toc.yaml

beyond-exception-handling.rmd:
- beyond-exception-handling-conditions-and-restarts
- the-r-way
- conditions
- condition-handlers
- java-style-exception-handling
- restarts
- providing-multiple-restarts
- other-uses-for-conditions
- writing-robust-software
C-interface.rmd:
- c-api
- introduction
- prerequisites
- calling-c
- c-data-structures
- c-vectors
- creating-vectors-and-garbage-collection
- missing-and-non-finite-values
- accessing-vector-data
- character-vectors-and-lists
- modifying-inputs
- coercing-scalars
- c-pairlists
- c-input-validation
- c-find-source
Computing-on-the-language.rmd:
- nse
- prereqs
- capturing-expressions
- exercises
- subset
- exercises-1
- scoping-issues
- exercises-2
- calling-from-another-function
- exercises-3
- substitute
- adding-an-escape-hatch-to-substitute
- capturing-dots
- exercises-4
- nse-downsides
- exercises-5
contribute.rmd: contributing
Data-structures.rmd:
- data-structures
- quiz
- vectors
- atomic-vectors
- types-and-tests
- coercion
- lists
- exercises
- attributes
- vector-names
- factors
- you-cant-use-values-that-are-not-in-the-levels
- nb-you-cant-combine-factors
- exercises-1
- matrices-and-arrays
- you-can-also-modify-an-object-in-place-by-setting-dim
- exercises-2
- data-frames
- creation
- testing-and-coercion
- combining-data-frames
- special-columns
Documenting-functions.rmd:
- documenting-functions
- help
- roxygen-process
- common-documentation-tags
- documenting-functions-and-methods
- documenting-s3-generic-functions-and-methods
- documenting-s4-generic-and-methods
- documenting-r5-methods
- documenting-classes
- documenting-a-s3-class
- documenting-an-s4-class
- documenting-an-r5-class
- documenting-datasets
- documenting-packages
- text-formatting
- lists
- tables
- mathematics
- character-formatting
- dynamic-help
Documenting-packages.rmd:
- package-level-documentation
- readme
- plyr
- stringr
- news
- citation
- vignettes
- demos
dsl.rmd:
- dsl
- prerequisites
- html
- goal
- escaping
- now-we-check-that-it-works
- double-escaping-is-not-a-problem
- and-text-we-know-is-html-doesnt-get-escaped.
- basic-tag-functions
- tag-functions
- processing-all-tags
- exercises
- latex
- latex-mathematics
- goal-1
- to_math
- known-symbols
- unknown-symbols
- known-functions
- grouping
- other-math-functions
- labelling
- unknown-functions
- exercises-1
Environments.rmd:
- environments
- introduction
- environment-basics
- what-is-an-environment
- manipulating-and-inspecting-environments
- special-environments
- where
- exercises
- function-environments
- the-environment-where-the-function-is-created
- the-environment-where-the-function-resides
- the-environment-created-when-a-function-is-run
- the-environment-where-the-function-is-called
- exercises-1
- explicit-scoping-with-local
- binding
- regular-binding
- constants
- section
- delayed-bindings
- active-bindings
- exercises-2
Exceptions-Debugging.rmd:
- debugging-condition-handling-and-defensive-programming
- debugging-techniques
- debugging-tools
- determining-the-sequence-of-calls
- browsing-on-error
- browsing-arbitrary-code
- the-call-stack-traceback-where-and-recover.
- other-types-of-failure
- condition-handling
- ignore-errors-with-try
- look-at-successful-results
- look-at-inputs-that-failed
- handle-conditions-with-trycatch
- if-no-condition-is-captured-trycatch-returns-the-value-of-the-input
- withcallinghandlers
- custom-signal-classes
- exercises
- defensive-programming
- exercises-1
Expressions.rmd:
- metaprogramming
- prerequisites
- structure-of-expressions
- exercises
- names
- exercises-1
- calls
- modifying-a-call
- creating-a-call-from-its-components
- exercises-2
- capturing-call
- exercises-3
- pairlists
- to-have-an-argument-with-no-default-you-need-an-explicit
- exercises-4
- parsing-and-deparsing
- exercises-5
- ast-funs
- finding-f-and-t
- finding-all-variables-created-by-assignment
- modifying-code
- exercises-6
Formulas.rmd:
- formulas
- formula-as-a-quoting-function
- xtabs
- formulas-for-modelling
Function-operators.rmd:
- function-operators
- in-other-languages
- behavioural-fos
- useful-behavioural-fos
- memoisation
- capturing-function-invocations
- the-location-where-the-function-is-evaluated
- exercises
- output-fos
- minor-modifications
- remove-failed-models-nulls-with-compact
- changing-what-a-function-does
- instead-of-using-an-anonymous-function-to-time-execution
- we-can-compose-function-operators
- exercises-1
- input-fos
- prefilling-function-arguments-partial-function-application
