Data Science: An Introduction/250 R Commands

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Appendix 2: 250 R Commands



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Chapter SummaryEdit

This is copied verbatim from Jeromy Anglim's Blog[1]

DiscussionEdit

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[2] 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 CommandsEdit


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 ReadingEdit

ReferencesEdit

  1. Jeromy Anglim (May 10, 2010). "Abbreviations of R Commands Explained: 250+ R Abbreviations". Jeromy Anglim's Blog: Psychology and Statistics. http://jeromyanglim.blogspot.com/2010/05/abbreviations-of-r-commands-explained.html. Retrieved 08 August 2012. 
  2. Tom Short (11 July 2004). "R Reference Card". The Comprehensive R Archive Network (CRAN). http://cran.r-project.org/doc/contrib/Short-refcard.pdf. Retrieved 08 August 2012. 

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Last modified on 12 August 2012, at 00:29