free book), have taken programming in R to an all-new level. Moreover, I just enjoy making pretty graphs : )

In this first blog (easier read), we will look at the sentiment throughout the books. In a second blog, we have examined the stereotypes behind the Hogwarts houses.

Setup

First, we need to set up our environment in RStudio. We will be needing several packages for our analyses. Most importantly, Bradley Boehmke was nice enough to gather all Harry Potter books in his harrypotter package on GitHub. We need devtools to install that package the first time, but from then on can load it in normally. Next, we load the tidytext package, which automates and tidies a lot of the text mining functionalities. We also need plyr for a specific function (ldply()). Other tidyverse packages we can load in a single bundle, including ggplot2dplyr, and tidyr, which I use in almost every of my projects. Finally, we load the wordcloud visualization package which draws on tm.

After loading these packages, I set some additional default options.

# LOAD IN PACKAGES
# library(devtools)
# devtools::install_github("bradleyboehmke/harrypotter")
library(harrypotter)
library(tidytext)
library(plyr)
library(tidyverse)
library(wordcloud)

# OPTIONS
options(stringsAsFactors = F, # do not convert upon loading
        scipen = 999, # do not convert numbers to e-values
        max.print = 200) # stop printing after 200 values

# VIZUALIZATION SETTINGS
theme_set(theme_light()) # set default ggplot theme to light
fs = 12 # default plot font size

Data preparation

With RStudio set, its time to the text of each book from the harrypotter package which we then “pipe” (%>% – another magical function from the tidyverse – specifically magrittr) along to bind all objects into a single dataframe. Here, each row represents a book with the text for each chapter stored in a separate columns. We want tidy data, so we use tidyr’s gather() function to turn each column into grouped rows. With tidytext’s unnest_tokens() function we can separate the tokens (in this case, single words) from these chapters.

# LOAD IN BOOK CHAPTERS
# TRANSFORM TO TOKENIZED DATASET
hp_words <- list(
 philosophers_stone = philosophers_stone,
 chamber_of_secrets = chamber_of_secrets,
 prisoner_of_azkaban = prisoner_of_azkaban,
 goblet_of_fire = goblet_of_fire,
 order_of_the_phoenix = order_of_the_phoenix,
 half_blood_prince = half_blood_prince,
 deathly_hallows = deathly_hallows
) %>%
 ldply(rbind) %>% # bind all chapter text to dataframe columns
 mutate(book = factor(seq_along(.id), labels = .id)) %>% # identify associated book
 select(-.id) %>% # remove ID column
 gather(key = 'chapter', value = 'text', -book) %>% # gather chapter columns to rows
 filter(!is.na(text)) %>% # delete the rows/chapters without text
 mutate(chapter = as.integer(chapter)) %>% # chapter id to numeric
 unnest_tokens(word, text, token = 'words') # tokenize data frame

Let’s inspect our current data format with head(), which prints the first rows (default n = 6).

# EXAMINE FIRST AND LAST WORDS OF SAGA
hp_words %>% head()
##                   book chapter  word
## 1   philosophers_stone       1   the
## 1.1 philosophers_stone       1   boy
## 1.2 philosophers_stone       1   who
## 1.3 philosophers_stone       1 lived
## 1.4 philosophers_stone       1    mr
## 1.5 philosophers_stone       1   and

Word frequency

A next step would be to examine word frequencies.

# PLOT WORD FREQUENCY PER BOOK
hp_words %>%
  group_by(book, word) %>%
  anti_join(stop_words, by = "word") %>% # delete stopwords
  count() %>% # summarize count per word per book
  arrange(desc(n)) %>% # highest freq on top
  group_by(book) %>% # 
  mutate(top = seq_along(word)) %>% # identify rank within group
  filter(top <= 15) %>% # retain top 15 frequent words
  # create barplot
  ggplot(aes(x = -top, fill = book)) + 
  geom_bar(aes(y = n), stat = 'identity', col = 'black') +
  # make sure words are printed either in or next to bar
  geom_text(aes(y = ifelse(n > max(n) / 2, max(n) / 50, n + max(n) / 50),
                label = word), size = fs/3, hjust = "left") +
  theme(legend.position = 'none', # get rid of legend
        text = element_text(size = fs), # determine fontsize
        axis.text.x = element_text(angle = 45, hjust = 1, size = fs/1.5), # rotate x text
        axis.ticks.y = element_blank(), # remove y ticks
        axis.text.y = element_blank()) + # remove y text
  labs(y = "Word count", x = "", # add labels
       title = "Harry Plotter: Most frequent words throughout the saga") +
  facet_grid(. ~ book) + # separate plot for each book
  coord_flip() # flip axes

download.png

Unsuprisingly, Harry is the most common word in every single book and Ron and Hermione are also present. Dumbledore’s role as an (irresponsible) mentor becomes greater as the storyline progresses. The plot also nicely depicts other key characters:

  • Lockhart and Dobby in book 2,
  • Lupin in book 3,
  • Moody and Crouch in book 4,
  • Umbridge in book 5,
  • Ginny in book 6,
  • and the final confrontation with He who must not be named in book 7.

