R reference card
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This document provides a summary of common functions and operations in R for input/output, data manipulation, indexing vectors and lists, and converting between data types. Key functions covered include print(), format(), write.table(), read.table(), c(), rep(), seq(), and data.frame() for creating and manipulating data. Indexing techniques allow extracting or replacing elements of vectors, matrices, data frames, and lists. Functions like str(), summary(), and dim() provide information about R objects.
![R Reference Card cat(..., file="", sep=" ") prints the arguments after coercing to Slicing and extracting data
character; sep is the character separator between arguments Indexing lists
by Tom Short, EPRI Solutions, Inc., tshort@eprisolutions.com 2005-07-12 print(a, ...) prints its arguments; generic, meaning it can have differ- x[n] list with elements n
Granted to the public domain. See www.Rpad.org for the source and latest ent methods for different objects x[[n]] nth element of the list
version. Includes material from R for Beginners by Emmanuel Paradis (with format(x,...) format an R object for pretty printing x[["name"]] element of the list named "name"
permission). write.table(x,file="",row.names=TRUE,col.names=TRUE, x$name id.
sep=" ") prints x after converting to a data frame; if quote is TRUE, Indexing vectors
character or factor columns are surrounded by quotes ("); sep is the x[n] nth element
field separator; eol is the end-of-line separator; na is the string for x[-n] all but the nth element
Help and basics missing values; use col.names=NA to add a blank column header to x[1:n] first n elements
get the column headers aligned correctly for spreadsheet input x[-(1:n)] elements from n+1 to the end
Most R functions have online documentation.
sink(file) output to file, until sink() x[c(1,4,2)] specific elements
help(topic) documentation on topic
Most of the I/O functions have a file argument. This can often be a charac- x["name"] element named "name"
?topic id.
ter string naming a file or a connection. file="" means the standard input or x[x > 3] all elements greater than 3
help.search("topic") search the help system
output. Connections can include files, pipes, zipped files, and R variables. x[x > 3 & x < 5] all elements between 3 and 5
apropos("topic") the names of all objects in the search list matching
On windows, the file connection can also be used with description = x[x %in% c("a","and","the")] elements in the given set
the regular expression ”topic”
"clipboard". To read a table copied from Excel, use Indexing matrices
help.start() start the HTML version of help
x <- read.delim("clipboard") x[i,j] element at row i, column j
str(a) display the internal *str*ucture of an R object
To write a table to the clipboard for Excel, use x[i,] row i
summary(a) gives a “summary” of a, usually a statistical summary but it is
write.table(x,"clipboard",sep="t",col.names=NA) x[,j] column j
generic meaning it has different operations for different classes of a
For database interaction, see packages RODBC, DBI, RMySQL, RPgSQL, and x[,c(1,3)] columns 1 and 3
ls() show objects in the search path; specify pat="pat" to search on a
ROracle. See packages XML, hdf5, netCDF for reading other file formats. x["name",] row named "name"
pattern
ls.str() str() for each variable in the search path Data creation Indexing data frames (matrix indexing plus the following)
dir() show files in the current directory x[["name"]] column named "name"
c(...) generic function to combine arguments with the default forming a
methods(a) shows S3 methods of a x$name id.
vector; with recursive=TRUE descends through lists combining all
methods(class=class(a)) lists all the methods to handle objects of elements into one vector
class a from:to generates a sequence; “:” has operator priority; 1:4 + 1 is “2,3,4,5”
options(...) set or examine many global options; common ones: width, seq(from,to) generates a sequence by= specifies increment; length=
digits, error
Variable conversion
specifies desired length
library(x) load add-on packages; library(help=x) lists datasets and as.array(x), as.data.frame(x), as.numeric(x),
seq(along=x) generates 1, 2, ..., length(x); useful for for loops
functions in package x. as.logical(x), as.complex(x), as.character(x),
rep(x,times) replicate x times; use each= to repeat “each” el-
attach(x) database x to the R search path; x can be a list, data frame, or R ... convert type; for a complete list, use methods(as)
ement of x each times; rep(c(1,2,3),2) is 1 2 3 1 2 3;
data file created with save. Use search() to show the search path. rep(c(1,2,3),each=2) is 1 1 2 2 3 3 Variable information
detach(x) x from the R search path; x can be a name or character string data.frame(...) create a data frame of the named or unnamed is.na(x), is.null(x), is.array(x), is.data.frame(x),
of an object previously attached or a package. arguments; data.frame(v=1:4,ch=c("a","B","c","d"),n=10); is.numeric(x), is.complex(x), is.character(x),
Input and output shorter vectors are recycled to the length of the longest ... test for type; for a complete list, use methods(is)
list(...) create a list of the named or unnamed arguments; length(x) number of elements in x
load() load the datasets written with save
list(a=c(1,2),b="hi",c=3i); dim(x) Retrieve or set the dimension of an object; dim(x) <- c(3,2)
data(x) loads specified data sets
array(x,dim=) array with data x; specify dimensions like dimnames(x) Retrieve or set the dimension names of an object
read.table(file) reads a file in table format and creates a data
dim=c(3,4,2); elements of x recycle if x is not long enough nrow(x) number of rows; NROW(x) is the same but treats a vector as a one-
frame from it; the default separator sep="" is any whitespace; use
matrix(x,nrow=,ncol=) matrix; elements of x recycle row matrix
header=TRUE to read the first line as a header of column names; use
factor(x,levels=) encodes a vector x as a factor ncol(x) and NCOL(x) id. for columns
as.is=TRUE to prevent character vectors from being converted to fac-
gl(n,k,length=n*k,labels=1:n) generate levels (factors) by spec- class(x) get or set the class of x; class(x) <- "myclass"
tors; use comment.char="" to prevent "#" from being interpreted as
ifying the pattern of their levels; k is the number of levels, and n is unclass(x) remove the class attribute of x
a comment; use skip=n to skip n lines before reading data; see the
the number of replications attr(x,which) get or set the attribute which of x
help for options on row naming, NA treatment, and others
