R: A Quick Reference

Transcription

1 R: A Quick Reference Colorado Reed January 17, 2012 Contents 1 Basics Arrays and Matrices Lists Loading Packages Loops Operators Vectors Usage Notes Data Loading Data Debugging Interactive Debugging Functions Anonymous Function Other Function Helpfuls Objects S4 Objects Methods and Generic Functions Creating an R package S3 Objects

2 6 Syntax 11 7 Plotting & Visualization D Plots Labels and Such Random The R Language Notes 12 9 Appendix: Handy Function Reference Appendix: Assorted Tips 14 1 Basics 1.1 Arrays and Matrices > a=array ( 1 : 1 2, dim=c ( 3, 4 ) ) > a [, 1 ] [, 2 ] [, 3 ] [, 4 ] [ 1, ] [ 2, ] [ 3, ] > m=matrix ( 1 : 1 2, nrow=3, ncol =4) # 2D array > m [, 1 ] [, 2 ] [, 3 ] [, 4 ] [ 1, ] [ 2, ] [ 3, ] Access elements of an array/matrix using commas (leave blank to access everything in the row/column/etc) or slice using a colon. > a=array ( 1 : 1 2, dim=c ( 3, 4 ) ) > a [, 2 : 3 ] [, 1 ] [, 2 ] [ 1, ] 4 7 [ 2, ] 5 8 2

3 [ 3, ] 6 9 Use negative indices to specify elements that should not be included. 1.2 Lists Lists can contain heterogeneous objects and named components. > h=l i s t ( myarray=array ( 1 : 6, dim=c ( 2, 3 ) ),myname= c o lorado ) > h $myarray [, 1 ] [, 2 ] [, 3 ] [ 1, ] [ 2, ] $myname [ 1 ] c o l o r a d o which can be accessed in a few different ways > h [ 2 ] $myname [ 1 ] c o l o r a d o > h$myname [ 1 ] c o l o r a d o A data frame is a list that contains multiple named vectors that are the same length (i.e. for experimental data). 1.3 Loading Packages Think of a package as a class in Java. Load a package via 3

4 l i b r a r y ( package. name) OR r e q u i r e ( package. name) Install a package via i n s t a l l. packages ( package. name ) view the currently loaded packages (. packages ( ) ) obtain help documentation for a given library l i b r a r y ( help= topicmodels ) view the vignette for a given library v i g n e t t e ( topicmodels ) to install a package, cd to the directory with the tgz file and issue the command R CMD INSTALL filename.tgz. 1.4 Loops Three types of loops in R: repeat, while, and for. Use break to exit a loop and next to continue to the next iteration. i < 5 # repeat loop repeat { i f ( i > 25) break 4

5 } e l s e { p r i n t ( i ) i < i + 5 } i < 5 # while loop while ( i <=25){ p r i n t ( i ) ; i < i + 5 } # f o r loop f o r ( i in seq ( from=5, to =25, by=5) p r i n t ( i ) Iterators and foreach loops are available through external packages 1.5 Operators %%: mod operator $: similar to the way Java uses dot. %*%: matrix multiply 1.6 Vectors Use sequence operator similar to Matlab to generate a vector > x=1:50 > x =1:2:50 #NO > x=seq ( from=1, to =50,by=2) #yes Use the c( ) function to form longer vectors of mismatched elements > x=c ( 5, 6, 9 : 1 0, h e l l o ) 5

6 Note that character vectors are indexed by the quoted string (a C string is a character in R) can use either single or double quotes for a character in R. > x=c ( bye you, h e l l o ) > x [ 1 ] [ 1 ] bye you Can use logical indexing: > b=1:12 > b [ b \%\% 3 == 0 ] [ 1 ] Usage Notes indexing starts at 1 2 Data 2.1 Loading Data 1. read.table: general delimited data 2. read.fwf: fixed width data To read data line-by-line use: con < f i l e ( i n p u t F i l e, open = r ) while ( l e n g t h ( oneline < readlines ( con, n = 1, warn = FALSE) ) > 0) { # do s t u f f } c l o s e ( con ) 6