Finally, why does J.K. seem obsessively writing about eyes that look at doors?

Estimating sentiment

Next, we turn to the sentiment of the text. tidytext includes three famous sentiment dictionaries:

  • AFINN: including bipolar sentiment scores ranging from -5 to 5
  • bing: including bipolar sentiment scores
  • nrc: including sentiment scores for many different emotions (e.g., anger, joy, and surprise)

The following script identifies all words that occur both in the books and the dictionaries and combines them into a long dataframe:

# EXTRACT SENTIMENT WITH THREE DICTIONARIES
hp_senti <- bind_rows(
  # 1 AFINN 
  hp_words %>% 
    inner_join(get_sentiments("afinn"), by = "word") %>%
    filter(score != 0) %>% # delete neutral words
    mutate(sentiment = ifelse(score < 0, 'negative', 'positive')) %>% # identify sentiment
    mutate(score = sqrt(score ^ 2)) %>% # all scores to positive
    group_by(book, chapter, sentiment) %>% 
    mutate(dictionary = 'afinn'), # create dictionary identifier
  # 2 BING 
  hp_words %>% 
    inner_join(get_sentiments("bing"), by = "word") %>%
    group_by(book, chapter, sentiment) %>%
    mutate(dictionary = 'bing'), # create dictionary identifier
  # 3 NRC 
  hp_words %>% 
    inner_join(get_sentiments("nrc"), by = "word") %>%
    group_by(book, chapter, sentiment) %>%
    mutate(dictionary = 'nrc') # create dictionary identifier
)

# EXAMINE FIRST SENTIMENT WORDS
hp_senti %>% head()
## # A tibble: 6 x 6
## # Groups:   book, chapter, sentiment [2]
##                 book chapter      word score sentiment dictionary
##                                   
## 1 philosophers_stone       1     proud     2  positive      afinn
## 2 philosophers_stone       1 perfectly     3  positive      afinn
## 3 philosophers_stone       1     thank     2  positive      afinn
## 4 philosophers_stone       1   strange     1  negative      afinn
## 5 philosophers_stone       1  nonsense     2  negative      afinn
## 6 philosophers_stone       1       big     1  positive      afinn

Wordcloud

Although wordclouds are not my favorite visualizations, they do allow for a quick display of frequencies among a large body of words.

hp_senti %>%
  group_by(word) %>%
  count() %>% # summarize count per word
  mutate(log_n = sqrt(n)) %>% # take root to decrease outlier impact
  with(wordcloud(word, log_n, max.words = 100))

download (1)

It appears we need to correct for some words that occur in the sentiment dictionaries but have a different meaning in J.K. Rowling’s books. Most importantly, we need to filter two character names.

# DELETE SENTIMENT FOR CHARACTER NAMES
hp_senti_sel <- hp_senti %>% filter(!word %in% c("harry","moody"))

Words per sentiment

Let’s quickly sketch the remaining words per sentiment.

# VIZUALIZE MOST FREQUENT WORDS PER SENTIMENT
hp_senti_sel %>% # NAMES EXCLUDED
  group_by(word, sentiment) %>%
  count() %>% # summarize count per word per sentiment
  group_by(sentiment) %>%
  arrange(sentiment, desc(n)) %>% # most frequent on top
  mutate(top = seq_along(word)) %>% # identify rank within group
  filter(top <= 15) %>% # keep top 15 frequent words
  ggplot(aes(x = -top, fill = factor(sentiment))) + 
  # create barplot
  geom_bar(aes(y = n), stat = 'identity', col = 'black') +
  # make sure words are printed either in or next to bar
  geom_text(aes(y = ifelse(n > max(n) / 2, max(n) / 50, n + max(n) / 50),
                label = word), size = fs/3, hjust = "left") +
  theme(legend.position = 'none', # remove legend
        text = element_text(size = fs), # determine fontsize
        axis.text.x = element_text(angle = 45, hjust = 1), # rotate x text
        axis.ticks.y = element_blank(), # remove y ticks
        axis.text.y = element_blank()) + # remove y text
  labs(y = "Word count", x = "", # add manual labels
       title = "Harry Plotter: Words carrying sentiment as counted throughout the saga",
       subtitle = "Using tidytext and the AFINN, bing, and nrc sentiment dictionaries") +
  facet_grid(. ~ sentiment) + # separate plot for each sentiment
  coord_flip() # flip axes

download (2).png

This seems ok. Let’s continue to plot the sentiment over time.

Positive and negative sentiment throughout the series

As positive and negative sentiment is included in each of the three dictionaries we can to compare and contrast scores.

