Data Science: An Introduction/250 R Commands

Data Science: An Introduction

Appendix 2: 250 R Commands

---

Chapter Summary

This is copied verbatim from Jeromy Anglim's Blog

Discussion

Dr. Anglim writes:

The R programming language includes many abbreviations. Abbreviations exist in function names, argument names, and allowed values for arguments. This post expands on over 150 R abbreviations with the aim of making it easier for users new to R who are trying to memorise R commands.

Abbreviations save time when typing and can make for less cumbersome code. However, abbreviations often make it more difficult to remember a command. This is especially true when the user does not know what the abbreviation stands for.

R has been developed by a group of technical experts with backgrounds in Linux and Unix, mathematics, statistics, and statistical computing. With gaining popularity, R is now being used by people with little to none of this background. Abbreviations which are intuitive to the experts are not necessarily intuitive to this broader audience.

The R help system does a reasonable job of explaining the abbreviations in R. However, I thought it would be useful to write a post listing some of the common abbreviations along with the expansion of the abbreviation. Whereas R sometimes errs on the side of assuming expertise, I thought I'd err on the side of assuming naivety. Thus, the table includes many abbreviations which are probably obvious to most readers.

I thank Tom Short for his R reference Card which provided some inspiration for a starting list of R commands. Feel free to reproduce or adapt this table elsewhere. For example, perhaps it could be included in an R Wiki with additional entries. If you spot an error in the table, let me know in the comments of this post.

I might expand the table in the future. At the moment, it's mainly function names with not many arguments or values of arguments. I also haven't put much time into grouping and ordering the functions.

