Basics of R. > x=2 (or x<-2) > y=x+3 (or y<-x+3)

Transcription

1 Basics of R 1. Arithmetic Operators > 2+2 > sqrt(2) # (2) >2^2 > sin(pi) # sin(π) >(1-2)*3 > exp(1) # e 1 >1-2*3 > log(10) # This is a short form of the full command, log(10, base=e). (Note) For log 10 7, use > log(10,7). (Note) Continuation prompt '+' Try >sqrt(2. Then you will see a prompt '+' on the next line. That means your command is incomplete, and R is waiting further action from you. Just type ) after '+' sign. 2. Assignment (= or <-) ; Mostly, naming a value is convenient for using it later. ; Put a name on the left-hand side of the equal sign and the value on the right of a equal sign (=) or the sign <-. > x=2 (or x<-2) > y=x+3 (or y<-x+3)

2 3. Entering data 3.1 Data vector using c( ) 3.1.a Numeric data Suppose you have a data set which is the number of whale beaching per year in Texas during the 1990s. The data set is > whales.tx=c(74, 122, 235, 111, 292, 111, 211, 133, 156, 79) ; The values are separated by a comma. Once stored, the values can be printed by typing the variable name. > whales.tx [1] (Note) '[1]' means the first observation. If more than one row is output, then this number refers to the first observation in each row of the output. (NOTE) The c( ) function can also combine data vectors. For example, > x=c(74,122,235,111,292) > y=c(111,211,133,156,79) > c(x,y) [1] (Note) Some functions with a numeric data vectors > sum(whales.tx) ; sum of data points in the data vector > length(whales,tx) ; length of data vector > sum(whales.tx)/length(whales.tx) ; average > mean(whales.tx) ; average (Note) Try other functions: sort(), min(), max(), range(), diff(), cusum() 3.1.b Character data If a data set consists of character values, then > simpsons=c( Homer, 'Marge', Bart ) ; character strins are made with maching quotes, either double,, or single, '. (Note) If we mix the type within a data vector, the data will be coerced into a common type, which is usually a character. This can prevent arithmetic operations Data vector using scan( ) You can use scan( ) function interactively on the screen. It reads data until a blank line is entered. For example, > x=scan() 1: : Read 8 items (Note) The scan ( ) function read an external (text or ASCII-formatted) data file. Suppose the Texas whale data were stored in a file named by whales_tx.txt in text or ASCII format. Then >whales.tx=scan(file= whale_tx.txt ) Read 10 items. (see '7. Importing/exporting data/output')

3 4. Element-by-element arithmetic operation with data vectors Suppose we also have another data set, which contains the number of whales that beached in Florida during the 1990s. The data set consists of 10 data points as follows >whales.fl=c(89, 254,292,274,233,294,204,204,90) >whales.tx+whales.tx [1] >whales.tx-whales.fl [1] Try the following command. > whales.tx-mean(whales.tx) (Example) Write an R program to calculate variance of the following data: > x=c(2,3,5,7,11) > n=length(x) > n [1] 5 > xbar=mean(x) > x-xbar [1] 5.6 >sum((x-xbar)^2) [1]51.2 >sum((x-xbar)^2)/(n-1) [1] 12.8 (Note) You can also use 'var()' function. Try 'var(x)'. You will get the same answer.

4 5. Matrix and matrix computation matrix (data, nrow=, ncol=, byrow=t) data: a list of the elements that fill the matrix nrow, ncol: the dimension of matrix byrow: specifies the rule that the matrix is to be filled. If byrow=f, then the matrix is filled column by column. Otherwise, it is filled row by row. The default is byrow=f. > p=seq(1:6) # seq(a:b) means a, a+1, a+2,..., b > p [1] > DF=matrix(p, nrow=2,ncol=3, byrow=f) # DF is filled by column by column [1,] [2,] > DT=matrix(p, nrow=2,ncol=3, byrow=t) # DT is filled by row by row [1,] [2,] > DD=matrix(p, nrow=2,ncol=3) # The default (if 'byrow' is not specified) is byrow=f [1,] [2,] > dim(dd) # the dimension of DD [1] 2 3 # 2 by 3 matrix > DD[2,] # elements of the 2 nd row [1] > DF[,3] # elements of the 3 rd column [1] 5 6 > DF[,2:3] # elements of the 2 nd to the 3 rd column [,1] [,2] [1,] 3 5 [2,] 4 6 > Y=matrix(c(1,2,3,4,5,6),nrow=3,ncol=2) # creating a 3-by-2 matrix Y > Y [,1] [,2] [1,] 1 4 [2,] 2 5 [3,] 3 6 > dim(y) [1] 3 2 # 3-by-2 matrix > X=matrix(c(7,8,9,10,11,12),nrow=2,ncol=3) # creating a 2-by-3 matrix X > X [1,] [2,] > t(y) # transpose of Y [1,] [2,] > Z=matrix(c(7,8,9),nrow=3,ncol=1) > Z [,1] [1,] 7 [2,] 8 [3,] 9