expand.grid() a data frame from all combinations of the supplied vec- attributes(obj) get or set the list of attributes of obj
read.csv("filename",header=TRUE) id. but with defaults set for
tors or factors
reading comma-delimited files
rbind(...) combine arguments by rows for matrices, data frames, and Data selection and manipulation
read.delim("filename",header=TRUE) id. but with defaults set which.max(x) returns the index of the greatest element of x
others
for reading tab-delimited files which.min(x) returns the index of the smallest element of x
cbind(...) id. by columns
read.fwf(file,widths,header=FALSE,sep="",as.is=FALSE) rev(x) reverses the elements of x
read a table of f ixed width f ormatted data into a ’data.frame’; widths sort(x) sorts the elements of x in increasing order; to sort in decreasing
is an integer vector, giving the widths of the fixed-width fields order: rev(sort(x))
save(file,...) saves the specified objects (...) in the XDR platform- cut(x,breaks) divides x into intervals (factors); breaks is the number
independent binary format of cut intervals or a vector of cut points
save.image(file) saves all objects](https://image.slidesharecdn.com/r-refcard-130212064839-phpapp01/85/R-reference-card-1-320.jpg)
![match(x, y) returns a vector of the same length than x with the elements cummin(x) id. for the minimum Strings
of x which are in y (NA otherwise) cummax(x) id. for the maximum paste(...) concatenate vectors after converting to character; sep= is the
which(x == a) returns a vector of the indices of x if the comparison op- union(x,y), intersect(x,y), setdiff(x,y), setequal(x,y), string to separate terms (a single space is the default); collapse= is
eration is true (TRUE), in this example the values of i for which x[i] is.element(el,set) “set” functions an optional string to separate “collapsed” results
== a (the argument of this function must be a variable of mode logi- Re(x) real part of a complex number substr(x,start,stop) substrings in a character vector; can also as-
cal) Im(x) imaginary part sign, as substr(x, start, stop) <- value
choose(n, k) computes the combinations of k events among n repetitions Mod(x) modulus; abs(x) is the same strsplit(x,split) split x according to the substring split
= n!/[(n − k)!k!] Arg(x) angle in radians of the complex number grep(pattern,x) searches for matches to pattern within x; see ?regex
na.omit(x) suppresses the observations with missing data (NA) (sup- Conj(x) complex conjugate gsub(pattern,replacement,x) replacement of matches determined
presses the corresponding line if x is a matrix or a data frame) convolve(x,y) compute the several kinds of convolutions of two se- by regular expression matching sub() is the same but only replaces
na.fail(x) returns an error message if x contains at least one NA quences the first occurrence.
unique(x) if x is a vector or a data frame, returns a similar object but with fft(x) Fast Fourier Transform of an array tolower(x) convert to lowercase
the duplicate elements suppressed mvfft(x) FFT of each column of a matrix toupper(x) convert to uppercase
table(x) returns a table with the numbers of the differents values of x filter(x,filter) applies linear filtering to a univariate time series or match(x,table) a vector of the positions of first matches for the elements
(typically for integers or factors) to each series separately of a multivariate time series of x among table
subset(x, ...) returns a selection of x with respect to criteria (..., Many math functions have a logical parameter na.rm=FALSE to specify miss- x %in% table id. but returns a logical vector
typically comparisons: x$V1 < 10); if x is a data frame, the option ing data (NA) removal. pmatch(x,table) partial matches for the elements of x among table
select gives the variables to be kept or dropped using a minus sign
sample(x, size) resample randomly and without replacement size ele-
Matrices nchar(x) number of characters
ments in the vector x, the option replace = TRUE allows to resample t(x) transpose Dates and times
with replacement diag(x) diagonal The class Date has dates without times. POSIXct has dates and times, includ-
prop.table(x,margin=) table entries as fraction of marginal table %*% matrix multiplication ing time zones. Comparisons (e.g. >), seq(), and difftime() are useful.
solve(a,b) solves a %*% x = b for x Date also allows + and −. ?DateTimeClasses gives more information. See
Math solve(a) matrix inverse of a also package chron.
sin,cos,tan,asin,acos,atan,atan2,log,log10,exp rowsum(x) sum of rows for a matrix-like object; rowSums(x) is a faster as.Date(s) and as.POSIXct(s) convert to the respective class;
max(x) maximum of the elements of x version format(dt) converts to a string representation. The default string
min(x) minimum of the elements of x colsum(x), colSums(x) id. for columns format is “2001-02-21”. These accept a second argument to specify a
range(x) id. then c(min(x), max(x)) rowMeans(x) fast version of row means format for conversion. Some common formats are:
sum(x) sum of the elements of x colMeans(x) id. for columns
diff(x) lagged and iterated differences of vector x
prod(x) product of the elements of x
Advanced data processing
apply(X,INDEX,FUN=) a vector or array or list of values obtained by %a, %A Abbreviated and full weekday name.
mean(x) mean of the elements of x %b, %B Abbreviated and full month name.
median(x) median of the elements of x applying a function FUN to margins (INDEX) of X
lapply(X,FUN) apply FUN to each element of the list X %d Day of the month (01–31).
quantile(x,probs=) sample quantiles corresponding to the given prob- %H Hours (00–23).
abilities (defaults to 0,.25,.5,.75,1) tapply(X,INDEX,FUN=) apply FUN to each cell of a ragged array given
by X with indexes INDEX %I Hours (01–12).
weighted.mean(x, w) mean of x with weights w %j Day of year (001–366).
rank(x) ranks of the elements of x by(data,INDEX,FUN) apply FUN to data frame data subsetted by INDEX
ave(x,...,FUN=mean) subsets of x are averaged (or other function %m Month (01–12).
var(x) or cov(x) variance of the elements of x (calculated on n − 1); if x is %M Minute (00–59).
a matrix or a data frame, the variance-covariance matrix is calculated specified by FUN), where each subset consist of those observations
with the same factor levels %p AM/PM indicator.
sd(x) standard deviation of x %S Second as decimal number (00–61).
cor(x) correlation matrix of x if it is a matrix or a data frame (1 if x is a merge(a,b) merge two data frames by common columns or row names
xtabs(a b,data=x) a contingency table from cross-classifying factors %U Week (00–53); the first Sunday as day 1 of week 1.