- changing-input-types
- exercises-2
- combining-fos
- function-composition
- logical-predicates-and-boolean-algebra
- exercises-3
- the-common-pattern-and-a-subtle-bug
- exercises-4
Functional-programming.rmd:
- functional-programming
- other-languages
- motivation
- anonymous-functions
- with-appropriate-parenthesis-the-function-is-called
- so-this-anonymous-function-syntax
- behaves-exactly-the-same-as
- exercises
- introduction-to-closures
- function-factories
- mutable-state
- exercises-1
- lists-of-functions
- or-use-a-named-function-instead-of-an-anonymous-function
- moving-lists-of-functions-to-the-global-environment
- exercises-2
- case-study-numerical-integration
- exercises-3
Functionals.rmd:
- functionals
- introduction
- lapply
- with-a-for-loop
- with-lapply
- divide-each-column-by-the-mean
- looping-patterns
- exercises
- for-loop-functionals-friends-of-lapply
- vector-output-sapply-and-vapply
- multiple-inputs-map-and-mapply
- in-this-case-equivalent-to
- rolling-computations
- parallelisation
- exercises-1
- data-structure-functionals
- matrix-and-array-operations
- group-apply
- the-plyr-package
- exercises-2
- functionals-fp
- reduce
- predicate-functionals
- exercises-3
- mathematical-functionals
- exercises-4
- converting-loops-to-functionals-and-when-its-not-possible
- modifying-in-place
- recursive-relationships
- while-loops
- a-family-of-functions
- both-versions-will-achieve-the-same-results
- exercises-5
Functions.rmd:
- functions
- components-of-a-function
- primitive-functions
- exercises
- lexical-scoping
- name-masking
- functions-vs.-variables
- a-fresh-start
- dynamic-lookup
- exercises-1
- every-operation-is-a-function-call
- equivalent-to
- function-arguments
- calling-functions
- can-abbreviate-long-argument-names
- but-this-doesnt-work-because-abbreviation-is-ambiguous
- calling-a-function-given-a-list-of-arguments
- default-and-missing-arguments
- lazy-evaluation
- ls-evaluated-inside-f
- ls-evaluated-in-global-environment
- section
- exercises-2
- special-calls
- infix-functions
- replacement-functions
- exercises-3
- return-values
- on.exit
- exercises-4
Git.rmd:
- git-and-github
- git
- the-basics
- github
index.rmd:
- welcome
- advanced-r-programming
- package-development
Introduction.rmd:
- introduction
- who-should-read-this-book
- what-you-will-get-out-of-this-book
- meta-techniques
- recommended-reading
- getting-help
- intro-ack
- conventions
- colophon
memory.rmd:
- memory
- packages
- object-size
- exercises
- total-memory-use
- garbarge-collection
- memory-profiling
- exercises-1
- modification-in-place
- touching-the-object-forces-an-increment
- sum-is-primitive-so-no-increment
- f-and-g-never-evaluate-x-so-refs-dont-increment
- loops
- exercises-2
Namespaces.rmd:
- namespaces
- how-do-namespaces-work
- exporting
- importing
- compiled-code
- how-do-they-work
OO-essentials.rmd:
- oo-field-guide
- introduction
- base-types
- s3
- recognising-objects-generic-functions-and-methods
- defining-classes-and-creating-objects
- create-then-set-class
- turn-it-into-a-data-frame
- creating-new-methods-and-generics
- method-dispatch
- exercises
- s4
- recognising-objects-generic-functions-and-methods-1
- from-examplemle
- an-s4-object
- an-s4-generic
- retrieve-an-s4-method-described-later
- defining-classes-and-creating-objects-1
- creating-new-methods-and-generics-1
- method-dispatch-1
- from-pryr-takes-an-unevaluated-function-call
- exercises-1
- rc
- defining-classes-and-creating-objects-2
- recognising-objects-and-methods
- method-dispatch-2
- exercises-2
- picking-a-system
Package-basics.rmd:
- package-basics
- package-essentials
- optional-components
- getting-started
- the-r-directory
- a-minimal-description-file
- other-description-components
- source-binary-and-bundled-packages
- package-libraries
- installing-packages
- exercises
Package-development-cycle.rmd:
- the-package-development-cycle
- dev-mode
- key-functions
- development-cycles
- confirmatory-programming
- exploratory-programming
Package-quick-reference.rmd:
- quick-reference-sheet-for-package-process
- create-a-new-package
- development-workflow
- deploying
- building-the-package-for-all-users-of-the-system
Performance.rmd:
- performance
- introduction
- why-is-r-slow
- microbenchmarking
- exercises
- language-performance
- extreme-dynamism
- name-lookup-with-mutable-environments
- lazy-evaluation-overhead
- exercises-1
- implementation-performance
- extracting-a-single-value-from-a-data-frame
- ifelse-pmin-and-pmax.