# VIZUALIZE POSTIVE/NEGATIVE SENTIMENT OVER TIME
plot_sentiment <- hp_senti_sel %>% # NAMES EXCLUDED
  group_by(dictionary, sentiment, book, chapter) %>%
  summarize(score = sum(score), # summarize AFINN scores
            count = n(), # summarize bing and nrc counts
            # move bing and nrc counts to score 
            score = ifelse(is.na(score), count, score))  %>%
  filter(sentiment %in% c('positive','negative')) %>%   # only retain bipolar sentiment
  mutate(score = ifelse(sentiment == 'negative', -score, score)) %>% # reverse negative values
  # create area plot
  ggplot(aes(x = chapter, y = score)) +    
  geom_area(aes(fill = score > 0),stat = 'identity') +
  scale_fill_manual(values = c('red','green')) + # change colors
  # add black smoothed line without standard error
  geom_smooth(method = "loess", se = F, col = "black") + 
  theme(legend.position = 'none', # remove legend
        text = element_text(size = fs)) + # change font size
  labs(x = "Chapter", y = "Sentiment score", # add labels
       title = "Harry Plotter: Sentiment during the saga",
       subtitle = "Using tidytext and the AFINN, bing, and nrc sentiment dictionaries") +
     # separate plot per book and dictionary and free up x-axes
  facet_grid(dictionary ~ book, scale = "free_x")
plot_sentiment

download (3).png

Let’s zoom in on the smoothed average.

plot_sentiment + coord_cartesian(ylim = c(-100,50)) # zoom in plot

download (4).png

Sentiment seems overly negative throughout the series. Particularly salient is that every book ends on a down note, except the Prisoner of Azkaban. Moreover, sentiment becomes more volatile in books four through six. These start out negative, brighten up in the middle, just to end in misery again. In her final book, J.K. Rowling depicts a world about to be conquered by the Dark Lord and the average negative sentiment clearly resembles this grim outlook.

The bing sentiment dictionary estimates the most negative sentiment on average, but that might be due to this specific text.

Other emotions throughout the series

Finally, let’s look at the other emotions that are included in the nrc dictionary.

# VIZUALIZE EMOTIONAL SENTIMENT OVER TIME
hp_senti_sel %>% # NAMES EXCLUDED 
  filter(!sentiment %in% c('negative','positive')) %>% # only retain other sentiments (nrc)
  group_by(sentiment, book, chapter) %>%
  count() %>% # summarize count
  # create area plot
  ggplot(aes(x = chapter, y = n)) +
  geom_area(aes(fill = sentiment), stat = 'identity') + 
  # add black smoothing line without standard error
  geom_smooth(aes(fill = sentiment), method = "loess", se = F, col = 'black') + 
  theme(legend.position = 'none', # remove legend
        text = element_text(size = fs)) + # change font size
  labs(x = "Chapter", y = "Emotion score", # add labels
       title = "Harry Plotter: Emotions during the saga",
       subtitle = "Using tidytext and the nrc sentiment dictionary") +
  # separate plots per sentiment and book and free up x-axes
  facet_grid(sentiment ~ book, scale = "free_x") 

download (5).png

This plot is less insightful as either the eight emotions are represented by similar words or J.K. Rowling combines all in her writing simultaneously. Patterns across emotions are highly similar, evidenced especially by the patterns in the Chamber of Secrets. In a next post, I will examine sentiment in a more detailed fashion, testing the differences over time and between characters statistically. For now, I hope you enjoyed these visualizations. Feel free to come back or subscribe to read my subsequent analyses.

The second blog in the Harry Plotter series examines the stereotypes behind the Hogwarts houses.

Text Mining: Shirin’s Twitter Feed

Text mining and analytics, natural language processing, and topic modelling have definitely become sort of an obsession of mine. I am just amazed by the insights one can retrieve from textual information, and with the ever increasing amounts of unstructured data on the internet, recreational analysts are coming up with the most amazing text mining projects these days.

Only last week, I came across posts talking about how the text in the Game of Thrones books to demonstrate a gender bias, how someone created an entire book with weirdly-satisfying computer-generated poems, and how to conduct a rather impressive analysis of your Twitter following. The latter, I copied below, with all props obviously for Shirin – the author.

For those of you who want to learn more about text mining and, specifically, how to start mining in R with tidytext, an new text-mining complement to the tidyverse, I can strongly recommend the new book by Julia Silge and David Robinson. This book has helped me greatly in learning the basics and you can definitely expect some blogs on my personal text mining projects soon.

===== COPIED FROM SHIRIN’S PLAYGROUND =====

Lately, I have been more and more taken with tidy principles of data analysis. They are elegant and make analyses clearer and easier to comprehend. Following the tidyverse and ggraph, I have been quite intrigued by applying tidy principles to text analysis with Julia Silge and David Robinson’s tidytext.

In this post, I will explore tidytext with an analysis of my Twitter followers’ descriptions to try and learn more about the people who are interested in my tweets, which are mainly about Data Science and Machine Learning.