vector) %w Weekday (0–6, Sunday is 0).
var(x, y) or cov(x, y) covariance between x and y, or between the aggregate(x,by,FUN) splits the data frame x into subsets, computes
summary statistics for each, and returns the result in a convenient %W Week (00–53); the first Monday as day 1 of week 1.
columns of x and those of y if they are matrices or data frames %y Year without century (00–99). Don’t use.
cor(x, y) linear correlation between x and y, or correlation matrix if they form; by is a list of grouping elements, each as long as the variables
in x %Y Year with century.
are matrices or data frames %z (output only.) Offset from Greenwich; -0800 is 8 hours west of.
round(x, n) rounds the elements of x to n decimals stack(x, ...) transform data available as separate columns in a data
frame or list into a single column %Z (output only.) Time zone as a character string (empty if not available).
log(x, base) computes the logarithm of x with base base
scale(x) if x is a matrix, centers and scales the data; to center only use unstack(x, ...) inverse of stack()
the option scale=FALSE, to scale only center=FALSE (by default reshape(x, ...) reshapes a data frame between ’wide’ format with
repeated measurements in separate columns of the same record and Where leading zeros are shown they will be used on output but are optional
center=TRUE, scale=TRUE) on input. See ?strftime.
pmin(x,y,...) a vector which ith element is the minimum of x[i], ’long’ format with the repeated measurements in separate records;
y[i], . . . use (direction=”wide”) or (direction=”long”)
pmax(x,y,...) id. for the maximum
cumsum(x) a vector which ith element is the sum from x[1] to x[i] Graphics devices
cumprod(x) id. for the product
x11(), windows() open a graphics window](https://image.slidesharecdn.com/r-refcard-130212064839-phpapp01/85/R-reference-card-2-320.jpg)
![postscript(file) starts the graphics device driver for produc- contour(x, y, z) contour plot (data are interpolated to draw the axis(side) adds an axis at the bottom (side=1), on the left (2), at the
ing PostScript graphics; use horizontal = FALSE, onefile = curves), x and y must be vectors and z must be a matrix so that top (3), or on the right (4); at=vect (optional) gives the abcissa (or
FALSE, paper = "special" for EPS files; family= specifies the dim(z)=c(length(x), length(y)) (x and y may be omitted) ordinates) where tick-marks are drawn
font (AvantGarde, Bookman, Courier, Helvetica, Helvetica-Narrow, filled.contour(x, y, z) id. but the areas between the contours are box() draw a box around the current plot
NewCenturySchoolbook, Palatino, Times, or ComputerModern); coloured, and a legend of the colours is drawn as well rug(x) draws the data x on the x-axis as small vertical lines
width= and height= specifies the size of the region in inches (for image(x, y, z) id. but with colours (actual data are plotted) locator(n, type="n", ...) returns the coordinates (x, y) after the
paper="special", these specify the paper size). persp(x, y, z) id. but in perspective (actual data are plotted) user has clicked n times on the plot with the mouse; also draws sym-
ps.options() set and view (if called without arguments) default values stars(x) if x is a matrix or a data frame, draws a graph with segments or a bols (type="p") or lines (type="l") with respect to optional graphic
for the arguments to postscript star where each row of x is represented by a star and the columns are parameters (...); by default nothing is drawn (type="n")
pdf, png, jpeg, bitmap, xfig, pictex; see ?Devices the lengths of the segments
dev.off() shuts down the specified (default is the current) graphics device; symbols(x, y, ...) draws, at the coordinates given by x and y, sym-
Graphical parameters
see also dev.cur, dev.set bols (circles, squares, rectangles, stars, thermometres or “boxplots”) These can be set globally with par(...); many can be passed as parameters
which sizes, colours . . . are specified by supplementary arguments to plotting commands.
Plotting termplot(mod.obj) plot of the (partial) effects of a regression model adj controls text justification (0 left-justified, 0.5 centred, 1 right-justified)
plot(x) plot of the values of x (on the y-axis) ordered on the x-axis (mod.obj) bg specifies the colour of the background (ex. : bg="red", bg="blue", . . .
plot(x, y) bivariate plot of x (on the x-axis) and y (on the y-axis) The following parameters are common to many plotting functions: the list of the 657 available colours is displayed with colors())
hist(x) histogram of the frequencies of x add=FALSE if TRUE superposes the plot on the previous one (if it exists) bty controls the type of box drawn around the plot, allowed values are: "o",
barplot(x) histogram of the values of x; use horiz=FALSE for horizontal axes=TRUE if FALSE does not draw the axes and the box "l", "7", "c", "u" ou "]" (the box looks like the corresponding char-
bars type="p" specifies the type of plot, "p": points, "l": lines, "b": points acter); if bty="n" the box is not drawn
dotchart(x) if x is a data frame, plots a Cleveland dot plot (stacked plots connected by lines, "o": id. but the lines are over the points, "h": cex a value controlling the size of texts and symbols with respect to the de-
line-by-line and column-by-column) vertical lines, "s": steps, the data are represented by the top of the fault; the following parameters have the same control for numbers on
pie(x) circular pie-chart vertical lines, "S": id. but the data are represented by the bottom of the axes, cex.axis, the axis labels, cex.lab, the title, cex.main,
boxplot(x) “box-and-whiskers” plot the vertical lines and the sub-title, cex.sub
sunflowerplot(x, y) id. than plot() but the points with similar coor- xlim=, ylim= specifies the lower and upper limits of the axes, for exam- col controls the color of symbols and lines; use color names: "red", "blue"
dinates are drawn as flowers which petal number represents the num- ple with xlim=c(1, 10) or xlim=range(x) see colors() or as "#RRGGBB"; see rgb(), hsv(), gray(), and
ber of points xlab=, ylab= annotates the axes, must be variables of mode character rainbow(); as for cex there are: col.axis, col.lab, col.main,
stripplot(x) plot of the values of x on a line (an alternative to main= main title, must be a variable of mode character col.sub
boxplot() for small sample sizes) sub= sub-title (written in a smaller font) font an integer which controls the style of text (1: normal, 2: italics, 3:
coplot(x˜y | z) bivariate plot of x and y for each value or interval of bold, 4: bold italics); as for cex there are: font.axis, font.lab,
