This is something of a compendium of all of base R. The intent here is to provide explanations (in as simple a manner as possible) of how to use them. There are numerous examples and explanations of use cases, and (wherever possible) links to relevant articles and posts.

.Call – Modern Interfaces to C/C++ code

.Device – Lists of Open/Active Graphics Devices

.Internal – Call an Internal Function

.Last.value – Value of Last Evaluated Expression

.Library – Search Paths for Packages

.Machine – Numerical Characteristics of the Machine

.Platform – Platform Specific Variables

.Primitive – Look Up a Primitive Function

.bincode – Bin a Numeric Vector

.deparseOpts – Options for Expression Deparsing

.onLoad – Hooks for Namespace Events

.packages – Listing of Packages

.standard_regexps – Miscellaneous Internal/Programming Utilities

: – Colon Operator

:: – Double Colon and Triple Colon Operators

@ – Extract or Replace a Slot

Arithmetic – Arithmetic Operators

AsIs – Inhibit Interpretation/Conversion of Objects

Bessel – Bessel Functions

Comparison – Relational Operators

Constants – Built-in Constants

Control – Control Flow

Cstack_info – Report Information on C Stack Size and Usage

DateTimeClasses – Date-Time Classes

Dates – Date Class

Defunct – Marking Objects as Defunct

Deprecated – Marking Objects as Deprecated

Encoding – Read or Set the Declared Encodings for a Character Vector

Extract – Extract or Replace Parts of an Object

Filter – Common Higher-Order Functions in Functional Programming Languages

Foreign – Foreign Function Interface

ISOdatetime – Date-time Conversion Functions from Numeric Representations

InternalMethods – Internal Generic Functions

La_version – LAPACK version

Logic – Logical Operators

Memory – Memory Available for Data Storage

Memory-limits – Memory Limits in R

NA – ‘Not Available’ / Missing Values

NULL – The Null Object

NotYetImplemented – Not Yet Implemented Functions and Unused Arguments

NumericConstants – Numeric Constants

Ops.Date – Operators on the Date Class

Paren – Parentheses and Braces

Quotes – Quotes

R.Version – Version Information

R.home – Return the R Home Directory

Random – Random Number Generation

Random.user – User-supplied Random Number Generation

Rdconv – Utilities for Processing Rd Files

Recall – Recursive Calling

Reserved – Reserved Words in R

Signals – Interrupting Execution of R

Special – Special Functions of Mathematics

Startup – Initialization at Start of an R Session

Syntax – Operator Syntax and Precedence

Sys.getenv – Get Environment Variables

Sys.getpid – Get the Process ID of the R Session

Sys.glob – Wildcard Expansion on File Paths

Sys.info – Extract System and User Information

Sys.localeconv – Find Details of the Numerical and Monetary Representations in the Current Locale

Sys.setFileTime – Set File Time

Sys.setenv – Set or Unset Environment Variables

Sys.sleep – Suspend Execution for a Time Interval

Sys.time – Get Current Date and Time

Sys.which – Find Full Paths to Executables

Trig – Trigonometric Functions

UseMethod – Class Methods

Vectorize – Vectorize a Scalar Function

.data.frame – Extract or Replace Parts of a Data Frame

.factor – Extract or Replace Parts of a Factor

abbreviate – Abbreviate Strings

abs – Miscellaneous Mathematical Functions

addTaskCallback – Add or Remove a Top-Level Task Callback

agrep – Approximate String Matching (Fuzzy Matching)

all – Are All Values True?

all.equal – Test if Two Objects are (Nearly) Equal

all.names – Find All Names in an Expression

any – Are Some Values True?