Resources I found useful for this analysis were http://www.rdatamining.com/docs/twitter-analysis-with-r and http://tidytextmining.com/tidytext.html

Retrieving Twitter data

I am using twitteR to retrieve data from Twitter (I have also tried rtweet but for some reason, my API key, secret and token (that worked with twitteR) resulted in a “failed to authorize” error with rtweet’s functions).

library(twitteR)

Once we have set up our Twitter REST API, we get the necessary information to authenticate our access.

consumerKey = "INSERT KEY HERE"
consumerSecret = "INSERT SECRET KEY HERE"
accessToken = "INSERT TOKEN HERE"
accessSecret = "INSERT SECRET TOKEN HERE"
options(httr_oauth_cache = TRUE)

setup_twitter_oauth(consumer_key = consumerKey, 
                    consumer_secret = consumerSecret, 
                    access_token = accessToken, 
                    access_secret = accessSecret)

Now, we can access information from Twitter, like timeline tweets, user timelines, mentions, tweets & retweets, followers, etc.

All the following datasets were retrieved on June 7th 2017, converted to a data frame for tidy analysis and saved for later use:

  • the last 3200 tweets on my timeline
my_name <- userTimeline("ShirinGlander", n = 3200, includeRts=TRUE)
my_name_df <- twListToDF(my_name)
save(my_name_df, file = "my_name.RData")
  • my last 3200 mentions and retweets
my_mentions <- mentions(n = 3200)
my_mentions_df <- twListToDF(my_mentions)
save(my_mentions_df, file = "my_mentions.RData")

my_retweets <- retweetsOfMe(n = 3200)
my_retweets_df <- twListToDF(my_retweets)
save(my_retweets_df, file = "my_retweets.RData")
  • the last 3200 tweets to me
tweetstome <- searchTwitter("@ShirinGlander", n = 3200)
tweetstome_df <- twListToDF(tweetstome)
save(tweetstome_df, file = "tweetstome.RData")
  • my friends and followers
user <- getUser("ShirinGlander")

friends <- user$getFriends() # who I follow
friends_df <- twListToDF(friends)
save(friends_df, file = "my_friends.RData")

followers <- user$getFollowers() # my followers
followers_df <- twListToDF(followers)
save(followers_df, file = "my_followers.RData")

Analyzing friends and followers

In this post, I will have a look at my friends and followers.

load("my_friends.RData")
load("my_followers.RData")

I am going to use packages from the tidyverse (tidyquant for plotting).

library(tidyverse)
library(tidyquant)
  • Number of friends (who I follow on Twitter): 225
  • Number of followers (who follows me on Twitter): 324
  • Number of friends who are also followers: 97

What languages do my followers speak?

One of the columns describing my followers is which language they have set for their Twitter account. Not surprisingly, English is by far the most predominant language of my followers, followed by German, Spanish and French.

followers_df %>%
  count(lang) %>%
  droplevels() %>%
  ggplot(aes(x = reorder(lang, desc(n)), y = n)) +
    geom_bar(stat = "identity", color = palette_light()[1], fill = palette_light()[1], alpha = 0.8) +
    theme_tq() +
    theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)) +
    labs(x = "language ISO 639-1 code",
         y = "number of followers")

Who are my most “influential” followers (i.e. followers with the biggest network)?

I also have information about the number of followers that each of my followers have (2nd degree followers). Most of my followers are followed by up to ~ 1000 people, while only a few have a very large network.

followers_df %>%
  ggplot(aes(x = log2(followersCount))) +
    geom_density(color = palette_light()[1], fill = palette_light()[1], alpha = 0.8) +
    theme_tq() +
    labs(x = "log2 of number of followers",
         y = "density")

How active are my followers (i.e. how often do they tweet)

The followers data frame also tells me how many statuses (i.e. tweets) each of followers have. To make the numbers comparable, I am normalizing them by the number of days that they have had their accounts to calculate the average number of tweets per day.

followers_df %>%
  mutate(date = as.Date(created, format = "%Y-%m-%d"),
         today = as.Date("2017-06-07", format = "%Y-%m-%d"),
         days = as.numeric(today - date),
         statusesCount_pDay = statusesCount / days) %>%
  ggplot(aes(x = log2(statusesCount_pDay))) +
    geom_density(color = palette_light()[1], fill = palette_light()[1], alpha = 0.8) +
    theme_tq()

Who are my followers with the biggest network and who tweet the most?

