![R Reference Card character or factor columns are surrounded by quotes ("); sep is the Indexing lists
field separator; eol is the end-of-line separator; na is the string for x[n] list with elements n
by Tom Short, EPRI PEAC, tshort@epri-peac.com 2004-11-07 missing values; use col.names=NA to add a blank column header to x[[n]] nth element of the list
Granted to the public domain. See www.Rpad.org for the source and latest get the column headers aligned correctly for spreadsheet input x[["name"]] element of the list named "name"
version. Includes material from R for Beginners by Emmanuel Paradis (with sink(file) output to file, until sink() x$name id.
permission). Most of the I/O functions have a file argument. This can often be a charac- Indexing matrices
ter string naming a file or a connection. file="" means the standard input or x[i,j] element at row i, column j
output. Connections can include files, pipes, zipped files, and R variables. x[i,] row i
On windows, the file connection can also be used with description = x[,j] column j
Getting help "clipboard". To read a table copied from Excel, use x[,c(1,3)] columns 1 and 3
x <- read.delim("clipboard") x["name",] row named "name"
Most R functions have online documentation. Indexing data frames (matrix indexing plus the following)
To write a table to the clipboard for Excel, use
help(topic) documentation on topic x[["name"]] column named "name"
write.table(x,"clipboard",sep="t",col.names=NA)
?topic id. id.
For database interaction, see packages RODBC, DBI, RMySQL, RPgSQL, and x$name
help.search("topic") search the help system
ROracle. See packages XML, hdf5, netCDF for reading other file formats.
apropos("topic") the names of all objects in the search list matching
the regular expression ”topic” Data creation
help.start() start the HTML version of help c(...) generic function to combine arguments with the default forming a Variable conversion
str(a) display the internal *str*ucture of an R object vector; with recursive=TRUE descends through lists combining all as.array(x), as.data.frame(x), as.numeric(x),
summary(a) gives a “summary” of a, usually a statistical summary but it is elements into one vector as.logical(x), as.complex(x), as.character(x),
generic meaning it has different operations for different classes of a from:to generates a sequence; “:” has operator priority; 1:4 + 1 is “2,3,4,5” ... convert type; for a complete list, use methods(as)
ls() show objects in the search path; specify pat="pat" to search on a seq(from,to) generates a sequence by= specifies increment; length=
pattern specifies desired length Variable information
ls.str() str() for each variable in the search path seq(along=x) generates 1, 2, ..., length(along); useful for for is.na(x), is.null(x), is.array(x), is.data.frame(x),
dir() show files in the current directory loops is.numeric(x), is.complex(x), is.character(x),
methods(a) shows S3 methods of a rep(x,times) replicate x times; use each= to repeat “each” el- ... test for type; for a complete list, use methods(is)
methods(class=class(a)) lists all the methods to handle objects of ement of x each times; rep(c(1,2,3),2) is 1 2 3 1 2 3; length(x) number of elements in x
class a rep(c(1,2,3),each=2) is 1 1 2 2 3 3 dim(x) Retrieve or set the dimension of an object; dim(x) <- c(3,2)
data.frame(...) create a data frame of the named or unnamed dimnames(x) Retrieve or set the dimension names of an object
Input and output arguments; data.frame(v=1:4,ch=c("a","B","c","d"),n=10); nrow(x) number of rows; NROW(x) is the same but treats a vector as a one-
load() load the datasets written with save row matrix
shorter vectors are recycled to the length of the longest
data(x) loads specified data sets ncol(x) and NCOL(x) id. for columns
list(...) create a list of the named or unnamed arguments;
library(x) load add-on packages class(x) get or set the class of x; class(x) <- "myclass"
list(a=c(1,2),b="hi",c=3i);
read.table(file) reads a file in table format and creates a data unclass(x) remove the class attribute of x
array(x,dim=) array with data x; specify dimensions like
frame from it; the default separator sep="" is any whitespace; use attr(x,which) get or set the attribute which of x
dim=c(3,4,2); elements of x recycle if x is not long enough
header=TRUE to read the first line as a header of column names; use attributes(obj) get or set the list of attributes of obj
matrix(x,nrow=,ncol=) matrix; elements of x recycle
as.is=TRUE to prevent character vectors from being converted to fac-
factor(x,levels=) encodes a vector x as a factor
tors; use comment.char="" to prevent "#" from being interpreted as
gl(n,k,length=n*k,labels=1:n) generate levels (factors) by spec-
Data selection and manipulation
a comment; use skip=n to skip n lines before reading data; see the which.max(x) returns the index of the greatest element of x
ifying the pattern of their levels; k is the number of levels, and n is
help for options on row naming, NA treatment, and others which.min(x) returns the index of the smallest element of x
the number of replications
read.csv("filename",header=TRUE) id. but with defaults set for rev(x) reverses the elements of x
expand.grid() a data frame from all combinations of the supplied vec-
reading comma-delimited files sort(x) sorts the elements of x in increasing order; to sort in decreasing
tors or factors
read.delim("filename",header=TRUE) id. but with defaults set order: rev(sort(x))
rbind(...) combine arguments by rows for matrices, data frames, and
for reading tab-delimited files cut(x,breaks) divides x into intervals (factors); breaks is the number
others
read.fwf(file,widths,header=FALSE,sep="",as.is=FALSE)
cbind(...) id. by columns of cut intervals or a vector of cut points
read a table of f ixed width f ormatted data into a ’data.frame’; widths match(x, y) returns a vector of the same length than x with the elements
is an integer vector, giving the widths of the fixed-width fields Slicing and extracting data of x which are in y (NA otherwise)
save(file,...) saves the specified objects (...) in the XDR platform- Indexing vectors which(x == a) returns a vector of the indices of x if the comparison op-
independent binary format x[n] nth element eration is true (TRUE), in this example the values of i for which x[i]
save.image(file) saves all objects x[-n] all but the nth element == a (the argument of this function must be a variable of mode logi-
cat(..., file="", sep=" ") prints the arguments after coercing to x[1:n] first n elements cal)
character; sep is the character separator between arguments x[-(1:n)] elements from n+1 to the end choose(n, k) computes the combinations of k events among n repetitions
print(a, ...) prints its arguments; generic, meaning it can have differ- x[c(1,4,2)] specific elements = n!/[(n − k)!k!]
