# Data Science: An Introduction/250 R Commands

Data Science: An Introduction
* Welcome to Data Science
** 01: A History of Data Science
** 02: A Mash-up of Disciplines
** 03: Definitions of Data
** 04: The Impact of Data Science
* Thinking about the World
** 05: Thinking Like a Visual Artist
** 06: Thinking Like a Data Engineer (Oct 13, 2012)
** 07: Thinking Like a Hacker
** 08: Thinking Like a Programmer
** 09: Thinking Like a Scientist
** 10: Thinking Like a Mathematician
** 11: Thinking Like a Statistician
** 12: Thinking Like a Domain Expert
* Analyzing and Visualizing, Part One
** 13: Single Variable Analysis
** 14: Single Variable Tables and Plots
* Setting up the Problem
** 15: Theory-Based Inquiry
** 16: Theoretical vs Measured Variables
** 17: Hypothesis Testing
* Collecting, Ingesting, Transforming Data
** 18: Collecting vs Finding Data
** 19: Data Dictionaries and Schemas
** 20: Data Preparation and Metadata
* Analyzing and Visualizing, Part Two
** Scientific data visualisation
** 21: Two Variable Analysis
** 22: Two Variable Tables
** 23: Two Variable Plots
* Emergent Answers to Free Form Problems
** 24: Non-Theory-Based Inquiry
** 25: Exploratory Analysis
* Analyzing and Visualizing, Part Three
** 26: Scientific data visualisation
** 26: Multiple Variable Analysis
** 27: Multiple Variable Tables
** 28: Multiple Variable Plots
* Presenting Results
** 29: Statistical Significance vs Substantive Significance
** 30: Telling the Story
** 31: Writing Good Data-Rich Paragraphs
** 32: Creating Good Data-Rich Slides
* Appendices
** 01. Glossary
** 02. Working in Groups
** 03. 250 R Commands
** 04. Research Design
** 05. Data Dictionary
Edit This Box

## 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 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 estimation | |
| 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 cumulative [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 package | [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). Retrieved 8 August 2012.{{cite web}}: CS1 maint: multiple names: authors list (link)

## References

* ↑ Jeromy Anglim (May 10, 2010). "Abbreviations of R Commands Explained: 250+ R Abbreviations". Jeromy Anglim's Blog: Psychology and Statistics. Retrieved 8 August 2012.
* ↑ Tom Short (11 July 2004). "R Reference Card" (PDF). The Comprehensive R Archive Network (CRAN). Retrieved 8 August 2012.

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