followers_df %>%
  mutate(date = as.Date(created, format = "%Y-%m-%d"),
         today = as.Date("2017-06-07", format = "%Y-%m-%d"),
         days = as.numeric(today - date),
         statusesCount_pDay = statusesCount / days) %>%
  select(screenName, followersCount, statusesCount_pDay) %>%
  arrange(desc(followersCount)) %>%
  top_n(10)
##         screenName followersCount statusesCount_pDay
## 1        dr_morton         150937           71.35193
## 2    Scientists4EU          66117           17.64389
## 3       dr_morton_          63467           46.57763
## 4   NewScienceWrld          60092           54.65874
## 5     RubenRabines          42286           25.99592
## 6  machinelearnbot          27427          204.67061
## 7  BecomingDataSci          16807           25.24069
## 8       joelgombin           6566           21.24094
## 9    renato_umeton           1998           19.58387
## 10 FranPatogenLoco            311           28.92593
followers_df %>%
  mutate(date = as.Date(created, format = "%Y-%m-%d"),
         today = as.Date("2017-06-07", format = "%Y-%m-%d"),
         days = as.numeric(today - date),
         statusesCount_pDay = statusesCount / days) %>%
  select(screenName, followersCount, statusesCount_pDay) %>%
  arrange(desc(statusesCount_pDay)) %>%
  top_n(10)
##         screenName followersCount statusesCount_pDay
## 1  machinelearnbot          27427          204.67061
## 2        dr_morton         150937           71.35193
## 3   NewScienceWrld          60092           54.65874
## 4       dr_morton_          63467           46.57763
## 5  FranPatogenLoco            311           28.92593
## 6     RubenRabines          42286           25.99592
## 7  BecomingDataSci          16807           25.24069
## 8       joelgombin           6566           21.24094
## 9    renato_umeton           1998           19.58387
## 10   Scientists4EU          66117           17.64389

Is there a correlation between number of followers and number of tweets?

Indeed, there seems to be a correlation that users with many followers also tend to tweet more often.

followers_df %>%
  mutate(date = as.Date(created, format = "%Y-%m-%d"),
         today = as.Date("2017-06-07", format = "%Y-%m-%d"),
         days = as.numeric(today - date),
         statusesCount_pDay = statusesCount / days) %>%
  ggplot(aes(x = followersCount, y = statusesCount_pDay, color = days)) +
    geom_smooth(method = "lm") +
    geom_point() +
    scale_color_continuous(low = palette_light()[1], high = palette_light()[2]) +
    theme_tq()

Tidy text analysis

Next, I want to know more about my followers by analyzing their Twitter descriptions with the tidytext package.

library(tidytext)
library(SnowballC)

To prepare the data, I am going to unnest the words (or tokens) in the user descriptions, convert them to the word stem, remove stop words and urls.

data(stop_words)

tidy_descr <- followers_df %>%
  unnest_tokens(word, description) %>%
  mutate(word_stem = wordStem(word)) %>%
  anti_join(stop_words, by = "word") %>%
  filter(!grepl("\\.|http", word))

What are the most commonly used words in my followers’ descriptions?

The first question I want to ask is what words are most common in my followers’ descriptions.

Not surprisingly, the most common word is “data”. I do tweet mostly about data related topics, so it makes sense that my followers are mostly likeminded. The rest is also related to data science, machine learning and R.

tidy_descr %>%
  count(word_stem, sort = TRUE) %>%
  filter(n > 20) %>%
  ggplot(aes(x = reorder(word_stem, n), y = n)) +
    geom_col(color = palette_light()[1], fill = palette_light()[1], alpha = 0.8) +
    coord_flip() +
    theme_tq() +
    labs(x = "",
         y = "count of word stem in all followers' descriptions")

This, we can also show with a word cloud.

library(wordcloud)
library(tm)
tidy_descr %>%
  count(word_stem) %>%
  mutate(word_stem = removeNumbers(word_stem)) %>%
  with(wordcloud(word_stem, n, max.words = 100, colors = palette_light()))

Instead of looking for the most common words, we can also look for the most common ngrams: here, for the most common word pairs (bigrams) in my followers’ descriptions.

tidy_descr_ngrams <- followers_df %>%
  unnest_tokens(bigram, description, token = "ngrams", n = 2) %>%
  filter(!grepl("\\.|http", bigram)) %>%
  separate(bigram, c("word1", "word2"), sep = " ") %>%
  filter(!word1 %in% stop_words$word) %>%
  filter(!word2 %in% stop_words$word)

bigram_counts <- tidy_descr_ngrams %>%
  count(word1, word2, sort = TRUE)
bigram_counts %>%
  filter(n > 10) %>%
  ggplot(aes(x = reorder(word1, -n), y = reorder(word2, -n), fill = n)) +
    geom_tile(alpha = 0.8, color = "white") +
    scale_fill_gradientn(colours = c(palette_light()[[1]], palette_light()[[2]])) +
    coord_flip() +
    theme_tq() +
    theme(legend.position = "right") +
    theme(axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)) +
    labs(x = "first word in pair",
         y = "second word in pair")

These, we can also show as a graph:

library(igraph)
library(ggraph)
bigram_graph <- bigram_counts %>%
  filter(n > 5) %>%
  graph_from_data_frame()

set.seed(1)

a <- grid::arrow(type = "closed", length = unit(.15, "inches"))
ggraph(bigram_graph, layout = "fr") +
  geom_edge_link(aes(edge_alpha = n), show.legend = FALSE,
                 arrow = a, end_cap = circle(.07, 'inches')) +
  geom_node_point(color =  palette_light()[1], size = 5, alpha = 0.8) +
  geom_node_text(aes(label = name), vjust = 1, hjust = 0.5) +
  theme_void()