- exercises-2
- faster-r
Philosophy.rmd:
- package-development-philosophy
- getting-started
- introduction-to-devtools
Profiling.rmd:
- profiling
- prerequisites
- measure-perf
- limitations
- exercises
- improve-perf
- code-organisation
- has-someone-already-solved-the-problem
- exercises-1
- do-as-little-as-possible
- step-1-assume-vector-input.-this-allows-me-to-remove-the-is.matrix
- test-and-the-method-that-use-matrix-subsetting.
- step-2-assume-difference-1l.-this-simplifies-input-checking
- and-eliminates-the-for-loop
- step-3-assume-lag-1l.-this-eliminates-input-checking-and-simplifies
- subsetting.
- generate-a-new-data-frame-containing-randomly-selected-rows
- generate-new-vectors-from-random-rows
- exercises-2
- vectorise
- exercises-3
- avoid-copies
- byte-code-compilation
- exercises-4
- case-study-t-test
- parallelise
- other-techniques
R5.rmd:
- reference-classes
- classes-and-instances
- methods
- common-methods
- documentation
- in-packages
- in-the-wild
Rcpp.rmd:
- rcpp
- getting-started
- getting-started-with-c
- no-inputs-scalar-output
- scalar-input-scalar-output
- vector-input-scalar-output
- vector-input-vector-output
- matrix-input-vector-output
- using-sourcecpp
- exercises
- rcpp-classes-and-methods
- rcpp-sugar
- arithmetic-and-logical-operators
- logical-summary-functions
- vector-views
- other-useful-functions
- missing-values
- scalars
- integers
- doubles
- strings
- boolean
- vectors
- exercises-1
- the-stl
- using-iterators
- algorithms
- data-structures-rcpp
- vectors-1
- sets
- include
- map
- exercises-2
- case-studies
- gibbs-sampler
- r-vectorisation-vs.-c-vectorisation
- using-rcpp-in-a-package
- adding-rcpp-to-an-existing-package
- more-details
- learning-more
- more-rcpp
- more-c
- acknowledgements
Release.rmd:
- releasing-a-package
- checking
- version-numbers
- publishing-on-cran
- publicising
Reproducibility.rmd:
- how-to-write-a-reproducible-example
- example
- save-the-data-structure-in-variable-bod
- some-example-code-that-uses-the-data
S3.rmd:
- the-s3-object-system
- object-class
- generic-functions-and-method-dispatch
- methods
- internal-generics
- inheritance
- double-dispatch
- object-styles
- best-practices
S4.rmd:
- the-s4-object-system
- classes-and-instances
- checking-validity
- generic-functions-and-methods
- method-dispatch
- inheritance
- method-dispatch-2
- in-the-wild
SoftwareSystems.rmd:
- writing-software-systems
- s3-ss
- s4-ss
- closures-as-s3-objects
- r5
Style.rmd:
- style-guide
- notation-and-naming
- file-names
- identifiers
- bad
- syntax
- spacing
- bad-1
- bad-2
- bad-3
- bad-4
- curly-braces
- bad-5
- line-length
- indentation
- assignment
- organisation
- commenting-guidelines
- plot-data----------------------------
Subsetting.rmd:
- subsetting
- data-types
- atomic-vectors
- lists
- matrices-and-arrays
- data-frames
- there-are-two-ways-to-select-columns-from-a-data-frame
- like-a-list
- theres-an-important-difference-if-you-select-a-single-column
- matrix-subsetting-simplifies-by-default-list-subsetting-does-not.
- s3-objects
- s4-objects
- exercises
- subsetting-operators
- if-you-do-supply-a-vector-it-indexes-recursively
- simplify-preserve
- section
- instead-use
- missingout-of-bounds-indices
- exercises-1
- subsetting-and-assignment
- the-length-of-the-lhs-needs-to-match-the-rhs
- note-that-theres-no-checking-for-duplicate-indices
- you-cant-combine-integer-indices-with-na
- this-is-mostly-useful-when-conditionally-modifying-vectors
- applications
- lookup-tables
- or-with-fewer-output-values
- matching-merging
- using-match
- using-rownames
- random-samplesbootstrap-integer-subsetting
- randomly-reorder
- ordering-integer-subsetting
- expanding-aggregated-counts-integer-subsetting
- removing-columns-from-data-frame-character-subsetting
- selecting-rows-based-on-a-condition-logical-subsetting
- boolean-algebra-vs-sets-logical-integer-subsetting
- x-y---intersectx-y
- x-y---unionx-y
- x-y---setdiffx-y
- xorx-y---setdiffunionx-y-intersectx-y
- exercises-2
Testing.rmd:
- testing
- motivation
- testthat-test-structure
- expectations
- tests
- contexts
- running-tests
- testing-files-and-directories
- autotest
- r-cmd-check
Vocabulary.rmd:
- vocabulary
- the-basics
- common-data-structures
- statistics
- working-with-r
- io