aperm – Array Transposition

append – Vector Merging

apply – Apply Functions Over Array Margins

args – Argument List of a Function

array – Multi-way Arrays

as.Date – Date Conversion Functions to and from Character

as.POSIXct – Date-time Conversion Functions

as.data.frame – Coerce to a Data Frame

as.environment – Coerce to an Environment Object

as.function – Convert Object to Function

assign – Assign a Value to a Name

assignOps – Assignment Operators

attach – Attach Set of R Objects to Search Path

attachNamespace – Loading and Unloading Name Spaces

attr – Object Attributes

attributes – Object Attribute Lists

autoload – On-demand Loading of Packages

backsolve – Solve an Upper or Lower Triangular System

base-package – The R Base Package

basename – Manipulate File Paths

bindenv – Binding and Environment Locking, Active Bindings

bitwNot – Bitwise Logical Operations

body – Access to and Manipulation of the Body of a Function

bquote – Partial substitution in expressions

browser – Environment Browser

browserText – Functions to Retrieve Values Supplied by Calls to the Browser

builtins – Returns the Names of All Built-in Objects

by – Apply a Function to a Data Frame Split by Factors

c – Combine Values into a Vector or List

call – Function Calls

callCC – Call With Current Continuation

capabilities – Report Capabilities of this Build of R

cat – Concatenate and Print

cbind – Combine R Objects by Rows or Columns

ceiling – Rounding of Numbers

char.expand – Expand a String with Respect to a Target Table

charToRaw – Convert to or from Raw Vectors

character – Character Vectors

charmatch – Partial String Matching

chartr – Character Translation and Casefolding

chol – The Choleski Decomposition

chol2inv – Inverse from Choleski (or QR) Decomposition

class – Object Classes

col – Column Indexes

colSums – Form Row and Column Sums and Means

commandArgs – Extract Command Line Arguments

comment – Query or Set a ‘Comment’ Attribute

complex – Complex Vectors

conditions – Condition Handling and Recovery

conflicts – Search for Masked Objects on the Search Path

connections – Functions to Manipulate Connections

contributors – R Project Contributors

copyright – Copyrights of Files Used to Build R

cosh – Hyperbolic Functions

crossprod – Matrix Crossproduct

cumsum – Cumulative Sums, Products, and Extremes

cut – Convert Numeric to Factor

cut.POSIXt – Convert a Date or Date-Time Object to a Factor

data.class – Object Classes

data.frame – Data Frames

data.matrix – Convert a Data Frame to a Numeric Matrix

date – System Date and Time

debug – Debug a Function

delayedAssign – Delay Evaluation

deparse – Expression Deparsing

det – Calculate the Determinant of a Matrix

detach – Detach Objects from the Search Path

diag – Matrix Diagonals

diff – Lagged Differences

difftime – Time Intervals

dim – Dimensions of an Object

dimnames – Dimnames of an Object

dir.create – Manipulaton of Directories and File Permissions

do.call – Execute a Function Call

double – Double-Precision Vectors

dput – Write an Object to a File or Recreate it

drop – Drop Redundant Extent Information

droplevels – Drop Levels

dump – Text Representations of R Objects

duplicated – Determine Duplicate Elements

dyn.load – Foreign Function Interface

eapply – Apply a Function Over Values in an Environment

eigen – Spectral Decomposition of a Matrix

encodeString – Encode Character Vector as for Printing

environment – Environment Access

environment variables – Environment Variables

eval – Evaluate an (Unevaluated) Expression

exists – Is an Object Defined?

expand.grid – Create a Data Frame from All Combinations of Factors

expression – Unevaluated Expressions

factor – Factors

file.access – Ascertain File Accessibility

file.choose – Choose a File Interactively

file.info – Extract File Information

file.path – Construct Path to File

file.show – Display One or More Files

files – File Manipulation

find.package – Find Packages

findInterval – Find Interval Numbers or Indices

force – Force Evaluation of an Argument

formals – Access to and Manipulation of the Formal Arguments

format – Encode in a Common Format

format.info – format(.) Information

format.pval – Format P Values

formatC – Formatting Using C-style Formats

formatDL – Format Description Lists

function – Function Definition

gc – Garbage Collection

gc.time – Report Time Spent in Garbage Collection

gctorture – Torture Garbage Collector

get – Return the Value of a Named Object

getDLLRegisteredRoutines – Reflectance Information for C/Fortran routines in a DLL

getHook – Functions to Get and Set Hooks for Load, Attach, Detach, and Unload

getLoadedDLLs – Get DLLs Loaded in Current Session

getNativeSymbolInfo – Obtain a Description of one or more Native (C/Fortran) Symbols

getTaskCallbackNames – Query the Names of the Current Internal Top-Level Task Callbacks

gettext – Translate Text Messages

getwd – Get or Set Working Directory

gl – Generate Factor Levels

grep – Pattern Matching and Replacement

grepRaw – Pattern Matching for Raw Vectors

groupGeneric – S3 Group Generic Functions

gzcon – (De)compress I/O Through Connections

hexmode – Display Numbers in Hexadecimal

iconv – Convert Character Vector between Encodings

icuSetCollate – Setup Collation by ICU

identical – Test Objects for Exact Equality

identity – Identity Function

ifelse – Conditional Element Selection

integer – Integer Vectors

interaction – Compute Factor Interactions

interactive – Is R Running Interactively?