ent methods for different objects x["name"] element named "name" na.omit(x) suppresses the observations with missing data (NA) (sup-
format(x,...) format an R object for pretty printing x[x > 3] all elements greater than 3 presses the corresponding line if x is a matrix or a data frame)
write.table(x,file="",row.names=TRUE,col.names=TRUE, x[x > 3 & x < 5] all elements between 3 and 5 na.fail(x) returns an error message if x contains at least one NA
sep=" ") prints x after converting to a data frame; if quote is TRUE, x[x %in% c("a","and","the")] elements in the given set](https://image.slidesharecdn.com/r-short-refcard-120708195910-phpapp02/85/R-short-refcard-1-320.jpg)
![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 nchar(x) number of characters
the duplicate elements suppressed mvfft(x) FFT of each column of a matrix
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
Dates and Times
(typically for integers or factors) to each series separately of a multivariate time series The class Date has dates without times. POSIXct has dates and times, includ-
subset(x, ...) returns a selection of x with respect to criteria (..., Many math functions have a logical parameter na.rm=FALSE to specify miss- ing time zones. Comparisons (e.g. >), seq(), and difftime() are useful.
typically comparisons: x$V1 < 10); if x is a data frame, the option ing data (NA) removal. Date also allows + and −. ?DateTimeClasses gives more information. See
select gives the variables to be kept or dropped using a minus sign also package chron.
sample(x, size) resample randomly and without replacement size ele-
Matrices as.Date(s) and as.POSIXct(s) convert to the respective class;
ments in the vector x, the option replace = TRUE allows to resample t(x) transpose format(dt) converts to a string representation. The default string
with replacement diag(x) diagonal format is “2001-02-21”. These accept a second argument to specify a
prop.table(x,margin=) table entries as fraction of marginal table %*% matrix multiplication format for conversion. Some common formats are:
solve(a,b) solves a %*% x = b for x
Math solve(a) matrix inverse of a %a, %A Abbreviated and full weekday name.
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 %b, %B Abbreviated and full month name.
max(x) maximum of the elements of x version %d Day of the month (01–31).
min(x) minimum of the elements of x colsum(x), colSums(x) id. for columns %H Hours (00–23).
range(x) id. then c(min(x), max(x)) rowMeans(x) fast version of row means %I Hours (01–12).
sum(x) sum of the elements of x colMeans(x) id. for columns %j Day of year (001–366).
diff(x) lagged and iterated differences of vector x
prod(x) product of the elements of x
Advanced data processing %m Month (01–12).
%M Minute (00–59).
mean(x) mean of the elements of x apply(X,INDEX,FUN=) a vector or array or list of values obtained by
%p AM/PM indicator.
median(x) median of the elements of x applying a function FUN to margins (INDEX) of X
%S Second as decimal number (00–61).
quantile(x,probs=) sample quantiles corresponding to the given prob- lapply(X,FUN) apply FUN to each element of the list X
%U Week (00–53); the first Sunday as day 1 of week 1.
abilities (defaults to 0,.25,.5,.75,1) tapply(X,INDEX,FUN=) apply FUN to each cell of a ragged array given
%w Weekday (0–6, Sunday is 0).
weighted.mean(x, w) mean of x with weights w by X with indexes INDEX
%W Week (00–53); the first Monday as day 1 of week 1.
rank(x) ranks of the elements of x by(data,INDEX,FUN) apply FUN to data frame data subsetted by INDEX
%y Year without century (00–99). Don’t use.
var(x) or cov(x) variance of the elements of x (calculated on n − 1); if x is merge(a,b) merge two data frames by common columns or row names
%Y Year with century.
a matrix or a data frame, the variance-covariance matrix is calculated xtabs(a b,data=x) a contingency table from cross-classifying factors
%z (output only.) Offset from Greenwich; -0800 is 8 hours west of.
sd(x) standard deviation of x aggregate(x,by,FUN) splits the data frame x into subsets, computes
%Z (output only.) Time zone as a character string (empty if not available).
cor(x) correlation matrix of x if it is a matrix or a data frame (1 if x is a summary statistics for each, and returns the result in a convenient
vector) form; by is a list of grouping elements, each as long as the variables
in x Where leading zeros are shown they will be used on output but are optional
var(x, y) or cov(x, y) covariance between x and y, or between the on input. See ?strftime.