We can also use bigram analysis to identify negated meanings (this will become relevant for sentiment analysis later). So, let’s look at which words are preceded by “not” or “no”.

bigrams_separated <- followers_df %>%
  unnest_tokens(bigram, description, token = "ngrams", n = 2) %>%
  filter(!grepl("\\.|http", bigram)) %>%
  separate(bigram, c("word1", "word2"), sep = " ") %>%
  filter(word1 == "not" | word1 == "no") %>%
  filter(!word2 %in% stop_words$word)

not_words <- bigrams_separated %>%
  filter(word1 == "not") %>%
  inner_join(get_sentiments("afinn"), by = c(word2 = "word")) %>%
  count(word2, score, sort = TRUE) %>%
  ungroup()
not_words %>%
  mutate(contribution = n * score) %>%
  arrange(desc(abs(contribution))) %>%
  head(20) %>%
  mutate(word2 = reorder(word2, contribution)) %>%
  ggplot(aes(word2, n * score, fill = n * score > 0)) +
    geom_col(show.legend = FALSE) +
    scale_fill_manual(values = palette_light()) +
    labs(x = "",
         y = "Sentiment score * number of occurrences",
         title = "Words preceded by \"not\"") +
    coord_flip() +
    theme_tq()

What’s the predominant sentiment in my followers’ descriptions?

For sentiment analysis, I will exclude the words with a negated meaning from nrc and switch their positive and negative meanings from bing (although in this case, there was only one negated word, “endorsement”, so it won’t make a real difference).

tidy_descr_sentiment <- tidy_descr %>%
  left_join(select(bigrams_separated, word1, word2), by = c("word" = "word2")) %>%
  inner_join(get_sentiments("nrc"), by = "word") %>%
  inner_join(get_sentiments("bing"), by = "word") %>%
  rename(nrc = sentiment.x, bing = sentiment.y) %>%
  mutate(nrc = ifelse(!is.na(word1), NA, nrc),
         bing = ifelse(!is.na(word1) & bing == "positive", "negative", 
                       ifelse(!is.na(word1) & bing == "negative", "positive", bing)))
tidy_descr_sentiment %>%
  filter(nrc != "positive") %>%
  filter(nrc != "negative") %>%
  gather(x, y, nrc, bing) %>%
  count(x, y, sort = TRUE) %>%
  filter(n > 10) %>%
  ggplot(aes(x = reorder(y, n), y = n)) +
    facet_wrap(~ x, scales = "free") +
    geom_col(color = palette_light()[1], fill = palette_light()[1], alpha = 0.8) +
    coord_flip() +
    theme_tq() +
    labs(x = "",
         y = "count of sentiment in followers' descriptions")

Are followers’ descriptions mostly positive or negative?

The majority of my followers have predominantly positive descriptions.

tidy_descr_sentiment %>%
  count(screenName, word, bing) %>%
  group_by(screenName, bing) %>%
  summarise(sum = sum(n)) %>%
  spread(bing, sum, fill = 0) %>%
  mutate(sentiment = positive - negative) %>%
  ggplot(aes(x = sentiment)) +
    geom_density(color = palette_light()[1], fill = palette_light()[1], alpha = 0.8) +
    theme_tq()

What are the most common positive and negative words in followers’ descriptions?

library(reshape2)
tidy_descr_sentiment %>%
  count(word, bing, sort = TRUE) %>%
  acast(word ~ bing, value.var = "n", fill = 0) %>%
  comparison.cloud(colors = palette_light()[1:2],
                   max.words = 100)

Topic modeling: are there groups of followers with specific interests?

Topic modeling can be used to categorize words into groups. Here, we can use it to see whether (some) of my followers can be grouped into subgroups according to their descriptions.

library(topicmodels)
dtm_words_count <- tidy_descr %>%
  mutate(word_stem = removeNumbers(word_stem)) %>%
  count(screenName, word_stem, sort = TRUE) %>%
  ungroup() %>%
  filter(word_stem != "") %>%
  cast_dtm(screenName, word_stem, n)

