Abbreviations of R Commands Explained: 250+ R Abbreviations

May 10, 2010
By

(This article was first published on Jeromy Anglim's Blog: Psychology and Statistics, and kindly contributed to R-bloggers)

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.

Context

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.

Table of R Commands

R Command Abbreviation Expanded Comments
ls[L]i[S]t objectscommon command in Unix-like operating systems
rm[R]e[M]ove objectscommon 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]essionWhy "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 applyrows [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]
xtabsCross (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 formatsi.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
catcon[CAT]enatestandard Unix command
aproposSearch 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 formati.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
seqGenerate [SEQ]uence
rep[REP]licate values of xperhaps also [REP]eat
dim[DIM]ension of an objectTypically, 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 opertionremainder 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]rintEtymology 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
parGraphics [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 parDefault 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 parNext [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 textPoint 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 parPerhaps: [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] distributionF 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
coefModel [COEF]ficients
dist[DIST]ance matrix
df as argument[D]egrees of [F]reedom
mad[M]edian [A]bsolute [D]eviation
sinkDivert 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]etworkAs 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.strShow [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
crossprodMatrix [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
logNatural [LOG]arithmDefault 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 functioni.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]asilyPerhaps, easy like a baby's rattle
StatET as softwareAnyone 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
S3R is a dialect of [S]; 3 is the version number
S4R is a dialect of [S]; 4 is the version number
Rterm as program[R] [TERM]inal
R CMD as programI think: [R] [C]o[m]man[D] prompt
repos as option[REPOS]itory locations
bin folder[BIN]ariesCommon 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]odeCommon Unix folder
doc folder[DOC]umentation
RGUI program[R] [G]rapical [U]ser [I]nterface
.site file extension[SITE] specific filee.g., RProfile.site
Hmisc packageFrank [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 packagePL[Y=ie][R]Double play on words: (1) package manipulates data like pliers manipulate materials; (2) last letter is R as in the program
aaplyinput [A]rray output [A]rray using [PLY]r package
daplyinput [D]ata frame output [A]rray using [PLY]r package
laplyinput [L]ist output [A]rray using [PLY]r package
adplyinput [A]rray output [D]ata frame using [PLY]r package
alplyinput [A]rray output [L]ist using [PLY]r package
a_plyinput [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]egressionNamed after book by John Fox
OpenMx packge[OPEN] Source [M]atri[X] algebra interpreterNeed 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 wordR [F]requently [A]sked [Q]uestions
DVI format[D]e[V]ice [I]ndependent file format
devel word[DEVEL]opmentas 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

Concluding Comments

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.

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