columns of x and those of y if they are matrices or data frames stack(x, ...) transform data available as separate columns in a data
cor(x, y) linear correlation between x and y, or correlation matrix if they frame or list into a single column
are matrices or data frames unstack(x, ...) inverse of stack()
round(x, n) rounds the elements of x to n decimals reshape(x, ...) reshapes a data frame between ’wide’ format with
log(x, base) computes the logarithm of x with base base repeated measurements in separate columns of the same record and Plotting
’long’ format with the repeated measurements in separate records; plot(x) plot of the values of x (on the y-axis) ordered on the x-axis
scale(x) if x is a matrix, centers and reduces the data; to center only use
use (direction=”wide”) or (direction=”long”) plot(x, y) bivariate plot of x (on the x-axis) and y (on the y-axis)
the option center=FALSE, to reduce only scale=FALSE (by default
hist(x) histogram of the frequencies of x
center=TRUE, scale=TRUE) Strings barplot(x) histogram of the values of x; use horiz=FALSE for horizontal
pmin(x,y,...) a vector which ith element is the minimum of x[i], paste(...) concatenate vectors after converting to character; sep= is the bars
y[i], . . . string to separate terms (a single space is the default); collapse= is dotchart(x) if x is a data frame, plots a Cleveland dot plot (stacked plots
pmax(x,y,...) id. for the maximum an optional string to separate “collapsed” results line-by-line and column-by-column)
cumsum(x) a vector which ith element is the sum from x[1] to x[i] substr(x,start,stop) substrings in a character vector; can also as- pie(x) circular pie-chart
cumprod(x) id. for the product sign, as substr(x, start, stop) <- value boxplot(x) “box-and-whiskers” plot
cummin(x) id. for the minimum strsplit(x,split) split x according to the substring split sunflowerplot(x, y) id. than plot() but the points with similar coor-
cummax(x) id. for the maximum grep(pattern,x) searches for matches to pattern within x; see ?regex dinates are drawn as flowers which petal number represents the num-
union(x,y), intersect(x,y), setdiff(x,y), setequal(x,y), gsub(pattern,replacement,x) replacement of matches determined ber of points
is.element(el,set) “set” functions by regular expression matching sub() is the same but only replaces stripplot(x) plot of the values of x on a line (an alternative to
Re(x) real part of a complex number the first occurrence. boxplot() for small sample sizes)
Im(x) imaginary part tolower(x) convert to lowercase coplot(x˜y | z) bivariate plot of x and y for each value or interval of
Mod(x) modulus; abs(x) is the same toupper(x) convert to uppercase values of z
Arg(x) angle in radians of the complex number match(x,table) a vector of the positions of first matches for the elements interaction.plot (f1, f2, y) if f1 and f2 are factors, plots the
Conj(x) complex conjugate of x among table means of y (on the y-axis) with respect to the values of f1 (on the
convolve(x,y) compute the several kinds of convolutions of two se- x %in% table id. but returns a logical vector x-axis) and of f2 (different curves); the option fun allows to choose
quences pmatch(x,table) partial matches for the elements of x among table the summary statistic of y (by default fun=mean)](https://image.slidesharecdn.com/r-short-refcard-120708195910-phpapp02/85/R-short-refcard-2-320.jpg)
![matplot(x,y) bivariate plot of the first column of x vs. the first one of y, mtext(text, side=3, line=0, ...) adds text given by text in lty controls the type of lines, can be an integer or string (1: "solid",
the second one of x vs. the second one of y, etc. the margin specified by side (see axis() below); line specifies the 2: "dashed", 3: "dotted", 4: "dotdash", 5: "longdash", 6:
fourfoldplot(x) visualizes, with quarters of circles, the association be- line from the plotting area "twodash", or a string of up to eight characters (between "0" and
tween two dichotomous variables for different populations (x must segments(x0, y0, x1, y1) draws lines from points (x0,y0) to points "9") which specifies alternatively the length, in points or pixels, of
be an array with dim=c(2, 2, k), or a matrix with dim=c(2, 2) if (x1,y1) the drawn elements and the blanks, for example lty="44" will have
k = 1) arrows(x0, y0, x1, y1, angle= 30, code=2) id. with arrows the same effect than lty=2
assocplot(x) Cohen–Friendly graph showing the deviations from inde- at points (x0,y0) if code=2, at points (x1,y1) if code=1, or both if lwd a numeric which controls the width of lines, default 1
pendence of rows and columns in a two dimensional contingency ta- code=3; angle controls the angle from the shaft of the arrow to the mar a vector of 4 numeric values which control the space between the axes
ble edge of the arrow head and the border of the graph of the form c(bottom, left, top,
mosaicplot(x) ‘mosaic’ graph of the residuals from a log-linear regres- abline(a,b) draws a line of slope b and intercept a right), the default values are c(5.1, 4.1, 4.1, 2.1)
sion of a contingency table abline(h=y) draws a horizontal line at ordinate y mfcol a vector of the form c(nr,nc) which partitions the graphic window
pairs(x) if x is a matrix or a data frame, draws all possible bivariate plots abline(v=x) draws a vertical line at abcissa x as a matrix of nr lines and nc columns, the plots are then drawn in
between the columns of x abline(lm.obj) draws the regression line given by lm.obj columns
plot.ts(x) if x is an object of class "ts", plot of x with respect to time, x rect(x1, y1, x2, y2) draws a rectangle which left, right, bottom, and mfrow id. but the plots are drawn by row
may be multivariate but the series must have the same frequency and top limits are x1, x2, y1, and y2, respectively pch controls the type of symbol, either an integer between 1 and 25, or any
dates polygon(x, y) draws a polygon linking the points with coordinates given single character within ""
ts.plot(x) id. but if x is multivariate the series may have different dates by x and y 1 q 2 3 4 5 6 7 8 9 10 q 11 12 13 q 14 15
and must have the same frequency legend(x, y, legend) adds the legend at the point (x,y) with the sym- 16 q 17 18 19 q 20 q 21 q 22 23 24 25 * * . X X a a ? ?
qqnorm(x) quantiles of x with respect to the values expected under a nor- bols given by legend ps an integer which controls the size in points of texts and symbols
mal law title() adds a title and optionally a sub-title pty a character which specifies the type of the plotting region, "s": square,
qqplot(x, y) quantiles of y with respect to the quantiles of x axis(side, vect) adds an axis at the bottom (side=1), on the left (2), "m": maximal
contour(x, y, z) contour plot (data are interpolated to draw the at the top (3), or on the right (4); vect (optional) gives the abcissa (or tck a value which specifies the length of tick-marks on the axes as a fraction
curves), x and y must be vectors and z must be a matrix so that ordinates) where tick-marks are drawn of the smallest of the width or height of the plot; if tck=1 a grid is
dim(z)=c(length(x), length(y)) (x and y may be omitted) rug(x) draws the data x on the x-axis as small vertical lines drawn
filled.contour(x, y, z) id. but the areas between the contours are locator(n, type="n", ...) returns the coordinates (x, y) after the tcl a value which specifies the length of tick-marks on the axes as a fraction
coloured, and a legend of the colours is drawn as well user has clicked n times on the plot with the mouse; also draws sym- of the height of a line of text (by default tcl=-0.5)
image(x, y, z) id. but with colours (actual data are plotted) bols (type="p") or lines (type="l") with respect to optional graphic xaxt if xaxt="n" the x-axis is set but not drawn (useful in conjonction with
persp(x, y, z) id. but in perspective (actual data are plotted) parameters (...); by default nothing is drawn (type="n") axis(side=1, ...))