# set a seed so that the output of the model is predictable
dtm_lda <- LDA(dtm_words_count, k = 5, control = list(seed = 1234))

topics_beta <- tidy(dtm_lda, matrix = "beta")
p1 <- topics_beta %>%
  filter(grepl("[a-z]+", term)) %>% # some words are Chinese, etc. I don't want these because ggplot doesn't plot them correctly
  group_by(topic) %>%
  top_n(10, beta) %>%
  ungroup() %>%
  arrange(topic, -beta) %>%
  mutate(term = reorder(term, beta)) %>%
  ggplot(aes(term, beta, color = factor(topic), fill = factor(topic))) +
    geom_col(show.legend = FALSE, alpha = 0.8) +
    scale_color_manual(values = palette_light()) +
    scale_fill_manual(values = palette_light()) +
    facet_wrap(~ topic, ncol = 5) +
    coord_flip() +
    theme_tq() +
    labs(x = "",
         y = "beta (~ occurrence in topics 1-5)",
         title = "The top 10 most characteristic words describe topic categories.")
user_topic <- tidy(dtm_lda, matrix = "gamma") %>%
  arrange(desc(gamma)) %>%
  group_by(document) %>%
  top_n(1, gamma)
p2 <- user_topic %>%
  group_by(topic) %>%
  top_n(10, gamma) %>%
  ggplot(aes(x = reorder(document, -gamma), y = gamma, color = factor(topic))) +
    facet_wrap(~ topic, scales = "free", ncol = 5) +
    geom_point(show.legend = FALSE, size = 4, alpha = 0.8) +
    scale_color_manual(values = palette_light()) +
    scale_fill_manual(values = palette_light()) +
    theme_tq() +
    coord_flip() +
    labs(x = "",
         y = "gamma\n(~ affiliation with topics 1-5)")
library(grid)
library(gridExtra)
grid.arrange(p1, p2, ncol = 1, heights = c(0.7, 0.3))

The upper of the two plots above show the words that were most strongly grouped to five topics. The lower plots show my followers with the strongest affiliation with these five topics.

Because in my tweets I only cover a relatively narrow range of topics (i.e. related to data), my followers are not very diverse in terms of their descriptions and the five topics are not very distinct.

If you find yourself in any of the topics, let me know if you agree with the topic that was modeled for you!

For more text analysis, see my post about text mining and sentiment analysis of a Stuff You Should Know Podcast.

tidyverse 101: Simplifying life for useRs

tidyverse 101: Simplifying life for useRs

Hadley Wickham‘s tidyverse has improved the workflow of analysts / data scientists, makes coding errors less likely and code more transparent. You’ve got to love the figure below, representing a simplified workflow of the average analysis project.

A simplified, standard cycle of data analysis

The tidyverse provides assistance in each of the stages. Various packages provide functionality to perform analytical tasks more effectively, in fewer lines, with fewer errors, and moreover in more transparent code. As a first step, the analyst will need to import (load) the data to his/her working environment (e.g., Excel, SPSS, R, RStudio, Spyder, Jupyter). In order to guarantee that the data are correct, a next step will be to clean up and tidy the data before continuing to the analysis part. In this early stage, the analyst can handle the explicit errors in the dataset, such as missing and nonsensical data points or records. After these preparatory steps, the main process starts. This consists of three interrelated tasks. (1) The analyst will need to transform the data in order to retrieve statistics, descriptives, and/or new features. (2) The analyst will need to visualize statistics, relations, and results. This is essential for storytelling and effective interpretation and communication of the results. (3) The analyst will try out different models to fit, explain, and predict the data. Finally, the results of this main process (leading to “understanding” of the data and the underlying processing) can be communicated to others.

 

I will run through each of these stages in separate posts, explaining the various packages, their inner workings, and demonstrating how they affect the process of data analysis in R:

  • Importing data (work in progress)
  • Tidying data (work in progress)
  • Transforming data (work in progress)
  • Visualizing data (work in progress)
  • Modeling data (work in progress)
  • Efficient programming (work in progress)

tidyverse1
Overview of the tidyverse packages that belong to each of the stages.

General tutorials:

 

tidyverse: Example: Trump Approval Rate

tidyverse: Example: Trump Approval Rate

For those of you unfamiliar with the tidyverse, it is a collection of R packages that share common philosophies and are designed to work together. Most if not all, are created by R-god Hadley Wickham, one of the leads at RStudio. I was introduced to the tidyverse-packages such as ggplot2 and dplyr in my second R-course, and they have cleaned and sped up my workflow tremendously ever since.

Although I don’t want to mix in the political debate, I came across such a wonderful example of how the tidyverse has simplified coding in R. On the downside, those unfamiliar with the syntax have trouble understanding what happens in the code the author uses.

Running the following R-code will install the core packages of the tidyverse:

install.packages(‘tidyverse’)

These consist among others of the following:

  • ggplot2: a more potent way of visualization
  • tibble: an upgrade to the standard data.frame
  • dplyr: adds great new functionality for manipulating data frames
  • tidyr: adds even more new functions for wrangling data frames
  • magrittr: adds piping functionality to improve code readability and workflow
  • readr: provides easier functions to load in data
  • purr: adds new functional programming functionality

There are several other packages included (e.g, stringr), but the above are the ones you are most likely to use in everyday projects.