values of z Low-level plotting commands font.main, font.sub
interaction.plot (f1, f2, y) if f1 and f2 are factors, plots the points(x, y) adds points (the option type= can be used) las an integer which controls the orientation of the axis labels (0: parallel to
means of y (on the y-axis) with respect to the values of f1 (on the lines(x, y) id. but with lines the axes, 1: horizontal, 2: perpendicular to the axes, 3: vertical)
x-axis) and of f2 (different curves); the option fun allows to choose text(x, y, labels, ...) adds text given by labels at coordi- lty controls the type of lines, can be an integer or string (1: "solid",
the summary statistic of y (by default fun=mean) nates (x,y); a typical use is: plot(x, y, type="n"); text(x, y, 2: "dashed", 3: "dotted", 4: "dotdash", 5: "longdash", 6:
matplot(x,y) bivariate plot of the first column of x vs. the first one of y, names) "twodash", or a string of up to eight characters (between "0" and
the second one of x vs. the second one of y, etc. mtext(text, side=3, line=0, ...) adds text given by text in "9") which specifies alternatively the length, in points or pixels, of
fourfoldplot(x) visualizes, with quarters of circles, the association be- the margin specified by side (see axis() below); line specifies the the drawn elements and the blanks, for example lty="44" will have
tween two dichotomous variables for different populations (x must line from the plotting area the same effect than lty=2
be an array with dim=c(2, 2, k), or a matrix with dim=c(2, 2) if segments(x0, y0, x1, y1) draws lines from points (x0,y0) to points lwd a numeric which controls the width of lines, default 1
k = 1) (x1,y1) mar a vector of 4 numeric values which control the space between the axes
assocplot(x) Cohen–Friendly graph showing the deviations from inde- arrows(x0, y0, x1, y1, angle= 30, code=2) id. with arrows and the border of the graph of the form c(bottom, left, top,
pendence of rows and columns in a two dimensional contingency ta- at points (x0,y0) if code=2, at points (x1,y1) if code=1, or both if right), the default values are c(5.1, 4.1, 4.1, 2.1)
ble code=3; angle controls the angle from the shaft of the arrow to the mfcol a vector of the form c(nr,nc) which partitions the graphic window
mosaicplot(x) ‘mosaic’ graph of the residuals from a log-linear regres- edge of the arrow head as a matrix of nr lines and nc columns, the plots are then drawn in
sion of a contingency table abline(a,b) draws a line of slope b and intercept a columns
pairs(x) if x is a matrix or a data frame, draws all possible bivariate plots abline(h=y) draws a horizontal line at ordinate y mfrow id. but the plots are drawn by row
between the columns of x abline(v=x) draws a vertical line at abcissa x pch controls the type of symbol, either an integer between 1 and 25, or any
plot.ts(x) if x is an object of class "ts", plot of x with respect to time, x abline(lm.obj) draws the regression line given by lm.obj single character within ""
may be multivariate but the series must have the same frequency and rect(x1, y1, x2, y2) draws a rectangle which left, right, bottom, and 1 q 2 3 4 5 6 7 8 9 10 q 11 12 13 q 14 15
dates top limits are x1, x2, y1, and y2, respectively 16 q 17 18 19 q 20 q 21 q 22 23 24 25 * * . X X a a ? ?
ts.plot(x) id. but if x is multivariate the series may have different dates polygon(x, y) draws a polygon linking the points with coordinates given ps an integer which controls the size in points of texts and symbols
and must have the same frequency by x and y pty a character which specifies the type of the plotting region, "s": square,
qqnorm(x) quantiles of x with respect to the values expected under a nor- legend(x, y, legend) adds the legend at the point (x,y) with the sym- "m": maximal
mal law bols given by legend tck a value which specifies the length of tick-marks on the axes as a fraction
qqplot(x, y) quantiles of y with respect to the quantiles of x title() adds a title and optionally a sub-title of the smallest of the width or height of the plot; if tck=1 a grid is
drawn](https://image.slidesharecdn.com/r-refcard-130212064839-phpapp01/85/R-reference-card-3-320.jpg)
R reference card
- 1. R Reference Card cat(..., file="", sep=" ") prints the arguments after coercing to Slicing and extracting data character; sep is the character separator between arguments Indexing lists by Tom Short, EPRI Solutions, Inc., [email protected] 2005-07-12 print(a, ...) prints its arguments; generic, meaning it can have differ- x[n] list with elements n Granted to the public domain. See www.Rpad.org for the source and latest ent methods for different objects x[[n]] nth element of the list version. Includes material from R for Beginners by Emmanuel Paradis (with format(x,...) format an R object for pretty printing x[["name"]] element of the list named "name" permission). write.table(x,file="",row.names=TRUE,col.names=TRUE, x$name id. sep=" ") prints x after converting to a data frame; if quote is TRUE, Indexing vectors character or factor columns are surrounded by quotes ("); sep is the x[n] nth element field separator; eol is the end-of-line separator; na is the string for x[-n] all but the nth element Help and basics missing values; use col.names=NA to add a blank column header to x[1:n] first n elements get the column headers aligned correctly for spreadsheet input x[-(1:n)] elements from n+1 to the end Most R functions have online documentation. sink(file) output to file, until sink() x[c(1,4,2)] specific elements help(topic) documentation on topic Most of the I/O functions have a file argument. This can often be a charac- x["name"] element named "name" ?topic id. ter string naming a file or a connection. file="" means the standard input or x[x > 3] all elements greater than 3 help.search("topic") search the help system output. Connections can include files, pipes, zipped files, and R variables. x[x > 3 & x < 5] all elements between 3 and 5 apropos("topic") the names of all objects in the search list matching On windows, the file connection can also be used with description = x[x %in% c("a","and","the")] elements in the given set the regular expression ”topic” "clipboard". To read a table copied from Excel, use Indexing matrices help.start() start the HTML version of help x <- read.delim("clipboard") x[i,j] element at row i, column j str(a) display the internal *str*ucture of an R object To write a table to the clipboard for Excel, use x[i,] row i summary(a) gives a “summary” of a, usually a statistical summary but it is write.table(x,"clipboard",sep="t",col.names=NA) x[,j] column j generic meaning it has different operations for different classes of a For database interaction, see packages RODBC, DBI, RMySQL, RPgSQL, and x[,c(1,3)] columns 1 and 3 ls() show objects in the search path; specify pat="pat" to search on a ROracle. See packages XML, hdf5, netCDF for reading other file formats. x["name",] row named "name" pattern ls.str() str() for each variable in the search path Data creation Indexing data frames (matrix indexing plus the following) dir() show files in the current directory x[["name"]] column named "name" c(...) generic function to combine arguments with the default forming a methods(a) shows S3 methods of a x$name id. vector; with recursive=TRUE descends through lists combining all methods(class=class(a)) lists all the methods to handle objects of elements into one vector class a from:to generates a sequence; “:” has operator priority; 1:4 + 1 is “2,3,4,5” options(...) set or examine many global options; common ones: width, seq(from,to) generates a sequence by= specifies increment; length= digits, error Variable conversion specifies desired length library(x) load add-on packages; library(help=x) lists datasets and as.array(x), as.data.frame(x), as.numeric(x), seq(along=x) generates 1, 2, ..., length(x); useful for for loops functions in package x. as.logical(x), as.complex(x), as.character(x), rep(x,times) replicate x times; use each= to repeat “each” el- attach(x) database x to the R search path; x can be a list, data frame, or R ... convert type; for a complete list, use methods(as) ement of x each times; rep(c(1,2,3),2) is 1 2 3 1 2 3; data file created with save. Use search() to show the search path. rep(c(1,2,3),each=2) is 1 1 2 2 3 3 Variable information detach(x) x from the R search path; x can be a name or character string data.frame(...) create a data frame of the named or unnamed is.na(x), is.null(x), is.array(x), is.data.frame(x), of an object previously attached or a package. arguments; data.frame(v=1:4,ch=c("a","B","c","d"),n=10); is.numeric(x), is.complex(x), is.character(x), Input and output shorter vectors are recycled to the length of the longest ... test for type; for a complete list, use methods(is) list(...) create a list of the named or unnamed arguments; length(x) number of elements in x load() load the datasets written with save list(a=c(1,2),b="hi",c=3i); dim(x) Retrieve or set the dimension of an object; dim(x) <- c(3,2) data(x) loads specified data sets array(x,dim=) array with data x; specify dimensions like dimnames(x) Retrieve or set the dimension names of an object read.table(file) reads a file in table format and creates a data dim=c(3,4,2); elements of x recycle if x is not long enough nrow(x) number of rows; NROW(x) is the same but treats a vector as a one- frame from it; the default separator sep="" is any whitespace; use matrix(x,nrow=,ncol=) matrix; elements of x recycle row matrix header=TRUE to read the first line as a header of column names; use factor(x,levels=) encodes a vector x as a factor ncol(x) and NCOL(x) id. for columns as.is=TRUE to prevent character vectors from being converted to fac- gl(n,k,length=n*k,labels=1:n) generate levels (factors) by spec- class(x) get or set the class of x; class(x) <- "myclass" tors; use comment.char="" to prevent "#" from being interpreted as ifying the pattern of their levels; k is the number of levels, and n is unclass(x) remove the class attribute of x a comment; use skip=n to skip n lines before reading data; see the the number of replications attr(x,which) get or set the attribute which of x help for options on row naming, NA treatment, and others expand.grid() a data frame from all combinations of the supplied vec- attributes(obj) get or set the list of attributes of obj read.csv("filename",header=TRUE) id. but with defaults set for tors or factors reading comma-delimited files rbind(...) combine arguments by rows for matrices, data frames, and Data selection and manipulation read.delim("filename",header=TRUE) id. but with defaults set which.max(x) returns the index of the greatest element of x others for reading tab-delimited files which.min(x) returns the index of the smallest element of x cbind(...) id. by columns read.fwf(file,widths,header=FALSE,sep="",as.is=FALSE) rev(x) reverses the elements of x read a table of f ixed width f ormatted data into a ’data.frame’; widths sort(x) sorts the elements of x in increasing order; to sort in decreasing is an integer vector, giving the widths of the fixed-width fields order: rev(sort(x)) save(file,...) saves the specified objects (...) in the XDR platform- cut(x,breaks) divides x into intervals (factors); breaks is the number independent binary format of cut intervals or a vector of cut points save.image(file) saves all objects
- 2. match(x, y) returns a vector of the same length than x with the elements cummin(x) id. for the minimum Strings of x which are in y (NA otherwise) cummax(x) id. for the maximum paste(...) concatenate vectors after converting to character; sep= is the which(x == a) returns a vector of the indices of x if the comparison op- union(x,y), intersect(x,y), setdiff(x,y), setequal(x,y), string to separate terms (a single space is the default); collapse= is eration is true (TRUE), in this example the values of i for which x[i] is.element(el,set) “set” functions an optional string to separate “collapsed” results == a (the argument of this function must be a variable of mode logi- Re(x) real part of a complex number substr(x,start,stop) substrings in a character vector; can also as- cal) Im(x) imaginary part sign, as substr(x, start, stop) <- value choose(n, k) computes the combinations of k events among n repetitions Mod(x) modulus; abs(x) is the same strsplit(x,split) split x according to the substring split = n!