stars(x) if x is a matrix or a data frame, draws a graph with segments or a yaxt if yaxt="n" the y-axis is set but not drawn (useful in conjonction with
star where each row of x is represented by a star and the columns are
Graphical parameters axis(side=2, ...))
the lengths of the segments These can be set globally with par(...); many can be passed as parameters
symbols(x, y, ...) draws, at the coordinates given by x and y, sym- to plotting commands.
bols (circles, squares, rectangles, stars, thermometres or “boxplots”) adj controls text justification (0 left-justified, 0.5 centred, 1 right-justified)
which sizes, colours . . . are specified by supplementary arguments bg specifies the colour of the background (ex. : bg="red", bg="blue", . . . Lattice (Trellis) graphics
termplot(mod.obj) plot of the (partial) effects of a regression model the list of the 657 available colours is displayed with colors())
bty controls the type of box drawn around the plot, allowed values are: "o", xyplot(y˜x) bivariate plots (with many functionalities)
(mod.obj) barchart(y˜x) histogram of the values of y with respect to those of x
The following parameters are common to many plotting functions: "l", "7", "c", "u" ou "]" (the box looks like the corresponding char-
acter); if bty="n" the box is not drawn dotplot(y˜x) Cleveland dot plot (stacked plots line-by-line and column-
add=FALSE if TRUE superposes the plot on the previous one (if it exists) by-column)
axes=TRUE if FALSE does not draw the axes and the box cex a value controlling the size of texts and symbols with respect to the de-
fault; the following parameters have the same control for numbers on densityplot(˜x) density functions plot
type="p" specifies the type of plot, "p": points, "l": lines, "b": points histogram(˜x) histogram of the frequencies of x
connected by lines, "o": id. but the lines are over the points, "h": the axes, cex.axis, the axis labels, cex.lab, the title, cex.main,
and the sub-title, cex.sub bwplot(y˜x) “box-and-whiskers” plot
vertical lines, "s": steps, the data are represented by the top of the qqmath(˜x) quantiles of x with respect to the values expected under a the-
vertical lines, "S": id. but the data are represented by the bottom of col controls the color of symbols and lines; use color names: "red", "blue"
see colors() or as "#RRGGBB"; see rgb(), hsv(), gray(), and oretical distribution
the vertical lines stripplot(y˜x) single dimension plot, x must be numeric, y may be a
xlim=, ylim= specifies the lower and upper limits of the axes, for exam- rainbow(); as for cex there are: col.axis, col.lab, col.main,
col.sub factor
ple with xlim=c(1, 10) or xlim=range(x) qq(y˜x) quantiles to compare two distributions, x must be numeric, y may
xlab=, ylab= annotates the axes, must be variables of mode character font an integer which controls the style of text (1: normal, 2: italics, 3:
bold, 4: bold italics); as for cex there are: font.axis, font.lab, be numeric, character, or factor but must have two ‘levels’
main= main title, must be a variable of mode character splom(˜x) matrix of bivariate plots
sub= sub-title (written in a smaller font) font.main, font.sub
las an integer which controls the orientation of the axis labels (0: parallel to parallel(˜x) parallel coordinates plot
Low-level plotting commands the axes, 1: horizontal, 2: perpendicular to the axes, 3: vertical) levelplot(z˜x*y|g1*g2) coloured plot of the values of z at the coor-
points(x, y) adds points (the option type= can be used) dinates given by x and y (x, y and z are all of the same length)
lines(x, y) id. but with lines wireframe(z˜x*y|g1*g2) 3d surface plot
text(x, y, labels, ...) adds text given by labels at coordi- cloud(z˜x*y|g1*g2) 3d scatter plot
nates (x,y); a typical use is: plot(x, y, type="n"); text(x, y,
names)](https://image.slidesharecdn.com/r-short-refcard-120708195910-phpapp02/85/R-short-refcard-3-320.jpg)
R short-refcard
- 1. R Reference Card character or factor columns are surrounded by quotes ("); sep is the Indexing lists field separator; eol is the end-of-line separator; na is the string for x[n] list with elements n by Tom Short, EPRI PEAC, tshort@epri-peac.com 2004-11-07 missing values; use col.names=NA to add a blank column header to x[[n]] nth element of the list Granted to the public domain. See www.Rpad.org for the source and latest get the column headers aligned correctly for spreadsheet input x[["name"]] element of the list named "name" version. Includes material from R for Beginners by Emmanuel Paradis (with sink(file) output to file, until sink() x$name id. permission). Most of the I/O functions have a file argument. This can often be a charac- Indexing matrices ter string naming a file or a connection. file="" means the standard input or x[i,j] element at row i, column j output. Connections can include files, pipes, zipped files, and R variables. x[i,] row i On windows, the file connection can also be used with description = x[,j] column j Getting help "clipboard". To read a table copied from Excel, use x[,c(1,3)] columns 1 and 3 x <- read.delim("clipboard") x["name",] row named "name" Most R functions have online documentation. Indexing data frames (matrix indexing plus the following) To write a table to the clipboard for Excel, use help(topic) documentation on topic x[["name"]] column named "name" write.table(x,"clipboard",sep="t",col.names=NA) ?topic id. id. For database interaction, see packages RODBC, DBI, RMySQL, RPgSQL, and x$name help.search("topic") search the help system ROracle. See packages XML, hdf5, netCDF for reading other file formats. apropos("topic") the names of all objects in the search list matching the regular expression ”topic” Data creation help.start() start the HTML version of help c(...) generic function to combine arguments with the default forming a Variable conversion str(a) display the internal *str*ucture of an R object vector; with recursive=TRUE descends through lists combining all as.array(x), as.data.frame(x), as.numeric(x), summary(a) gives a “summary” of a, usually a statistical summary but it is elements into one vector as.logical(x), as.complex(x), as.character(x), generic