Now, how about dissecting the code in the post. The author (1) loads some functionality in R,  (2) scrapes data on approval rates from the web, (3) cleans it up, and creates a wonderful visualization. S/He does this all in only 35 lines of code! Better even, 2 of these code lines are blank, 3 are setup, 6 have aesthetic purposes, and many others could be combined being only several characters long. Due to the tidyverse syntax, the code is easy to read, transparent, and reproducible (it only consists of two chained code blocks, after loading the packages), and takes only 7 seconds to run!

   user  system elapsed 
   5.67    0.85    6.53

In the rest of this article, I walk you through the code of this post to explain what’s happening:

  • hrbrthemes includes additional ggplot2 themes (plot colors, etc.)
  • rvest includes functionalities for web scraping
  • tidyverse we discussed earlier
library(hrbrthemes) 
library(rvest)
library(tidyverse)

Below, the author then creates a list containing the links to the online data to scrape and run it through a magrittr pipe (%>%) to apply the next bit of code to it.

map_df() comes from the purrr package and applies the subsequent code to every element in the earlier list:

  • Read in the html files specified earlier in the list %>%
  • Convert them to a table %>%
  • Store the name of the list (this is the name of the president) as .id %>%
  • Store that as a data.frame %>%
  • Select columns (and rename them) %>%
  • Use the earlier stored president id and add it as a column (‘who’) %>%
  • Save the output as a dataframe called ratings.
list(
  Obama="http://m.rasmussenreports.com/public_content/politics/obama_administration/obama_approval_index_history",
  Trump="http://m.rasmussenreports.com/public_content/politics/trump_administration/trump_approval_index_history"
) %>% 
map_df(~{
    read_html(.x) %>%
      html_table() %>%
      .[[1]] %>%
      tbl_df() %>%
      select(date=Date, approve=`Total Approve`, disapprove=`Total Disapprove`)
  }, .id="who") -> ratings

Below, the author then starts a new chained code block. S/He first changes (mutate()), from the ratings dataframe, the approval & disapproval data with a custom function (get rid of the % sign and divide by 100), which is then piped through:

  • Mutate dates to a data format (lubridate is yet another tidyverse package) %>%
  • Filter out any missing values %>%
  • Group by the ‘who’-column (President name) %>%
  • Sort the data file by earlier specified date %>%
  • Give every line an id number, from 1 up to the number of records (n() returns the sample size per President due to the earlier group_by()) %>%
  • Ungroup the data %>%

For readability, I split the code here, but it actually still continues as depicted by the %>% at the end.

mutate_at(ratings, c("approve", "disapprove"), function(x) as.numeric(gsub("%", "", x, fixed=TRUE))/100) %>%
  mutate(date = lubridate::dmy(date)) %>%
  filter(!is.na(approve)) %>%
  group_by(who) %>%
  arrange(date) %>%
  mutate(dnum = 1:n()) %>%
  ungroup() %>%

The output is now entered into the ggplot2 visualization function below:

  • ggplot() creates a layered plot, where the aes(thetics) (parameters) are defined as
    • x = the id number,
    • y = the approval rate,
    • and the color = the President name

Layers and details to this plot are specified/added using +

  • The first (bottom) layer of the plot is geom_hline() which creates a horizontal line at [x = 0; y = 0.5] with a size = 0.5. +
  • The 2nd layer is a scatterplot as geom_point() adds points with size = 0.25 on the x & y predefined in ggplot(aes()) +
  • Next the limits of the Y-axis are set to run from 0 to 1 +
  • A custom/manual color scheme is set +
  • Custom titles and labels are applied to the axis +
  • A predefined theme for the plot is used, drawn from hrbrthemes-package loading in at the start +
  • The direction of the legend is set +
  • The position of the legend is set
  ggplot(aes(dnum, approve, color=who)) +
  geom_hline(yintercept = 0.5, size=0.5) +
  geom_point(size=0.25) +
  scale_y_percent(limits=c(0,1)) +
  scale_color_manual(name=NULL, values=c("Obama"="#313695", "Trump"="#a50026")) +
  labs(x="Day in office", y="Approval Rating",
       title="Presidential approval ratings from day 1 in office",
       subtitle="For fairness, data was taken solely from Trump's favorite polling site (Ramussen)",
       caption="Data Source: \nCode: ") +
  theme_ipsum_rc(grid="XY", base_size = 16) +
  theme(legend.direction = "horizontal") +
  theme(legend.position=c(0.8, 1.05))

Theggplot()command at the start automatically prints the plot when it is finished (when no more + is found). The result is just wonderful, isn’t it? With only 35 lines, 2 chained commands, and 7 seconds runtime.

Rplot

Found on https://www.r-bloggers.com.

Animated GIFs in R

Sometimes, it can be of interest to examine how two variables correlate over time. For example, how people in a social network (e.g., an organization) behave or move over the course of time. However, it can be hard to display multi-dimensional data in a single plot. Instead of including time as an additional dimension and providing stakeholders with complicated 3-D plots, ggplot2 now has a support package called gganimate, which allows you to create custom GIFs. Particularly helpful when you seek to demonstrate trends over time.

See this recent post by Analytics Vidhya for a tutorial on the implementation.