/[(n − k)!k!] Arg(x) angle in radians of the complex number grep(pattern,x) searches for matches to pattern within x; see ?regex na.omit(x) suppresses the observations with missing data (NA) (sup- Conj(x) complex conjugate gsub(pattern,replacement,x) replacement of matches determined presses the corresponding line if x is a matrix or a data frame) convolve(x,y) compute the several kinds of convolutions of two se- by regular expression matching sub() is the same but only replaces na.fail(x) returns an error message if x contains at least one NA quences the first occurrence. unique(x) if x is a vector or a data frame, returns a similar object but with fft(x) Fast Fourier Transform of an array tolower(x) convert to lowercase the duplicate elements suppressed mvfft(x) FFT of each column of a matrix toupper(x) convert to uppercase table(x) returns a table with the numbers of the differents values of x filter(x,filter) applies linear filtering to a univariate time series or match(x,table) a vector of the positions of first matches for the elements (typically for integers or factors) to each series separately of a multivariate time series of x among table subset(x, ...) returns a selection of x with respect to criteria (..., Many math functions have a logical parameter na.rm=FALSE to specify miss- x %in% table id. but returns a logical vector typically comparisons: x$V1 < 10); if x is a data frame, the option ing data (NA) removal. pmatch(x,table) partial matches for the elements of x among table select gives the variables to be kept or dropped using a minus sign sample(x, size) resample randomly and without replacement size ele- Matrices nchar(x) number of characters ments in the vector x, the option replace = TRUE allows to resample t(x) transpose Dates and times with replacement diag(x) diagonal The class Date has dates without times. POSIXct has dates and times, includ- prop.table(x,margin=) table entries as fraction of marginal table %*% matrix multiplication ing time zones. Comparisons (e.g. >), seq(), and difftime() are useful. solve(a,b) solves a %*% x = b for x Date also allows + and −. ?DateTimeClasses gives more information. See Math solve(a) matrix inverse of a also package chron. sin,cos,tan,asin,acos,atan,atan2,log,log10,exp rowsum(x) sum of rows for a matrix-like object; rowSums(x) is a faster as.Date(s) and as.POSIXct(s) convert to the respective class; max(x) maximum of the elements of x version format(dt) converts to a string representation. The default string min(x) minimum of the elements of x colsum(x), colSums(x) id. for columns format is “2001-02-21”. These accept a second argument to specify a range(x) id. then c(min(x), max(x)) rowMeans(x) fast version of row means format for conversion. Some common formats are: sum(x) sum of the elements of x colMeans(x) id. for columns diff(x) lagged and iterated differences of vector x prod(x) product of the elements of x Advanced data processing apply(X,INDEX,FUN=) a vector or array or list of values obtained by %a, %A Abbreviated and full weekday name. mean(x) mean of the elements of x %b, %B Abbreviated and full month name. median(x) median of the elements of x applying a function FUN to margins (INDEX) of X lapply(X,FUN) apply FUN to each element of the list X %d Day of the month (01–31). quantile(x,probs=) sample quantiles corresponding to the given prob- %H Hours (00–23). abilities (defaults to 0,.25,.5,.75,1) tapply(X,INDEX,FUN=) apply FUN to each cell of a ragged array given by X with indexes INDEX %I Hours (01–12). weighted.mean(x, w) mean of x with weights w %j Day of year (001–366). rank(x) ranks of the elements of x by(data,INDEX,FUN) apply FUN to data frame data subsetted by INDEX ave(x,...,FUN=mean) subsets of x are averaged (or other function %m Month (01–12). var(x) or cov(x) variance of the elements of x (calculated on n − 1); if x is %M Minute (00–59). a matrix or a data frame, the variance-covariance matrix is calculated specified by FUN), where each subset consist of those observations with the same factor levels %p AM/PM indicator. sd(x) standard deviation of x %S Second as decimal number (00–61). cor(x) correlation matrix of x if it is a matrix or a data frame (1 if x is a merge(a,b) merge two data frames by common columns or row names xtabs(a b,data=x) a contingency table from cross-classifying factors %U Week (00–53); the first Sunday as day 1 of week 1. vector) %w Weekday (0–6, Sunday is 0). var(x, y) or cov(x, y) covariance between x and y, or between the aggregate(x,by,FUN) splits the data frame x into subsets, computes summary statistics for each, and returns the result in a convenient %W Week (00–53); the first Monday as day 1 of week 1. columns of x and those of y if they are matrices or data frames %y Year without century (00–99). Don’t use. cor(x, y) linear correlation between x and y, or correlation matrix if they form; by is a list of grouping elements, each as long as the variables in x %Y Year with century. are matrices or data frames %z (output only.) Offset from Greenwich; -0800 is 8 hours west of. round(x, n) rounds the elements of x to n decimals stack(x, ...) transform data available as separate columns in a data frame or list into a single column %Z (output only.) Time zone as a character string (empty if not available). log(x, base) computes the logarithm of x with base base scale(x) if x is a matrix, centers and scales the data; to center only use unstack(x, ...) inverse of stack() the option scale=FALSE, to scale only center=FALSE (by default reshape(x, ...) reshapes a data frame between ’wide’ format with repeated measurements in separate columns of the same record and Where leading zeros are shown they will be used on output but are optional center=TRUE, scale=TRUE) on input. See ?strftime. pmin(x,y,...) a vector which ith element is the minimum of x[i], ’long’ format with the repeated measurements in separate records; y[i], . . . use (direction=”wide”) or (direction=”long”) pmax(x,y,...) id. for the maximum cumsum(x) a vector which ith element is the sum from x[1] to x[i] Graphics devices cumprod(x) id. for the product x11(), windows() open a graphics window
- 3. postscript(file) starts the graphics device driver for produc- contour(x, y, z) contour plot (data are interpolated to draw the axis(side) adds an axis at the bottom (side=1), on the left (2), at the ing PostScript graphics; use horizontal = FALSE, onefile = curves), x and y must be vectors and z must be a matrix so that top (3), or on the right (4); at=vect (optional) gives the abcissa (or FALSE, paper = "special" for EPS files; family= specifies the dim(z)=c(length(x), length(y)) (x and y may be omitted) ordinates) where tick-marks are drawn font (AvantGarde, Bookman, Courier, Helvetica, Helvetica-Narrow, filled.contour(x, y, z) id. but the areas between the contours are box() draw a box around the current plot NewCenturySchoolbook, Palatino, Times, or ComputerModern); coloured, and a legend of the colours is drawn as well rug(x) draws the data x on the x-axis as small vertical lines width= and height= specifies the size of the region in inches (for image(x, y, z) id. but with colours (actual data are plotted) locator(n, type="n", ...) returns