meaning it has different operations for different classes of a from:to generates a sequence; “:” has operator priority; 1:4 + 1 is “2,3,4,5” ... convert type; for a complete list, use methods(as) ls() show objects in the search path; specify pat="pat" to search on a seq(from,to) generates a sequence by= specifies increment; length= pattern specifies desired length Variable information ls.str() str() for each variable in the search path seq(along=x) generates 1, 2, ..., length(along); useful for for is.na(x), is.null(x), is.array(x), is.data.frame(x), dir() show files in the current directory loops is.numeric(x), is.complex(x), is.character(x), methods(a) shows S3 methods of a rep(x,times) replicate x times; use each= to repeat “each” el- ... test for type; for a complete list, use methods(is) methods(class=class(a)) lists all the methods to handle objects of ement of x each times; rep(c(1,2,3),2) is 1 2 3 1 2 3; length(x) number of elements in x class a rep(c(1,2,3),each=2) is 1 1 2 2 3 3 dim(x) Retrieve or set the dimension of an object; dim(x) <- c(3,2) data.frame(...) create a data frame of the named or unnamed dimnames(x) Retrieve or set the dimension names of an object Input and output arguments; data.frame(v=1:4,ch=c("a","B","c","d"),n=10); nrow(x) number of rows; NROW(x) is the same but treats a vector as a one- load() load the datasets written with save row matrix shorter vectors are recycled to the length of the longest data(x) loads specified data sets ncol(x) and NCOL(x) id. for columns list(...) create a list of the named or unnamed arguments; library(x) load add-on packages class(x) get or set the class of x; class(x) <- "myclass" list(a=c(1,2),b="hi",c=3i); read.table(file) reads a file in table format and creates a data unclass(x) remove the class attribute of x array(x,dim=) array with data x; specify dimensions like frame from it; the default separator sep="" is any whitespace; use attr(x,which) get or set the attribute which of x dim=c(3,4,2); elements of x recycle if x is not long enough header=TRUE to read the first line as a header of column names; use attributes(obj) get or set the list of attributes of obj matrix(x,nrow=,ncol=) matrix; elements of x recycle as.is=TRUE to prevent character vectors from being converted to fac- factor(x,levels=) encodes a vector x as a factor tors; use comment.char="" to prevent "#" from being interpreted as gl(n,k,length=n*k,labels=1:n) generate levels (factors) by spec- Data selection and manipulation a comment; use skip=n to skip n lines before reading data; see the which.max(x) returns the index of the greatest element of x ifying the pattern of their levels; k is the number of levels, and n is help for options on row naming, NA treatment, and others which.min(x) returns the index of the smallest element of x the number of replications read.csv("filename",header=TRUE) id. but with defaults set for rev(x) reverses the elements of x expand.grid() a data frame from all combinations of the supplied vec- reading comma-delimited files sort(x) sorts the elements of x in increasing order; to sort in decreasing tors or factors read.delim("filename",header=TRUE) id. but with defaults set order: rev(sort(x)) rbind(...) combine arguments by rows for matrices, data frames, and for reading tab-delimited files cut(x,breaks) divides x into intervals (factors); breaks is the number others read.fwf(file,widths,header=FALSE,sep="",as.is=FALSE) cbind(...) id. by columns of cut intervals or a vector of cut points read a table of f ixed width f ormatted data into a ’data.frame’; widths match(x, y) returns a vector of the same length than x with the elements is an integer vector, giving the widths of the fixed-width fields Slicing and extracting data of x which are in y (NA otherwise) save(file,...) saves the specified objects (...) in the XDR platform- Indexing vectors which(x == a) returns a vector of the indices of x if the comparison op- independent binary format x[n] nth element eration is true (TRUE), in this example the values of i for which x[i] save.image(file) saves all objects x[-n] all but the nth element == a (the argument of this function must be a variable of mode logi- cat(..., file="", sep=" ") prints the arguments after coercing to x[1:n] first n elements cal) character; sep is the character separator between arguments x[-(1:n)] elements from n+1 to the end choose(n, k) computes the combinations of k events among n repetitions print(a, ...) prints its arguments; generic, meaning it can have differ- x[c(1,4,2)] specific elements = n!/[(n − k)!k!] ent methods for different objects x["name"] element named "name" na.omit(x) suppresses the observations with missing data (NA) (sup- format(x,...) format an R object for pretty printing x[x > 3] all elements greater than 3 presses the corresponding line if x is a matrix or a data frame) write.table(x,file="",row.names=TRUE,col.names=TRUE, x[x > 3 & x < 5] all elements between 3 and 5 na.fail(x) returns an error message if x contains at least one NA sep=" ") prints x after converting to a data frame; if quote is TRUE, x[x %in% c("a","and","the")] elements in the given set
- 2. 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 nchar(x) number of characters the duplicate elements suppressed mvfft(x) FFT of each column of a matrix 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 Dates and Times (typically for integers or factors) to each series separately of a multivariate time series The class Date has dates without times. POSIXct has dates and times, includ- subset(x, ...) returns a selection of x with respect to criteria (..., Many math functions have a logical parameter na.rm=FALSE to specify miss- ing time zones. Comparisons (e.g. >), seq(), and difftime() are useful. typically comparisons: x$V1 < 10); if x is a data frame, the option ing data (NA) removal. Date also allows + and −. ?DateTimeClasses gives more information. See select gives the variables to be kept or dropped using a minus sign also package chron. sample(x, size) resample randomly and without replacement size ele- Matrices as.Date(s) and as.POSIXct(s) convert to the respective class; ments in the vector x, the option replace = TRUE allows to resample t(x) transpose format(dt) converts to a string representation. The default string with replacement diag(x) diagonal format is “2001-02-21”. These accept a second argument to specify a prop.table(x,margin=) table entries as fraction of marginal table %*% matrix multiplication format for conversion. Some common formats are: solve(a,b) solves a %*% x = b for x Math solve(a) matrix inverse of a %a, %A Abbreviated and full weekday name. 