Table of R Commands

R Command	Abbreviation Expanded	Comments
ls	[L]i[S]t objects	common command in Unix-like operating systems
rm	[R]e[M]ove objects	common command in Unix-like operating systems
str	[STR]ucture of an object
unz	[UNZ]ip
getwd	[GET] [W]orking [D]irectory
dir	[DIR]ectory
sprintf	[S]tring [PRINT] [F]ormatted
c	[C]ombine values
regexpr	[REG]ular [EXPR]ession	Why "regular"? See regular sets, regular language
diag	[DIAG]onal values of a matrix
col	[COL]umn
lapply	[L]ist [APPLY]	Apply function to each element and return a list
sapply	[S]implify [APPLY ]	Apply function to each element and attempt to return a vector (i.e., a vector is "simpler" than a list)
mapply	[M]ultivariate [APPLY]	Multivariate version of sapply
tapply	[T]able [APPLY]	Apply function to sets of values as defined by an index
apply	[APPLY] function to sets of values as defined by an index
MARGIN = 1 or 2 in apply	rows [1] come before columns [2]	e.g., a 2 x 3 matrix has 2 rows and 3 columns (note: row count is stated first)
rmvnorm	[R]andom number generator for [M]ulti[V]ariate [NORM]al data
rle	[R]un [L]ength [E]ncoding
ftable	[F]ormat [TABLE]
xtabs	Cross (i.e., [X]) [TAB]ulation	[X] is the symbol of a cross; [X] is sometimes spoken as "by". Cross-tabulating means to cross one variable with another
xtable	[TABLE] of the object [X]
formatC	[FORMAT] using [C] style formats	i.e., [C] the programming language
Sweave	[S] [WEAVE]	The R Programming language is a dialect of S. Weaving involves combining code and documentation
cor	[COR]relation
ancova	[AN]alysis [O]f [COVA]riance
manova	[M]ultivariate [AN]alysis [O]f [VA]riance
aov	[A]nalysis [O]f [V]ariance
TukeyHSD	[T]ukey's [H]onestly [S]ignificant [D]ifference
hclust	[H]ierarchical [CLUST]er analysis
cmdscale	[C]lassical metric [M]ulti[D]imensional [SCAL]ing
factanal	[FACT]or [ANAL]ysis
princomp	[PRIN]cipal [COMP]onents analysis
prcomp	[PR]incipal [COMP]onents analysis
lme	[L]inear [M]ixed [E]ffects model
resid	[RESID]uals
ranef	[RAN]dom [EF]fects
anova	[AN]alysis [O]f [VA]riance
fixef	[FIX]ed [EF]ffects
vcov	[V]ariance-[COV]ariance matrix
logLik	[LOG] [LIK]elihood
BIC	[B]ayesian [I]nformation [C]riteria
mcmcsamp	[M]arkov [Chain] [Monte] [C]arlo [SAMP]ling
eval	[EVAL]uate an R expression
cat	con[CAT]enate	standard Unix command
apropos	Search documentation for a purpose or on a topic (i.e., [APROPOS])	Unix command for search documentation;
read.csv	[READ] a file in [C]omma [S]eperated [V]alues format	i.e., in each row of the data commas separate values for each variable
read.fwf	[READ] a file in [F]ixed [W]idth [F]ormat
seq	Generate [SEQ]uence
rep	[REP]licate values of x	perhaps also [REP]eat
dim	[DIM]ension of an object	Typically, number of rows and columns in a matrix
gl	[G]enerate factor [L]evels
rbind	[R]ows [BIND]
cbind	[C]olumns [BIND]
is.na	[IS] [N]ot [A]vailable
nrow	[N]umber of [ROW]s
ncol	[N]umber of [COL]umns
attr	[ATTR]ibute
rev	[REV]erse
diff	[DIFF]erence between x and a lag of x
prod	[PROD]uct
var	[VAR]iance
sd	[S]tandard [D]eviation
cumsum	[CUM]ulative [SUM]
cumprod	[CUM]ulative [PROD]uct
setdiff	[SET] [DIFF]erence
intersect	[INTERSECT]ion
Re	[RE]al part of a number
Im	[IM]aginary part of a number
Mod	[MOD]ulo opertion	remainder of division of one number by another
t	[T]ranspose of a vector or matrix
substr	[SUBSTR]ing
strsplit	[STR]ing [SPLIT]
grep	[G]lobal / [R]egular [E]xpression / [P]rint	Etymology based on text editor instructions in programs such as ed
sub	[SUB]stitute identified pattern found in string
gsub	[G]lobal [SUB]stitute identified pattern found in string
pmatch	[P]artial string [MATCH]ing
nchar	[N]umber of [CHAR]acters in a string
ps.options	[P]ost-[S]cript [OPTIONS]
win.metafile	[WIN]dows [METAFILE] graphic
dev.off	[DEV]ice [OFF]
dev.cur	[CUR]rent [DEV]ice
dev.set	[SET] the current [DEV]ice
hist	[HIST]ogram
pie	[PIE] Chart
coplot	[CO]nditioning [PLOT]
matplot	[PLOT] colums of [MAT]rices
assocplot	[ASSOC]iation [PLOT]
plot.ts	[PLOT] [T]ime [S]eries
qqnorm	[Q]uantile-[Q]uantile [P]lot based on normal distribution
persp	[PERSP]ective [P]lot
xlim	[LIM]it of the [X] axis
ylim	[LIM]it of the [Y] axis
xlab	[LAB]el for the [X] axis
ylab	[LAB]el for the [Y] axis
main	[MAIN] title for the plot
sub	[SUB] title for the plot
mtext	[M]argin [TEXT]
abline	[LINE] on plot often of the form y = [A] + [B] x
h argument in abline	[H]orizontal line
v argument in abline	[V]ertical line
par	Graphics [PAR]ameter