invisible – Change the Print Mode to Invisible

is.R – Are we using R, rather than S?

is.finite – Finite, Infinite, and NaN Numbers

is.function – Is an Object of Type (Primitive) Function?

is.language – Is an Object a Language Object?

is.object – Is an Object ‘internally classed’?

is.recursive – Is an Object Atomic or Recursive?

is.single – Is an Object of Single Precision Type?

is.unsorted – Test if an Object is Not Sorted

isS4 – Test for an S4 Object

isSymmetric – Test if a Matrix or other Object is Symmetric

jitter – ‘Jitter’ (Add Noise) to Numbers

kappa – Compute or Estimate the Condition Number of a Matrix

kronecker – Kronecker Products on Arrays

l10n_info – Localization Information

labels – Find Labels from Object

lapply – Apply a Function over a List or Vector

length – Length of an Object

levels – Levels Attributes

library – Loading/Attaching and Listing of Packages

library.dynam – Loading DLLs from Packages

license – The R License Terms

list – Lists - Generic and Dotted Pairs

list.files – List the Files in a Directory/Folder

list2env – From a List, Build or Add to an Environment

load – Reload Saved Datasets

locales – Query or Set Aspects of the Locale

log – Logarithms and Exponentials

logical – Logical Vectors

long vector – Long Vectors

lower.tri – Lower and Upper Triangular Part of a Matrix

ls – List Objects

make.names – Make Syntactically Valid Names

make.unique – Make Character Strings Unique

mapply – Apply a Function to Multiple List or Vector Arguments

margin.table – Compute Table Margin

mat.or.vec – Create a Matrix or a Vector

match – Value Matching

match.arg – Argument Verification Using Partial Matching

match.call – Argument Matching

match.fun – Extract a Function Specified by Name

matmult – Matrix Multiplication

matrix – Matrices

max – Maxima and Minima

max.col – Find Maximum Position in Matrix

mean – Arithmetic Mean

memCompress – In-memory Compression and Decompression

memory.profile – Profile the Usage of Cons Cells

merge – Merge Two Data Frames

message – Diagnostic Messages

missing – Does a Formal Argument have a Value?

mode – The (Storage) Mode of an Object

name – Names and Symbols

names – The Names of an Object

nargs – The Number of Arguments to a Function

nchar – Count the Number of Characters (or Bytes or Width)