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 %b, %B Abbreviated and full month name. max(x) maximum of the elements of x version %d Day of the month (01–31). min(x) minimum of the elements of x colsum(x), colSums(x) id. for columns %H Hours (00–23). range(x) id. then c(min(x), max(x)) rowMeans(x) fast version of row means %I Hours (01–12). sum(x) sum of the elements of x colMeans(x) id. for columns %j Day of year (001–366). diff(x) lagged and iterated differences of vector x prod(x) product of the elements of x Advanced data processing %m Month (01–12). %M Minute (00–59). mean(x) mean of the elements of x apply(X,INDEX,FUN=) a vector or array or list of values obtained by %p AM/PM indicator. median(x) median of the elements of x applying a function FUN to margins (INDEX) of X %S Second as decimal number (00–61). quantile(x,probs=) sample quantiles corresponding to the given prob- lapply(X,FUN) apply FUN to each element of the list X %U Week (00–53); the first Sunday as day 1 of week 1. abilities (defaults to 0,.25,.5,.75,1) tapply(X,INDEX,FUN=) apply FUN to each cell of a ragged array given %w Weekday (0–6, Sunday is 0). weighted.mean(x, w) mean of x with weights w by X with indexes INDEX %W Week (00–53); the first Monday as day 1 of week 1. rank(x) ranks of the elements of x by(data,INDEX,FUN) apply FUN to data frame data subsetted by INDEX %y Year without century (00–99). Don’t use. var(x) or cov(x) variance of the elements of x (calculated on n − 1); if x is merge(a,b) merge two data frames by common columns or row names %Y Year with century. a matrix or a data frame, the variance-covariance matrix is calculated xtabs(a b,data=x) a contingency table from cross-classifying factors %z (output only.) Offset from Greenwich; -0800 is 8 hours west of. sd(x) standard deviation of x aggregate(x,by,FUN) splits the data frame x into subsets, computes %Z (output only.) Time zone as a character string (empty if not available). cor(x) correlation matrix of x if it is a matrix or a data frame (1 if x is a summary statistics for each, and returns the result in a convenient vector) form; by is a list of grouping elements, each as long as the variables in x Where leading zeros are shown they will be used on output but are optional var(x, y) or cov(x, y) covariance between x and y, or between the on input. See ?strftime. columns of x and those of y if they are matrices or data frames stack(x, ...) transform data available as separate columns in a data cor(x, y) linear correlation between x and y, or correlation matrix if they frame or list into a single column are matrices or data frames unstack(x, ...) inverse of stack() round(x, n) rounds the elements of x to n decimals reshape(x, ...) reshapes a data frame between ’wide’ format with log(x, base) computes the logarithm of x with base base repeated measurements in separate columns of the same record and Plotting ’long’ format with the repeated measurements in separate records; plot(x) plot of the values of x (on the y-axis) ordered on the x-axis scale(x) if x is a matrix, centers and reduces the data; to center only use use (direction=”wide”) or (direction=”long”) plot(x, y) bivariate plot of x (on the x-axis) and y (on the y-axis) the option center=FALSE, to reduce only scale=FALSE (by default hist(x) histogram of the frequencies of x center=TRUE, scale=TRUE) Strings barplot(x) histogram of the values of x; use horiz=FALSE for horizontal pmin(x,y,...) a vector which ith element is the minimum of x[i], paste(...) concatenate vectors after converting to character; sep= is the bars y[i], . . . string to separate terms (a single space is the default); collapse= is dotchart(x) if x is a data frame, plots a Cleveland dot plot (stacked plots pmax(x,y,...) id. for the maximum an optional string to separate “collapsed” results line-by-line and column-by-column) cumsum(x) a vector which ith element is the sum from x[1] to x[i] substr(x,start,stop) substrings in a character vector; can also as- pie(x) circular pie-chart cumprod(x) id. for the product sign, as substr(x, start, stop) <- value boxplot(x) “box-and-whiskers” plot cummin(x) id. for the minimum strsplit(x,split) split x according to the substring split sunflowerplot(x, y) id. than plot() but the points with similar coor- cummax(x) id. for the maximum grep(pattern,x) searches for matches to pattern within x; see ?regex dinates are drawn as flowers which petal number represents the num- union(x,y), intersect(x,y), setdiff(x,y), setequal(x,y), gsub(pattern,replacement,x) replacement of matches determined ber of points is.element(el,set) “set” functions by regular expression matching sub() is the same but only replaces stripplot(x) plot of the values of x on a line (an alternative to Re(x) real part of a complex number the first occurrence. boxplot() for small sample sizes) Im(x) imaginary part tolower(x) convert to lowercase coplot(x˜y | z) bivariate plot of x and y for each value or interval of Mod(x) modulus; abs(x) is the same toupper(x) convert to uppercase values of z Arg(x) angle in radians of the complex number match(x,table) a vector of the positions of first matches for the elements interaction.plot (f1, f2, y) if f1 and f2 are factors, plots the Conj(x) complex conjugate of x among table means of y (on the y-axis) with respect to the values of f1 (on the convolve(x,y) compute the several kinds of convolutions of two se- x %in% table id. but returns a logical vector x-axis) and of f2 (different curves); the option fun allows to choose quences pmatch(x,table) partial matches for the elements of x among table the summary statistic of y (by default fun=mean)