5 > V=matrix(c(10,20,30),nrow=1,ncol=3) > V [1,] > A=cbind(Y,Z) # combining the columns of Y and Z > A [1,] [2,] [3,] > B=rbind(X,V) # combining the rows of X and V > B [1,] [2,] [3,] > X=matrix(c(1,2,3,4,5,6),nrow=3,ncol=2) > y=matrix(c(7,8,9), nrow=3, ncol=1) > betahat=solve(t(x) %*% X) %*% t(x) %*% y # calculating ( X ' X ) 1 X ' y > betahat [,1] [1,] -1 [2,] 2 > m=nrow(x) # the number of rows of X > n=ncol(x) # the number of columns of X > m [1] 3 > n [1] 2 > y^2 # element-wise calculation [,1] [1,] 49 [2,] 64 [3,] 81 > y*y # element-wise calculation [,1] [1,] 49 [2,] 64 [3,] 81 > c(b) # deconstructing the matrix B; combining all column vectors of B [1]

6 6. Changing working directory Working directory is a directory in which a data file to be read or an output file to be written is located. Once you specify a working directory in the beginning of your program, you can read a data file or write an output file by specifying its file name only (without its directory path). > getwd( ) # checking the current working directory > setwd( directory path ) # setting a working directory Note: Forward slash (/) should be used as the path separator (Example) If you want to set a subdirectory new_dir under the Users directory in your computer to a new working directory, > setwd( /Users/new_dir ) 7. Importing/exporting data/output 7.1 Importing external data scan( ) ; reads logical, integer, numeric, complex, character,... scan(file = " ", what =, sep = "", skip =,quiet=,nlines=) file: the external file name to be read what: data type (logical, integer, numeric, complex, character); sep: delimiter between data (or field separator character). Sep = means that the separator is white space (one or more spaces, tabs). Sep= \t means the separator is tab. skip: specifies the number of lines to skip before beginning to read data values quiet: if FALSE (default), scan() will print a line, saying how many items have been read. nlines: if positive, the maximum number of lines of data to be read (Example 1) Suppose that a data file, 'a.txt', in the current working directory has the following format: b b b b4 Then, we can read the file using scan( ) function: > q=scan(file="a.txt",what="character") > q[3] [1] b1 > q[4] [1] 200 (Example 2) Suppose that a data file, 'b.txt', in the current working directory has the following format: x y z b b b b4 Then, we can read the file using scan( ) function: > q=scan(file="b.txt",what="character",skip=1) > q[3] [1] b1 > q[4] [1] 200

7 7.1.2 read.table( ) ; reads a file in table format read.table(file, header = FALSE, sep = "", dec = ".", skip=, row.names, col.names) header: indicates whether the file to be read contains variable names in the first line row.names: a vector of row names col.names: a vector of column names (Example 1) Suppose that a data file, 'b.txt', in the current working directory has the following format: x y z b b b b4 > r1=read.table("b.txt",header=t) > r1 x y z b b b b4 > dim(r1) [1] 4 3 # b.txt was read as a 4 by 3 matrix > r1[2,3] # accessing the (2,3) element [1] b2 > r1[,2] # accessing the 2 nd column elements [1] > r1[,"y"] # accessing the 2 nd column elements [1] read.csv ( ) ; reads data file in which data are separated by comma read.csv(file, header = TRUE, sep = ",", dec=".") 7.2 Exporting data write( ) ; writes a matrix or vector in a specified number of columns. write (x, file = "x.txt", ncolumns =, append = FALSE, sep = " ") x: the data in R to be exported file: x is exported with a name x.txt ncolumns: the number of columns append: if append=true, x is appended to the file x.txt write.table( ) ; writes a data frame with row and column labels write.table(x, file = "", append = FALSE, sep = " ", na = "NA", dec = ".") na: specify the string for missing values in the data (default is NA)

8 8. Writing outputs from an R session into an external file > sink( sinkout.txt ) > a=5 >a # The value of a, 5, is not shown in the screen but stored in the external file, sinkout.txt. > b=a+10 > b >sink() >unlink( sinkout.txt ) # Writing outputs into sinkout.txt is terminated. > a [1] 5 > b [1] Batch execution of an R program ; useful for executing a simulation program and storing its output to an external file. Outside R, R --vanilla <input file> output file&