adj as par	[ADJ]ust text [J]ustification
bg as par	[B]ack[G]round colour
bty as par	[B]ox [TY]pe
cex as par	[C]haracter [EX]tension or [EX]pansion of plotting objects
cex.sub as par	[C]haracter [EX]tension or [EX]pansion of [SUB]title
cex.axis as par	[C]haracter [EX]tension or [EX]pansion of [AXIS] annotation
cex.lab as par	[C]haracter [EX]tension or [EX]pansion X and Y [LAB]els
cex.main as par	[C]haracter [EX]tension or [EX]pansion of [MAIN] title
col as par	Default plotting [COL]our
las as par	[L]abel of [A]xis [S]tyle
lty as par	[L]ine [TY]pe
lwd as par	[L]ine [W]i[D]th
mar as par	[MAR]gin width in lines
mfg as par	Next [G]raph for [M]atrix of [F]igures
mfcol as par	[M]atrix of [F]igures entered [COL]umn-wise
mfrow as par	[M]atrix of [F]igures entered [ROW]-wise
pch as par	[P]lotting [CH]aracter
ps as par	[P]oint [S]ize of text	Point is a printing measurement
pty as par	[P]lot region [TY]pe
tck as par	[T]i[CK] mark length
tcl as par	[T]i[C]k mark [L]ength
xaxs as par	[X] [AX]is [S]tyle
yaxs as par	[Y] [AX]is [S]tyle
xaxt as par	[X] [AX]is [T]ype
yaxt as par	[Y] [AX]is [T]ype
asp as par	[ASP]ect ratio
xlog as par	[X] axis as [LOG]arithm scale
ylog as par	[Y] axis as [LOG]arithm scale
omi as par	[O]uter [M]argin width in [I]nches
mai as par	[MA]rgin width in [I]nches
pin as par	[P]lot size in [IN]ches
xpd as par		Perhaps: [X = Cut] [P]lot ? Perhaps D for device
xyplot	[X] [Y] [PLOT]	[X] for horizontal axis; [Y] for vertical axis
bwplot	[B]ox and [W]hisker plot
qq	[Q]uantile-[Quantile] plot'
splom	[S]catter[PLO]t [M]atrix
optim	[OPTIM]isation
lm	[L]inear [M]odel
glm	[G]eneralised [L]inear [M]odel
nls	[N]onlinear [L]east [S]quare parameter esetimation
loess	[LO]cally [E]stimated [S]catterplot [S]moothing
prop.test	[TEST] null hypothesis that [PROP]ortions in several gropus are the same
rnorm	[R]andom number drawn from [NORM]al distribution
dnorm	[D]ensity of a given quantile in a [NORM]al distribution
pnorm	[D]istribution function for [NORM]al distribution returning cumulaive [P]robability
qnorm	[Q]uantile function based on [NORM]al distribution
rexp	[R]andom number generation from [EXP]onential distribution
rgamma	[R]andom number generation from [GAMMA] distribution
rpois	[R]andom number generation from [POIS]on distribution
rweibull	[R]andom number generation from [WEIBULL] distribution
rcauchy	[R]andom number generation from [CAUCHY] distribution
rbeta	[R]andom number generation from [BETA] distribution
rt	[R]andom number generation from [t] distribution
rf	[R]andom number generation from [F] distribution	F for Ronald [F]isher
rchisq	[R]andom number generation from [CHI] [SQ]uare distribution
rbinom	[R]andom number generation from [BINOM]ial distribution
rgeom	[R]andom number generation from [EXP]onential distribution
rhyper	[R]andom number generation from [HYPER]geometric distribution
rlogis	[R]andom number generation from [LOGIS]tic distribution
rlnorm	[R]andom number generation from [L]og [NOR]mal distribution
rnbinom	[R]andom number generation from [N]egative [BINOM]ial distribution
runif	[R]andom number generation from [UNIF]orm distribution
rwilcox	[R]andom number generation from [WILCOX]on distribution
ggplot in ggplot2	[G]rammar of [G]raphics [PLOT]	See Leland Wilkinson (1999)
aes in ggplot2	[AES]thetic mapping
geom_ in ggplot2	[GEOM]etric object
stat_ in ggplot2	[STAT]istical summary
coord_ in ggplot2	[COORD]inate system
qplot in ggplot2	[Q]uick [PLOT]
x as argument	[X] is common letter for unknown variable in math
FUN as argument	[FUN]ction
pos as argument	[POS]ition
lib.loc in library	[LIB]rary folder [LOC]ation
sep as argument	[SEP]erator character
comment.char in read.table	[COMMENT] [CHAR]acter(s)
I	[I]nhibit [I]nterpretation or [I]nsulate
T value	[T]rue
F value	[F]alse
na.rm as argument	[N]ot [A]vailable [R]e[M]oved
fivenum	[FIVE] [NUM]ber summary
IQR	[I]nter [Q]uartile [R]ange
coef	Model [COEF]ficients
dist	[DIST]ance matrix
df as argument	[D]egrees of [F]reedom
mad	[M]edian [A]bsolute [D]eviation
sink		Divert R output to a connection (i.e., like connecting a pipe to a [SINK])
eol in write.table	[End] [O]f [L]ine character(s)
R as software	[R]oss Ihaka and [R]obert Gentleman or [R] is letter before S
CRAN as word	[C]omprehensive [R] [A]rchive [N]etwork	As I understand it: Inpsired by CTAN (Comprehensive TeX Archive Network); pronunciation of CRAN rhymes with CTAN (i.e., "See" ran as in Iran; "See tan")
Sexpr	[S] [EXPR]ession