the coordinates (x, y) after the paper="special", these specify the paper size). persp(x, y, z) id. but in perspective (actual data are plotted) user has clicked n times on the plot with the mouse; also draws sym- ps.options() set and view (if called without arguments) default values stars(x) if x is a matrix or a data frame, draws a graph with segments or a bols (type="p") or lines (type="l") with respect to optional graphic for the arguments to postscript star where each row of x is represented by a star and the columns are parameters (...); by default nothing is drawn (type="n") pdf, png, jpeg, bitmap, xfig, pictex; see ?Devices the lengths of the segments dev.off() shuts down the specified (default is the current) graphics device; symbols(x, y, ...) draws, at the coordinates given by x and y, sym- Graphical parameters see also dev.cur, dev.set bols (circles, squares, rectangles, stars, thermometres or “boxplots”) These can be set globally with par(...); many can be passed as parameters which sizes, colours . . . are specified by supplementary arguments to plotting commands. Plotting termplot(mod.obj) plot of the (partial) effects of a regression model adj controls text justification (0 left-justified, 0.5 centred, 1 right-justified) plot(x) plot of the values of x (on the y-axis) ordered on the x-axis (mod.obj) bg specifies the colour of the background (ex. : bg="red", bg="blue", . . . plot(x, y) bivariate plot of x (on the x-axis) and y (on the y-axis) The following parameters are common to many plotting functions: the list of the 657 available colours is displayed with colors()) hist(x) histogram of the frequencies of x add=FALSE if TRUE superposes the plot on the previous one (if it exists) bty controls the type of box drawn around the plot, allowed values are: "o", barplot(x) histogram of the values of x; use horiz=FALSE for horizontal axes=TRUE if FALSE does not draw the axes and the box "l", "7", "c", "u" ou "]" (the box looks like the corresponding char- bars type="p" specifies the type of plot, "p": points, "l": lines, "b": points acter); if bty="n" the box is not drawn dotchart(x) if x is a data frame, plots a Cleveland dot plot (stacked plots connected by lines, "o": id. but the lines are over the points, "h": cex a value controlling the size of texts and symbols with respect to the de- line-by-line and column-by-column) vertical lines, "s": steps, the data are represented by the top of the fault; the following parameters have the same control for numbers on pie(x) circular pie-chart vertical lines, "S": id. but the data are represented by the bottom of the axes, cex.axis, the axis labels, cex.lab, the title, cex.main, boxplot(x) “box-and-whiskers” plot the vertical lines and the sub-title, cex.sub sunflowerplot(x, y) id. than plot() but the points with similar coor- xlim=, ylim= specifies the lower and upper limits of the axes, for exam- col controls the color of symbols and lines; use color names: "red", "blue" dinates are drawn as flowers which petal number represents the num- ple with xlim=c(1, 10) or xlim=range(x) see colors() or as "#RRGGBB"; see rgb(), hsv(), gray(), and ber of points xlab=, ylab= annotates the axes, must be variables of mode character rainbow(); as for cex there are: col.axis, col.lab, col.main, stripplot(x) plot of the values of x on a line (an alternative to main= main title, must be a variable of mode character col.sub boxplot() for small sample sizes) sub= sub-title (written in a smaller font) font an integer which controls the style of text (1: normal, 2: italics, 3: coplot(x˜y | z) bivariate plot of x and y for each value or interval of bold, 4: bold italics); as for cex there are: font.axis, font.lab, values of z Low-level plotting commands font.main, font.sub interaction.plot (f1, f2, y) if f1 and f2 are factors, plots the points(x, y) adds points (the option type= can be used) las an integer which controls the orientation of the axis labels (0: parallel to means of y (on the y-axis) with respect to the values of f1 (on the lines(x, y) id. but with lines the axes, 1: horizontal, 2: perpendicular to the axes, 3: vertical) x-axis) and of f2 (different curves); the option fun allows to choose text(x, y, labels, ...) adds text given by labels at coordi- lty controls the type of lines, can be an integer or string (1: "solid", the summary statistic of y (by default fun=mean) nates (x,y); a typical use is: plot(x, y, type="n"); text(x, y, 2: "dashed", 3: "dotted", 4: "dotdash", 5: "longdash", 6: matplot(x,y) bivariate plot of the first column of x vs. the first one of y, names) "twodash", or a string of up to eight characters (between "0" and the second one of x vs. the second one of y, etc. mtext(text, side=3, line=0, ...) adds text given by text in "9") which specifies alternatively the length, in points or pixels, of fourfoldplot(x) visualizes, with quarters of circles, the association be- the margin specified by side (see axis() below); line specifies the the drawn elements and the blanks, for example lty="44" will have tween two dichotomous variables for different populations (x must line from the plotting area the same effect than lty=2 be an array with dim=c(2, 2, k), or a matrix with dim=c(2, 2) if segments(x0, y0, x1, y1) draws lines from points (x0,y0) to points lwd a numeric which controls the width of lines, default 1 k = 1) (x1,y1) mar a vector of 4 numeric values which control the space between the axes assocplot(x) Cohen–Friendly graph showing the deviations from inde- arrows(x0, y0, x1, y1, angle= 30, code=2) id. with arrows and the border of the graph of the form c(bottom, left, top, pendence of rows and columns in a two dimensional contingency ta- at points (x0,y0) if code=2, at points (x1,y1) if code=1, or both if right), the default values are c(5.1, 4.1, 4.1, 2.1) ble code=3; angle controls the angle from the shaft of the arrow to the mfcol a vector of the form c(nr,nc) which partitions the graphic window mosaicplot(x) ‘mosaic’ graph of the residuals from a log-linear regres- edge of the arrow head as a matrix of nr lines and nc columns, the plots are then drawn in sion of a contingency table abline(a,b) draws a line of slope b and intercept a columns pairs(x) if x is a matrix or a data frame, draws all possible bivariate plots abline(h=y) draws a horizontal line at ordinate y mfrow id. but the plots are drawn by row between the columns of x abline(v=x) draws a vertical line at abcissa x pch controls the type of symbol, either an integer between 1 and 25, or any