R for Data Science: Import, Tidy, Transform, Visualize, and Model Data. 2 Ed

 Introduction....5 Preface to the second edition....5 What you will learn....6 How this book is organized....8 What you won’t learn....9 Modeling....9 Big data....10 Python, Julia, and friends....10 Prerequisites....10 R....11 RStudio....11 The tidyverse....12 Other packages....13 Running R code....14 Conventions Used in This Book....15 Using Code Examples....16 O’Reilly Online Learning....17 How to Contact Us....17 Acknowledgments....18 Online Edition....21 I. Whole game....23 1. Data visualization....25 Introduction....25 Prerequisites....26 First steps....27 The penguins data frame....27 Ultimate goal....29 Creating a ggplot....30 Adding aesthetics and layers....34 Exercises....39 ggplot2 calls....41 Visualizing distributions....42 A categorical variable....42 A numerical variable....44 Exercises....47 Visualizing relationships....48 A numerical and a categorical variable....48 Two categorical variables....52 Two numerical variables....54 Three or more variables....55 Exercises....57 Saving your plots....58 Exercises....59 Common problems....59 Summary....60 2. Workflow: basics....62 Coding basics....62 Comments....64 What’s in a name?....65 Calling functions....66 Exercises....68 Summary....68 3. Data transformation....70 Introduction....70 Prerequisites....71 nycflights13....71 dplyr basics....74 Rows....75 filter()....75 Common mistakes....78 arrange()....79 distinct()....80 Exercises....83 Columns....84 mutate()....84 select()....87 rename()....88 relocate()....89 Exercises....90 The pipe....91 Groups....94 group_by()....94 summarize()....95 The slice_ functions....97 Grouping by multiple variables....98 Ungrouping....99 .by....101 Exercises....101 Case study: aggregates and sample size....103 Summary....106 4. Workflow: code style....107 Names....108 Spaces....109 Pipes....110 ggplot2....112 Sectioning comments....113 Exercises....114 Summary....114 5. Data Tidying....116 Introduction....116 Prerequisites....116 Tidy data....116 Exercises....119 Lengthening data....119 Data in column names....120 How does pivoting work?....122 Many variables in column names....124 Data and variable names in the column headers....126 Widening data....127 How does pivot_wider() work?....129 Summary....131 6. Workflow: scripts and projects....133 Scripts....133 Running code....134 RStudio diagnostics....135 Saving and naming....136 Projects....137 What is the source of truth?....138 Where does your analysis live?....140 RStudio projects....141 Relative and absolute paths....143 Exercises....144 Summary....144 7. Data import....146 Introduction....146 Prerequisites....146 Reading data from a file....146 Practical advice....148 Other arguments....151 Other file types....153 Exercises....153 Controlling column types....154 Guessing types....154 Missing values, column types, and problems....155 Column types....156 Reading data from multiple files....157 Writing to a file....158 Data entry....160 Summary....161 8. Workflow: getting help....162 Google is your friend....162 Making a reprex....163 Investing in yourself....166 Summary....166 II. Visualize....167 9. Layers....169 Introduction....169 Prerequisites....170 Aesthetic mappings....170 Exercises....175 Geometric objects....176 Exercises....185 Facets....187 Exercises....190 Statistical transformations....191 Exercises....196 Position adjustments....197 Exercises....203 Coordinate systems....204 Exercises....206 The layered grammar of graphics....207 Summary....208 10. Exploratory data analysis....210 Introduction....210 Prerequisites....211 Questions....211 Variation....212 Typical values....213 Unusual values....215 Exercises....218 Unusual values....219 Exercises....221 Covariation....222 A categorical and a numerical variable....222 Exercises....227 Two categorical variables....228 Exercises....230 Two numerical variables....231 Exercises....234 Patterns and models....235 Summary....238 11. Communication....239 Introduction....239 Prerequisites....240 Labels....240 Exercises....242 Annotations....243 Exercises....249 Scales....250 Default scales....250 Axis ticks and legend keys....251 Legend layout....256 Replacing a scale....259 Zooming....267 Exercises....273 Themes....273 Exercises....277 Layout....277 