- 3. matplot(x,y) bivariate plot of the first column of x vs. the first one of y, mtext(text, side=3, line=0, ...) adds text given by text in lty controls the type of lines, can be an integer or string (1: "solid", the second one of x vs. the second one of y, etc. the margin specified by side (see axis() below); line specifies the 2: "dashed", 3: "dotted", 4: "dotdash", 5: "longdash", 6: fourfoldplot(x) visualizes, with quarters of circles, the association be- line from the plotting area "twodash", or a string of up to eight characters (between "0" and tween two dichotomous variables for different populations (x must segments(x0, y0, x1, y1) draws lines from points (x0,y0) to points "9") which specifies alternatively the length, in points or pixels, of be an array with dim=c(2, 2, k), or a matrix with dim=c(2, 2) if (x1,y1) the drawn elements and the blanks, for example lty="44" will have k = 1) arrows(x0, y0, x1, y1, angle= 30, code=2) id. with arrows the same effect than lty=2 assocplot(x) Cohen–Friendly graph showing the deviations from inde- at points (x0,y0) if code=2, at points (x1,y1) if code=1, or both if lwd a numeric which controls the width of lines, default 1 pendence of rows and columns in a two dimensional contingency ta- code=3; angle controls the angle from the shaft of the arrow to the mar a vector of 4 numeric values which control the space between the axes ble edge of the arrow head and the border of the graph of the form c(bottom, left, top, mosaicplot(x) ‘mosaic’ graph of the residuals from a log-linear regres- abline(a,b) draws a line of slope b and intercept a right), the default values are c(5.1, 4.1, 4.1, 2.1) sion of a contingency table abline(h=y) draws a horizontal line at ordinate y mfcol a vector of the form c(nr,nc) which partitions the graphic window pairs(x) if x is a matrix or a data frame, draws all possible bivariate plots abline(v=x) draws a vertical line at abcissa x as a matrix of nr lines and nc columns, the plots are then drawn in between the columns of x abline(lm.obj) draws the regression line given by lm.obj columns plot.ts(x) if x is an object of class "ts", plot of x with respect to time, x rect(x1, y1, x2, y2) draws a rectangle which left, right, bottom, and mfrow id. but the plots are drawn by row may be multivariate but the series must have the same frequency and top limits are x1, x2, y1, and y2, respectively pch controls the type of symbol, either an integer between 1 and 25, or any dates polygon(x, y) draws a polygon linking the points with coordinates given single character within "" ts.plot(x) id. but if x is multivariate the series may have different dates by x and y 1 q 2 3 4 5 6 7 8 9 10 q 11 12 13 q 14 15 and must have the same frequency legend(x, y, legend) adds the legend at the point (x,y) with the sym- 16 q 17 18 19 q 20 q 21 q 22 23 24 25 * * . X X a a ? ? qqnorm(x) quantiles of x with respect to the values expected under a nor- bols given by legend ps an integer which controls the size in points of texts and symbols mal law title() adds a title and optionally a sub-title pty a character which specifies the type of the plotting region, "s": square, qqplot(x, y) quantiles of y with respect to the quantiles of x axis(side, vect) adds an axis at the bottom (side=1), on the left (2), "m": maximal contour(x, y, z) contour plot (data are interpolated to draw the at the top (3), or on the right (4); vect (optional) gives the abcissa (or tck a value which specifies the length of tick-marks on the axes as a fraction curves), x and y must be vectors and z must be a matrix so that ordinates) where tick-marks are drawn of the smallest of the width or height of the plot; if tck=1 a grid is dim(z)=c(length(x), length(y)) (x and y may be omitted) rug(x) draws the data x on the x-axis as small vertical lines drawn filled.contour(x, y, z) id. but the areas between the contours are locator(n, type="n", ...) returns the coordinates (x, y) after the tcl a value which specifies the length of tick-marks on the axes as a fraction coloured, and a legend of the colours is drawn as well user has clicked n times on the plot with the mouse; also draws sym- of the height of a line of text (by default tcl=-0.5) image(x, y, z) id. but with colours (actual data are plotted) bols (type="p") or lines (type="l") with respect to optional graphic xaxt if xaxt="n" the x-axis is set but not drawn (useful in conjonction with persp(x, y, z) id. but in perspective (actual data are plotted) parameters (...); by default nothing is drawn (type="n") axis(side=1, ...)) stars(x) if x is a matrix or a data frame, draws a graph with segments or a yaxt if yaxt="n" the y-axis is set but not drawn (useful in conjonction with star where each row of x is represented by a star and the columns are Graphical parameters axis(side=2, ...)) the lengths of the segments These can be set globally with par(...); many can be passed as parameters symbols(x, y, ...) draws, at the coordinates given by x and y, sym- to plotting commands. bols (circles, squares, rectangles, stars, thermometres or “boxplots”) adj controls text justification (0 left-justified, 0.5 centred, 1 right-justified) which sizes, colours . . . are specified by supplementary arguments bg specifies the colour of the background (ex. : bg="red", bg="blue", . . . Lattice (Trellis) graphics termplot(mod.obj) plot of the (partial) effects of a regression model the list of the 657 available colours is displayed with colors()) bty controls the type of box drawn around the plot, allowed values are: "o", xyplot(y˜x) bivariate plots (with many functionalities) (mod.obj) barchart(y˜x) histogram of the values of y with respect to those of x The following parameters are common to many plotting functions: "l", "7", "c", "u" ou "]" (the box looks like the corresponding char- acter); if bty="n" the box is not drawn dotplot(y˜x) Cleveland dot plot (stacked plots line-by-line and column- add=FALSE if TRUE superposes the plot on the previous one (if it exists) by-column) axes=TRUE if FALSE does not draw the axes and the box cex a value controlling the size of texts and symbols with respect to the de- fault; the