7 3 Debugging 3.1 Interactive Debugging The five important interactive debugging functions are traceback, debug, browser, trace, recover. Use traceback() after an error to figure out what caused the error. Use debug() on a function then call the function to step through it. Like pdb, type n to go to the next line, use Q to quit. Use undebug() to switch the debug off. To switch to browser mode on error do: o p t i o n s ( e r r o r=r e c o v e r ) 4 Functions In R you can specify function arguments by name: > l o g ( x=64, base =4) Functions are just another object that are assigned to a symbol: > f = f u n c t i o n ( x, y ) { c ( x+1, y+1)} > f ( 1, 2 ) [ 1 ] 2 3 It s possible to provide default values for the arguments > g < f u n c t i o n ( x, y=10) {x+y} > g ( 1 ) [ 1 ] 11 7

8 An ellipses (...) is a special object in R that can only be accessed inside a function and means all of the other arguments. Use etc, to specify the first, second, etc element in... > v < c ( s q r t ( 1 : ) ) > f < f u n c t i o n ( x,... ) { p r i n t ( x ) ; summary (... ) } > f ( Here i s the summary f o r v., v, d i g i t s =2) [ 1 ] Here i s the summary f o r v. Min. 1 s t Qu. Median Mean 3 rd Qu. Max A return() function can be used to return values, however, if no return statement is provided R will return the last evaluated expression (so many programmers omit the return statement). All work in R is accomplished via functions (just with lots of syntactic sugar): > animals [ 4 ]< duck > [< ( animals, 4, duck ) # same e x p r e s s i o n 4.1 Anonymous Function Functions do not need a name, e.g. it s possible to define a function and apply it directly to an argument or sappily, etc. > ( f u n c t i o n ( x ) {x+1}) ( 1 ) [ 1 ] 2 > a < c ( 1, 2, 3, 4, 5) > sapply ( a, f u n c t i o n ( x ) {x+1}) [ 1 ] Other Function Helpfuls Can define binary operators using two %: 8

9 \%myop\% < f u n c t i o n ( a, b ) {2 a + 2 b} Can obtain the arguments of a function via the args() command. 5 Objects R has three types of object oriented systems: S3, S4, R S4 Objects To create a new class use the setclass function: s e t C l a s s ( Class, r e p r e s e n t a t i o n, prototype, c o n t a i n s=c h a r a c t e r ( ), v a l i d i t y, access, where, version, sealed, package, S3methods = FALSE) the readily important parameters are: Class: string specifying the name for the new class. (only required argument) representation: A beamed list of the different slots in the class, specify ANY to allow arbitrary objects to be stored in the slot. prototype: an object containing the default objects for slots in the class contains: character vector with the names of the classes this class extends (superclasses) package: specify the package name of the class s e t C l a s s ( Person, r e p r e s e n t a t i o n (name= c h a r a c t e r, age= numeric ) ) create an instance of the class with new 9

10 hadley < new ( Person,name= Hadley, age =31) Unlike S3, S4 validates the slot types (you can t enter age="cat"). Access the ia > hadley@name [ 1 ] Hadley > s l o t ( hadley, age ) [ 1 ] Methods and Generic Functions properly initialize a generic function a: i f (! i s G e n e r i c ( a ) ) { i f ( i s. f u n c t i o n ( a ) ) fun < a e l s e fun < f u n c t i o n ( o b j e c t ) standardgeneric ( a ) s e t G e n e r i c ( a, fun ) } setmethod ( a, foo, f u n c t i o n ( o b j e c t ) { object@a }) It is also possible to use the method.skeleton() function to generate a setmethod function. 5.3 Creating an R package TODO: See for the definitive guide. Create the appropriate directory package for an R package via: 10

