Data Science: An Introduction/250 R Commands
Contents
Chapter Summary[edit]
This is copied verbatim from Jeromy Anglim's Blog^{[1]}
Discussion[edit]
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 Commands[edit]
R Command  Abbreviation Expanded  Comments 
ls 
[L]i[S]t objects  common command in Unixlike operating systems 
rm 
[R]e[M]ove objects  common command in Unixlike 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". Crosstabulating 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]umnwise  
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 "hostspecific systemwide 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[edit]
 Anonymous, Bill Venables, and David M. Smith (22 June 2012). "An Introduction to R". The Comprehensive R Archive Network (CRAN). http://cran.rproject.org/doc/manuals/Rintro.html. Retrieved 08 August 2012.
References[edit]
 ↑ 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/abbreviationsofrcommandsexplained.html. Retrieved 08 August 2012.
 ↑ Tom Short (11 July 2004). "R Reference Card". The Comprehensive R Archive Network (CRAN). http://cran.rproject.org/doc/contrib/Shortrefcard.pdf. Retrieved 08 August 2012.
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