following parameters have the same control for numbers on densityplot(˜x) density functions plot type="p" specifies the type of plot, "p": points, "l": lines, "b": points histogram(˜x) histogram of the frequencies of x connected by lines, "o": id. but the lines are over the points, "h": the axes, cex.axis, the axis labels, cex.lab, the title, cex.main, and the sub-title, cex.sub bwplot(y˜x) “box-and-whiskers” plot vertical lines, "s": steps, the data are represented by the top of the qqmath(˜x) quantiles of x with respect to the values expected under a the- vertical lines, "S": id. but the data are represented by the bottom of col controls the color of symbols and lines; use color names: "red", "blue" see colors() or as "#RRGGBB"; see rgb(), hsv(), gray(), and oretical distribution the vertical lines stripplot(y˜x) single dimension plot, x must be numeric, y may be a xlim=, ylim= specifies the lower and upper limits of the axes, for exam- rainbow(); as for cex there are: col.axis, col.lab, col.main, col.sub factor ple with xlim=c(1, 10) or xlim=range(x) qq(y˜x) quantiles to compare two distributions, x must be numeric, y may xlab=, ylab= annotates the axes, must be variables of mode character font an integer which controls the style of text (1: normal, 2: italics, 3: bold, 4: bold italics); as for cex there are: font.axis, font.lab, be numeric, character, or factor but must have two ‘levels’ main= main title, must be a variable of mode character splom(˜x) matrix of bivariate plots sub= sub-title (written in a smaller font) font.main, font.sub las an integer which controls the orientation of the axis labels (0: parallel to parallel(˜x) parallel coordinates plot Low-level plotting commands the axes, 1: horizontal, 2: perpendicular to the axes, 3: vertical) levelplot(z˜x*y|g1*g2) coloured plot of the values of z at the coor- points(x, y) adds points (the option type= can be used) dinates given by x and y (x, y and z are all of the same length) lines(x, y) id. but with lines wireframe(z˜x*y|g1*g2) 3d surface plot text(x, y, labels, ...) adds text given by labels at coordi- cloud(z˜x*y|g1*g2) 3d scatter plot nates (x,y); a typical use is: plot(x, y, type="n"); text(x, y, names)
- 4. In the normal Lattice formula, y x|g1*g2 has combinations of optional con- rpois(n, lambda) Poisson ditioning variables g1 and g2 plotted on separate panels. Lattice functions rweibull(n, shape, scale=1) Weibull take many of the same arguments as base graphics plus also data= the data rcauchy(n, location=0, scale=1) Cauchy frame for the formula variables and subset= for subsetting. Use panel= rbeta(n, shape1, shape2) beta to define a custom panel function (see apropos("panel") and ?llines). rt(n, df) ‘Student’ (t) Lattice functions return an object of class trellis and have to be print-ed to rf(n, df1, df2) Fisher–Snedecor (F) (χ2 ) produce the graph. Use print(xyplot(...)) inside functions where auto- rchisq(n, df) Pearson matic printing doesn’t work. Use lattice.theme and lset to change Lattice rbinom(n, size, prob) binomial defaults. rgeom(n, prob) geometric rhyper(nn, m, n, k) hypergeometric Optimization and model fitting rlogis(n, location=0, scale=1) logistic optim(par, fn, method = c("Nelder-Mead", "BFGS", rlnorm(n, meanlog=0, sdlog=1) lognormal "CG", "L-BFGS-B", "SANN") general-purpose optimization; rnbinom(n, size, prob) negative binomial par is initial values, fn is function to optimize (normally minimize) runif(n, min=0, max=1) uniform nlm(f,p) minimize function f using a Newton-type algorithm with starting rwilcox(nn, m, n), rsignrank(nn, n) Wilcoxon’s statistics values p All these functions can be used by replacing the letter r with d, p or q to lm(formula) fit linear models; formula is typically of the form response get, respectively, the probability density (dfunc(x, ...)), the cumulative termA + termB + ...; use I(x*y) + I(xˆ2) for terms made of probability density (pfunc(x, ...)), and the value of quantile (qfunc(p, nonlinear components ...), with 0 < p < 1). glm(formula,family=) fit generalized linear models, specified by giv- ing a symbolic description of the linear predictor and a description of the error distribution; family is a description of the error distribution and link function to be used in the model; see ?family Programming nls(formula) nonlinear least-squares estimates of the nonlinear model function( arglist ) expr function definition parameters return(value) approx(x,y=) linearly interpolate given data points; x can be an xy plot- if(cond) expr ting structure if(cond) cons.expr else alt.expr spline(x,y=) cubic spline interpolation for(var in seq) expr loess(formula) fit a polynomial surface using local fitting while(cond) expr Many of the formula-based modeling functions have several common argu- repeat expr ments: data= the data frame for the formula variables, subset= a subset of break variables used in the fit, na.action= action for missing values: "na.fail", next "na.omit", or a function. The following generics often apply to model fitting Use braces {} around statements functions: ifelse(test, yes, no) a value with the same shape as test filled predict(fit,...) predictions from fit based on input data with elements from either yes or no df.residual(fit) returns the number of residual degrees of freedom do.call(funname, args) executes a function call from the name of coef(fit) returns the estimated coefficients (sometimes with their the function and a list of arguments to be passed to it standard-errors) residuals(fit) returns the residuals deviance(fit) returns the deviance fitted(fit) returns the fitted values logLik(fit) computes the logarithm of the likelihood and the number of parameters AIC(fit) computes the Akaike information criterion or AIC Statistics aov(formula) analysis of variance model anova(fit,...) analysis of variance (or deviance) tables for one or more fitted model objects density(x) kernel density estimates of x binom.test(), pairwise.t.test(), power.t.test(), prop.test(), t.test(), ... use help.search("test") Distributions rnorm(n, mean=0, sd=1) Gaussian (normal) rexp(n, rate=1) exponential rgamma(n, shape, scale=1) gamma