plot.ts(x) if x is an object of class "ts", plot of x with respect to time, x abline(lm.obj) draws the regression line given by lm.obj single character within "" may be multivariate but the series must have the same frequency and rect(x1, y1, x2, y2) draws a rectangle which left, right, bottom, and 1 q 2 3 4 5 6 7 8 9 10 q 11 12 13 q 14 15 dates top limits are x1, x2, y1, and y2, respectively 16 q 17 18 19 q 20 q 21 q 22 23 24 25 * * . X X a a ? ? ts.plot(x) id. but if x is multivariate the series may have different dates polygon(x, y) draws a polygon linking the points with coordinates given ps an integer which controls the size in points of texts and symbols and must have the same frequency by x and y pty a character which specifies the type of the plotting region, "s": square, qqnorm(x) quantiles of x with respect to the values expected under a nor- legend(x, y, legend) adds the legend at the point (x,y) with the sym- "m": maximal mal law bols given by legend tck a value which specifies the length of tick-marks on the axes as a fraction qqplot(x, y) quantiles of y with respect to the quantiles of x title() adds a title and optionally a sub-title of the smallest of the width or height of the plot; if tck=1 a grid is drawn
- 4. tcl a value which specifies the length of tick-marks on the axes as a fraction Optimization and model fitting Distributions of the height of a line of text (by default tcl=-0.5) optim(par, fn, method = c("Nelder-Mead", "BFGS", rnorm(n, mean=0, sd=1) Gaussian (normal) xaxs, yaxs style of axis interval calculation; default "r" for an extra "CG", "L-BFGS-B", "SANN") general-purpose optimization; rexp(n, rate=1) exponential space; "i" for no extra space par is initial values, fn is function to optimize (normally minimize) rgamma(n, shape, scale=1) gamma xaxt if xaxt="n" the x-axis is set but not drawn (useful in conjunction with nlm(f,p) minimize function f using a Newton-type algorithm with starting rpois(n, lambda) Poisson axis(side=1, ...)) values p rweibull(n, shape, scale=1) Weibull yaxt if yaxt="n" the y-axis is set but not drawn (useful in conjonction with lm(formula) fit linear models; formula is typically of the form response rcauchy(n, location=0, scale=1) Cauchy axis(side=2, ...)) termA + termB + ...; use I(x*y) + I(xˆ2) for terms made of rbeta(n, shape1, shape2) beta nonlinear components rt(n, df) ‘Student’ (t) glm(formula,family=) fit generalized linear models, specified by giv- rf(n, df1, df2) Fisher–Snedecor (F) (χ2 ) ing a symbolic description of the linear predictor and a description of rchisq(n, df) Pearson Lattice (Trellis) graphics the error distribution; family is a description of the error distribution rbinom(n, size, prob) binomial xyplot(y˜x) bivariate plots (with many functionalities) and link function to be used in the model; see ?family rgeom(n, prob) geometric barchart(y˜x) histogram of the values of y with respect to those of x nls(formula) nonlinear least-squares estimates of the nonlinear model rhyper(nn, m, n, k) hypergeometric dotplot(y˜x) Cleveland dot plot (stacked plots line-by-line and column- parameters rlogis(n, location=0, scale=1) logistic by-column) approx(x,y=) linearly interpolate given data points; x can be an xy plot- rlnorm(n, meanlog=0, sdlog=1) lognormal densityplot(˜x) density functions plot ting structure rnbinom(n, size, prob) negative binomial histogram(˜x) histogram of the frequencies of x spline(x,y=) cubic spline interpolation runif(n, min=0, max=1) uniform bwplot(y˜x) “box-and-whiskers” plot loess(formula) fit a polynomial surface using local fitting rwilcox(nn, m, n), rsignrank(nn, n) Wilcoxon’s statistics qqmath(˜x) quantiles of x with respect to the values expected under a the- Many of the formula-based modeling functions have several common argu- All these functions can be used by replacing the letter r with d, p or q to oretical distribution ments: data= the data frame for the formula variables, subset= a subset of get, respectively, the probability density (dfunc(x, ...)), the cumulative stripplot(y˜x) single dimension plot, x must be numeric, y may be a variables used in the fit, na.action= action for missing values: "na.fail", probability density (pfunc(x, ...)), and the value of quantile (qfunc(p, factor "na.omit", or a function. The following generics often apply to model fitting ...), with 0 < p < 1). qq(y˜x) quantiles to compare two distributions, x must be numeric, y may functions: be numeric, character, or factor but must have two ‘levels’ predict(fit,...) predictions from fit based on input data splom(˜x) matrix of bivariate plots df.residual(fit) returns the number of residual degrees of freedom parallel(˜x) parallel coordinates plot coef(fit) returns the estimated coefficients (sometimes with their Programming levelplot(z˜x*y|g1*g2) coloured plot of the values of z at the coor- standard-errors) function( arglist ) expr function definition dinates given by x and y (x, y and z are all of the same length) residuals(fit) returns the residuals return(value) wireframe(z˜x*y|g1*g2) 3d surface plot deviance(fit) returns the deviance if(cond) expr cloud(z˜x*y|g1*g2) 3d scatter plot fitted(fit) returns the fitted values if(cond) cons.expr else alt.expr In the normal Lattice formula, y x|g1*g2 has combinations of optional con- logLik(fit) computes the logarithm of the likelihood and the number of for(var in seq) expr ditioning variables g1 and g2 plotted on separate panels. Lattice functions parameters while(cond) expr take many of the same arguments as base graphics plus also data= the data AIC(fit) computes the Akaike information criterion or AIC repeat expr frame for the formula variables and subset= for subsetting. Use panel= to define a custom panel function (see apropos("panel") and ?llines). Statistics break next Lattice functions return an object of class trellis and have to be print-ed to aov(formula) analysis of variance model Use braces {} around statements produce the graph. Use print(xyplot(...)) inside functions where auto- anova(fit,...) analysis of variance (or deviance) tables for one or more ifelse(test, yes, no) a value with the same shape as test filled matic printing doesn’t work. Use lattice.theme and lset to change Lattice fitted model objects with elements from either yes or no defaults. density(x) kernel density estimates of x do.call(funname, args) executes a function call from the name of binom.test(), pairwise.t.test(), power.t.test(), the function and a list of arguments to be passed to it prop.test(), t.test(), ... use help.search("test")