# Data Science: An Introduction/250 R Commands

**Appendix 2: 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 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 operation | 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] columns 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]etc. 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 groups 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: Inspired 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; also 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[edit]

- 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 8 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/abbreviations-of-r-commands-explained.html. Retrieved 8 August 2012. - ↑ 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 8 August 2012.

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