11 package. s k e l e t o n (name= anrpackage, l i s t, environment =.GlobalEnv, path=., f o r c e=false, namespace=false, code f i l e s =c h a r a c t e r ( ) ) Create a file (traditionally) named zzz.r with a method.first.lib. When loading a new package, R searches for a.first.lib function and evaluates it if found. This method should call another function that initializes all classes and methods. From S4Objects.pdf this function should look something like:. F i r s t. l i b < f u n c t i o n ( libname, pkgname, where ) { i f (! r e q u i r e ( methods ) ) stop ( we r e q u i r e methods f o r package Foo ) where < match ( paste ( package :, pkgname, sep= ), search ( ) ). i n i t F o o ( where ) where.initfoo is the function in initialize the classes/methods. i n i t F o o < f u n c t i o n ( where ) { s e t C l a s s ( foo, r e p r e s e n t a t i o n ( a= c h a r a c t e r, b= numeric ), where=where ) s e t C l a s s ( bar, r e p r e s e n t a t i o n ( d= numeric, c= numeric ), where=where ) s e t C l a s s ( baz, c o n t a i n s=c ( foo, bar ), where=where ) } 5.4 S3 Objects S3 is the old-school OOP in R. S3 implements a style of OOP call genericfunction OO. 6 Syntax Curly braces are used to evaluate a sequence of expressions where the last expression is returned. 11

12 7 Plotting & Visualization 7.1 3D Plots Create a 3d interactive scatterplot: l i b r a r y (MCMCpack) x < r d i r i c h l e t (2000, c ( 1, 1, 1 ) ) l i b r a r y ( r g l ) plot3d ( x ) 7.2 Labels and Such Use title to add labels to a plot t i t l e ( main= main t i t l e, sub= sub t i t l e, xlab= x a x i s l a b e l, ylab= y a x i s l a b e l ) 7.3 Random Open a new plot window via p l o t ( 1, 1, xlim=c ( 0.2,2.2), ylim=c ( 0, 0. 5 ), type= n, ann=false) 8 The R Language Notes R is an interpreted language (like Perl or Lisp) Everything in R is an object Objects are copied by value in assignment statements 12

13 NA values are used to represent missing values, Inf and -Inf are infinity, NaN is not a number, and NULL represents no object. Automatic coercion roughly occurs as follows: logical < integer < numeric < complex < character < list. Inhibit coercion using the AsIs function. showmethods(classes=class(ldm)) 9 Appendix: Handy Function Reference as.integer(): convert to integer class(): determine the class of an object dim(): dimension of object dput(): dump an object as R-readable text. fix(): open an object to fix its content (or just view them) ginv(): computes the generalized (pseudo) inverse of a matrix. lapply():when you want to apply a function to each element of a list in turn and get a list back (compare to sappily). ls(): list the names elements of an object (or the current workspace) mode(): Get or set the type of storage mode of an object names(): lists all the $ accessible names of a complex variable par(): adjusts graphical parameters, e.g. lay two plots on top of each othe paste(): use to concatenate strings with each other and other objects print(): print to console rm(list = ls()): clears the current workspace sapply(): when you want to apply a function to each element of a list in turn, but you want a vector back, rather than a list (compare to lapply()). 13

14 showmethods(classes=class(objectvar)): show methods for a given object named objectvar slotnames(): lists all the slots of an object sprintf(): formatted printing into an object str(): shows the structure of any object summary(): provide a description of a model system.time(): time a command typeof(): display the type of an object 10 Appendix: Assorted Tips.Last.value: same as ans in Matlab enclose special symbols with a single quote to refer to them, e.g.?? plot multiple lines and such on the same figure by first issuing plot() then either lines() or points(). use length() to preallocate a vector e.g. l e n g t h ( h ) < 500 use lists like hash maps overwrite the show() method to change how an object is printed draw a 3x1 plot by first calling par(mfrow = c(1, 3)) 14