ls.str	Show [STR]ucture of [L]i[S]ted objects
browseEnv	[BROWSE] [ENV]ironment
envir as argument	[ENVIR]onment
q	[Q]uit
cancor	[CAN]onical [COR]relation
ave	[AVE]rage
min	[MIN]imum
max	[MAX]imum
sqrt	[SQ]uare [R]oo[T]
%o%	[O]uter product
&		& is ampersand meaning [AND]
|		| often used to represent OR in computing (http://en.wikipedia.org /wiki /Logical_disjunction)
:		sequence generator; aslo used in MATLAB
nlevels	[N]umber of [LEVELS] in a factor
det	[DET]erminant of a matrix
crossprod	Matrix [CROSSPROD]uct
gls	[G]eneralised [L]east [S]quares
dwtest in lmtest	[D]urbin-[W]atson Test
sem in sem	[S]tructural [E]quation [M]odel
betareg in betareg	[BETA] [REG]ression
log	Natural [LOG]arithm	Default base is e consistent with most mathematics (http://en.wikipedia.org /wiki /Logarithm#Implicit_bases)
log10	[LOG]arithm base 10
fft	[F]ast [F]ourier [T]ransform
exp	[EXP]onential function	i.e., e^x
df.residual	[D]egrees of [F]reedom of the [R]esidual
sin	[SIN]e function
cos	[COS]ine function
tan	[TAN]gent function
asin	[A]rc[SIN]e function
acos	[A]rc[COS]ine function
atan	[A]rc[TAN]gent function
deriv	[DERIV]ative
chol	[Choleski] decomposition
chol2inv	[CHOL]eski [2=TO] [INV]erse
svd	[S]ingular [V]alue [D]ecomposition
eigen	[EIGEN]value or [EIGEN]vector
lower.tri	[LOWER] [TRI]angle of a matrix
upper.tri	[UPPER] [TRI]angle of a matrix
acf	[A]uto [C]orrelation or [C]ovariance [F]unction
pacf	[P]artial A]uto [C]orrelation or [C]ovariance [F]unction
ccf	[C]ross [C]orrelation or [C]ovariance [F]unction
Rattle as software	[R] [A]nalytical [T]ool [T]o [L]earn [E]asily	Perhaps, easy like a baby's rattle
StatET as software		Anyone know? Statistics Eclipse?
JGR as software	[J]ava [G]UI for [R]	pronounced "Jaguar" like the cat
ESS as software	[E]macs [S]peaks [S]tatistics
Rcmdr package	[R] [C]o[m]man[d]e[r] GUI
prettyNum	[PRETTY] [NUM]ber
Inf value	[Inf]inite
NaN value	[N]ot [A] [N]umber
is.nan	[IS] [N]ot [A] [N]umber
S3		R is a dialect of [S]; 3 is the version number
S4		R is a dialect of [S]; 4 is the version number
Rterm as program	[R] [TERM]inal
R CMD as program		I think: [R] [C]o[m]man[D] prompt
repos as option	[REPOS]itory locations
bin folder	[BIN]aries	Common Unix folder for "essential command binaries"
etc folder	[et cetera]	Common Unix folder for "host-specific system-wide configuration files
src folder	[S]ou[RC]e [C]ode	Common Unix folder
doc folder	[DOC]umentation
RGUI program	[R] [G]rapical [U]ser [I]nterface
.site file extension	[SITE] specific file	e.g., RProfile.site
Hmisc package	Frank [HARRELL]'s package of [MISC]elaneous functions
n in debug	[N]ext step
c in debug	[C]ontinue
Q in debug	[Q]uit
MASS package	[M]odern [A]pplied [S]tatistics with [S]	Based on book of same name by Venables and Ripley
plyr package	PL[Y=ie][R]	Double play on words: (1) package manipulates data like pliers manipulate materials; (2) last letter is R as in the program
aaply	input [A]rray output [A]rray using [PLY]r package
daply	input [D]ata frame output [A]rray using [PLY]r package
laply	input [L]ist output [A]rray using [PLY]r package
adply	input [A]rray output [D]ata frame using [PLY]r package
alply	input [A]rray output [L]ist using [PLY]r package
a_ply	input [A]rray output Discarded (i.e., _ is blank) using [PLY]r package
RODBC package	[R] [O]bject [D]ata[B]ase [C]onnectivity
psych package	[PSYCH]ology related functions
zelig package		"Zelig is named after a Woody Allen movie about a man who had the strange ability to become the physical and psychological reflection of anyone he met and thus to fit perfectly in any situation." - http://gking. harvard.edu/ zelig/
strucchange package	[STRUC]tural [CHANGE]
relaimpo package	[RELA]tive [IMPO]rtance
car package	[C]ompanion to [A]pplied [R]egression	Named after book by John Fox
OpenMx packge	[OPEN] Source [M]atri[X] algebra interpreter	Need confirmation that [Mx] means matrix
df in write.foreign	[D]ata [F]rame
GNU S word	[GNU] is [N]ot [U]nix [S]
R FAQ word	R [F]requently [A]sked [Q]uestions
DVI format	[D]e[V]ice [I]ndependent file format
devel word	[DEVEL]opment	as in code under development
GPL word	[G]eneral [P]ublic [L]icense
utils package	[UTIL]itie[S]
mle	[M]aximum [L]ikelihood [E]stimation
rpart package	[R]ecursive [PART]itioning
sna package	[S]ocial [N]etwork [A]nalysis
ergm package	[E]xponential [R]andom [G]raph [M]odels
rbugs package	[R] interface to program [B]ayesian inference [Using] [G]ibbs [S]ampling