Exercises....281 Summary....282 III. Transform....284 12. Logical Vectors....286 Introduction....286 Prerequisites....286 Comparisons....287 Floating point comparison....289 Missing values....290 is.na()....291 Exercises....294 Boolean algebra....294 Missing values....295 Order of operations....295 %in%....297 Exercises....298 Summaries....299 Logical summaries....299 Numeric summaries of logical vectors....300 Logical subsetting....300 Exercises....302 Conditional transformations....302 if_else()....303 case_when()....304 Compatible types....306 Exercises....307 Summary....308 13. Numbers....309 Introduction....309 Prerequisites....309 Making numbers....310 Counts....310 Exercises....314 Numeric transformations....314 Arithmetic and recycling rules....314 Minimum and maximum....316 Modular arithmetic....317 Logarithms....319 Rounding....320 Cutting numbers into ranges....321 Cumulative and rolling aggregates....322 Exercises....323 General transformations....323 Ranks....323 Offsets....325 Consecutive identifiers....326 Exercises....328 Numeric summaries....329 Center....329 Minimum, maximum, and quantiles....331 Spread....332 Distributions....332 Positions....334 With mutate()....336 Exercises....336 Summary....337 14. Strings....338 Introduction....338 Prerequisites....338 Creating a string....339 Escapes....340 Raw strings....340 Other special characters....341 Exercises....342 Creating many strings from data....342 str_c()....343 str_glue()....344 str_flatten()....345 Exercises....345 Extracting data from strings....346 Separating into rows....347 Separating into columns....348 Diagnosing widening problems....350 Letters....354 Length....354 Subsetting....355 Exercises....356 Non-English text....356 Encoding....357 Letter variations....358 Locale-dependent functions....359 Summary....360 15. Regular Expressions....362 Introduction....362 Prerequisites....362 Pattern basics....363 Key functions....366 Detect matches....366 Count matches....368 Replace values....370 Extract variables....371 Exercises....372 Pattern details....373 Escaping....373 Anchors....375 Character classes....376 Quantifiers....378 Operator precedence and parentheses....378 Grouping and capturing....379 Exercises....381 Pattern control....382 Regex flags....383 Fixed matches....384 Practice....385 Check your work....385 Boolean operations....387 Creating a pattern with code....390 Exercises....392 Regular expressions in other places....392 tidyverse....392 Base R....393 Summary....394 16. Factors....396 Introduction....396 Prerequisites....396 Factor basics....397 General Social Survey....399 Exercise....400 Modifying factor order....401 Exercises....407 Modifying factor levels....407 Exercises....411 Ordered factors....411 Summary....412 17. Dates and Times....414 Introduction....414 Prerequisites....415 Creating date/times....415 During import....416 From strings....420 From individual components....421 From other types....424 Exercises....425 Date-time components....425 Getting components....426 Rounding....430 Modifying components....433 Exercises....434 Time spans....435 Durations....435 Periods....437 Intervals....440 Exercises....441 Time zones....441 Summary....444 18. Missing Values....446 Introduction....446 Prerequisites....446 Explicit missing values....447 Last observation carried forward....447 Fixed values....448 NaN....448 Implicit missing values....449 Pivoting....450 Complete....451 Joins....452 Exercises....453 Factors and empty groups....453 Summary....457 19. Joins....458 Introduction....458 Prerequisites....458 Keys....459 Primary and foreign keys....459 Checking primary keys....462 Surrogate keys....463 Exercises....465 Basic joins....466 Mutating joins....466 Specifying join keys....469 Filtering joins....472 Exercises....474 How do joins work?....475 Row matching....482 Filtering joins....483 Non-equi joins....484 Cross joins....486 Inequality joins....488 Rolling joins....489 Overlap joins....492 Exercises....494 Summary....494 IV. Import....496 20. Spreadsheets....498 Introduction....498 Excel....498 Prerequisites....498 Getting started....499 Reading Excel spreadsheets....499 Reading worksheets....504 Reading part of a sheet....507 Data types....509 Writing to Excel....510 Formatted output....512 Exercises....512 Google