nlevels – The Number of Levels of a Factor

noquote – Class for ‘no quote’ Printing of Character Strings

norm – Compute the Norm of a Matrix

normalizePath – Express File Paths in Canonical Form

nrow – The Number of Rows/Columns of an Array

numeric – Numeric Vectors

numeric_version – Numeric Versions

octmode – Display Numbers in Octal

on.exit – Function Exit Code

options – Options Settings

order – Ordering Permutation

outer – Outer Product of Arrays

parse – Parse Expressions

paste – Concatenate Strings

path.expand – Expand File Paths

pmatch – Partial String Matching

polyroot – Find Zeros of a Real or Complex Polynomial

pos.to.env – Convert Positions in the Search Path to Environments

pretty – Pretty Breakpoints

print – Print Values

print.data.frame – Printing Data Frames

print.default – Default Printing

prmatrix – Print Matrices, Old-style

proc.time – Running Time of R

prod – Product of Vector Elements

prop.table – Express Table Entries as Fraction of Marginal Table

pushBack – Push Text Back on to a Connection

qr – The QR Decomposition of a Matrix

qr.X – Reconstruct the Q, R, or X Matrices from a QR Object

quit – Terminate an R Session

range – Range of Values

rank – Sample Ranks

rapply – Recursively Apply a Function to a List

raw – Raw Vectors

rawConnection – Raw Connections

read.dcf – Read and Write Data in DCF Format

readBin – Transfer Binary Data to and from Connections

readChar – Transfer Character Strings to and from Connections

readLines – Read Text Lines from a Connection

readRDS – Serialization Interface for Single Objects

readRenviron – Set Environment Variables from a File

readline – Read a Line from the Terminal

reg.finalizer – Finalization of Objects

regex – Regular Expressions as used in R

regmatches – Extract or Replace Matched Substrings

remove – Remove Objects from a Specified Environment

rep – Replicate Elements of Vectors and Lists

replace – Replace Values in a Vector

rev – Reverse Elements

rle – Run Length Encoding

round.POSIXt – Round/Truncate Data-Time Objects

row – Row Indexes

row.names – Get and Set Row Names for Data Frames

rownames – Row and Column Names

rowsum – Give Column Sums of a Matrix or Data Frame, Based on a Grouping Variable

sQuote – Quote Text

sample – Random Samples and Permutations

save – Save R Objects

scale – Scaling and Centering of Matrix-like Objects

scan – Read Data Values

search – Give Search Path for R Objects

seek – Functions to Reposition Connections

seq – Sequence Generation

seq.Date – Generate Regular Sequences of Dates

seq.POSIXt – Generate Regular Sequences of Times

sequence – Create a Vector of Sequences

serialize – Simple Serialization Interface

setTimeLimit – Set CPU and/or Elapsed Time Limits

shQuote – Quote Strings for Use in OS Shells

showConnections – Display Connections

sign – Sign Function

sink – Send R Output to a File

slice.index – Slice Indexes in an Array

socketSelect – Wait on Socket Connections

solve – Solve a System of Equations

sort – Sorting or Ordering Vectors

source – Read R Code from a File or a Connection

split – Divide into Groups and Reassemble

sprintf – Use C-style String Formatting Commands

srcfile – References to Source Files

stop – Stop Function Execution

stopifnot – Ensure the Truth of R Expressions

strptime – Date-time Conversion Functions to and from Character

strsplit – Split the Elements of a Character Vector

strtoi – Convert Strings to Integers

strtrim – Trim Character Strings to Specified Display Widths

structure – Attribute Specification

strwrap – Wrap Character Strings to Format Paragraphs

subset – Subsetting Vectors, Matrices, and Data Frames

substitute – Substituting and Quoting Expressions

substr – Substrings of a Character Vector

sum – Sum of Vector Elements

summary – Object Summaries

svd – Singular Value Decomposition of a Matrix

sweep – Sweep out Array Summaries

switch – Select One of a List of Alternatives

sys.parent – Functions to Access the Function Call Stack

sys.source – Parse and Evaluate Expressions from a File

system – Invoke a System Command - 1

system.file – Find Names of R System Files

system.time – CPU Time Used

system2 – Invoke a System Command - 2

t – Matrix Transpose

table – Cross Tabulation and Table Creation

tabulate – Tabulation for Vectors

tapply – Apply a Function Over a Ragged Array

taskCallbackManager – Create an R-level Task Callback Manager

tempfile – Create Names for Temporary Files

textConnection – Text Connections

tilde – Tilde Operator

timezones – Time Zones

toString – Convert an R Object to a Character String

topenv – Top Level Environment

trace – Interactive Tracing and Debugging of Calls to a Function or Method

traceback – Print Call Stacks

tracemem – Trace Copying of Objects

transform – Transform an Object, for Example a Data Frame

try – Try an Expression Allowing Error Recovery

typeof – The Type of an Object

union – Set Operations

unique – Extract Unique Elements

unlist – Flatten Lists

unname – Remove ‘names’ or ‘dimnames’

utf8ToInt – Convert to or from UTF-8-encoded Character Vectors

vector – Vectors

warning – Warning Messages

warnings – Print Warning Messages

weekdays – Extract Parts of a POSIXt or Date Object

which – Which indices are TRUE?

which.min – Where is the Min() or Max() or first TRUE or FALSE?

with – Evaluate an Expression in a Data Environment

withVisible – Return both a value and its visibility

write – Write Data to a File

writeLines – Write Lines to a Connection

xtfrm – Auxiliary Function for Sorting and Ranking

zapsmall – Rounding of Numbers