More Reading

• Anonymous, Bill Venables, and David M. Smith (22 June 2012). "An Introduction to R". The Comprehensive R Archive Network (CRAN). http://cran.r-project.org/doc/manuals/R-intro.html. Retrieved 08 August 2012. 

Copyright Notice

You are free:

• to Share — to copy, distribute, display, and perform the work (pages from this wiki)
• to Remix — to adapt or make derivative works

Under the following conditions:

• Attribution — You must attribute this work to Wikibooks. You may not suggest that Wikibooks, in any way, endorses you or your use of this work.
• Share Alike — If you alter, transform, or build upon this work, you may distribute the resulting work only under the same or similar license to this one.
• Waiver — Any of the above conditions can be waived if you get permission from the copyright holder.
• Public Domain — Where the work or any of its elements is in the public domain under applicable law, that status is in no way affected by the license.
• Other Rights — In no way are any of the following rights affected by the license:

• Your fair dealing or fair use rights, or other applicable copyright exceptions and limitations;
• The author's moral rights;
• Rights other persons may have either in the work itself or in how the work is used, such as publicity or privacy rights.

• Notice — For any reuse or distribution, you must make clear to others the license terms of this work.The best way to do this is with a link to the following web page.

http://creativecommons.org/licenses/by-nc-sa/3.0/