Sheets....515 Prerequisites....515 Getting started....516 Reading Google Sheets....516 Writing to Google Sheets....520 Authentication....520 Exercises....520 Summary....521 21. Databases....522 Introduction....522 Prerequisites....523 Database basics....523 Connecting to a database....524 In this book....525 Load some data....526 DBI basics....526 dbplyr basics....528 SQL....531 SQL basics....531 SELECT....533 FROM....535 GROUP BY....536 WHERE....536 ORDER BY....539 Subqueries....539 Joins....540 Other verbs....542 Exercises....542 Function translations....543 Summary....547 22. Arrow....549 Introduction....549 Prerequisites....550 Getting the data....550 Opening a dataset....551 The parquet format....553 Advantages of parquet....553 Partitioning....554 Rewriting the Seattle library data....555 Using dplyr with arrow....556 Performance....557 Using dbplyr with arrow....558 Summary....559 23. Hierarchical Data....561 Introduction....561 Prerequisites....561 Lists....562 Hierarchy....563 List-columns....565 Unnesting....567 unnest_wider()....568 unnest_longer()....569 Inconsistent types....570 Other functions....570 Exercises....571 Case studies....571 Very wide data....572 Relational data....575 Deeply nested....579 Exercises....583 JSON....584 Data types....584 jsonlite....585 Starting the rectangling process....587 Exercises....588 Summary....589 24. Web Scraping....590 Introduction....590 Prerequisites....591 Scraping ethics and legalities....591 Terms of service....591 Personally identifiable information....592 Copyright....592 HTML basics....593 Elements....594 Attributes....595 Extracting data....595 Find elements....596 Nesting selections....597 Text and attributes....599 Tables....600 Finding the right selectors....601 Putting it all together....602 StarWars....602 IMDB top films....605 Dynamic sites....609 Summary....610 V. Program....612 25. Functions....614 Introduction....614 Prerequisites....615 Vector functions....615 Writing a function....616 Improving our function....618 Mutate functions....619 Summary functions....621 Exercises....623 Data frame functions....624 Indirection and tidy evaluation....624 When to embrace?....627 Common use cases....627 Data-masking vs. tidy-selection....630 Exercises....633 Plot functions....634 More variables....635 Combining with other tidyverse....637 Labeling....639 Exercises....641 Style....641 Exercises....643 Summary....643 26. Iteration....645 Introduction....645 Prerequisites....646 Modifying multiple columns....646 Selecting columns with .cols....647 Calling a single function....648 Calling multiple functions....649 Column names....651 Filtering....653 across() in functions....654 Vs pivot_longer()....655 Exercises....658 Reading multiple files....659 Listing files in a directory....660 Lists....660 purrr::map() and list_rbind()....662 Data in the path....664 Save your work....667 Many simple iterations....667 Heterogeneous data....669 Handling failures....670 Saving multiple outputs....671 Writing to a database....671 Writing csv files....674 Saving plots....676 Summary....678 27. A field guide to base R....680 Introduction....680 Prerequisites....681 Selecting multiple elements with [....681 Subsetting vectors....681 Subsetting data frames....683 dplyr equivalents....685 Exercises....686 Selecting a single element with $ and [[....687 Data frames....687 Tibbles....688 Lists....689 Exercises....691 Apply family....691 For loops....694 Plots....696 Summary....698 VI. Communicate....699 28. Quarto....701 Introduction....701 Prerequisites....702 Quarto basics....702 Exercises....707 Visual editor....707 Exercises....710 Source editor....710 Exercises....712 Code chunks....713 Chunk label....713 Chunk options....714 Global options....716 Inline code....717 Exercises....718 Figures....719 Figure sizing....719 Other important options....721 Exercises....722 Tables....722 Exercises....724 Caching....724 Exercises....727 Troubleshooting....727 YAML header....728 Self-contained....728 Parameters....728 Bibliographies and Citations....730 Workflow....731 Summary....733 29. Quarto Formats....735 Introduction....735 Output options....736 Documents....737 Presentations....738 Interactivity....738 htmlwidgets....738 Shiny....740 Websites and books....741 Other formats....743 Summary....743