SYNTAX EXAMPLES FOR R STATISTICAL PROGRAM
by Matthew Keller, [Link]@[Link]. 6/20/2006. Distribute freely.
R PROGRAMMING ENVIRONMENT
DEAL WITH OBJECTS:
ls()
length(ls()) #how many objects in memory?
remove(list = ls()) #remove all objects
remove(“dataset”) #remove a particular object
DEAL WITH ATTACHED FILES
search()
attach(myfile) #attach objects in myfile to 2nd position
attach(myfile, pos=5) #attach them to 5th position
detach (5) #to detach objects in 5th position (if possible)
LOAD A SCRIPT
source("C:/Program Files/R/functions/mckeller/[Link].R")
CHANGE DIRECTORY
getwd() #get the current working directory
setwd("c:/temp")
SAVE R IMAGE & HISTORY
[Link]("[Link]")
savehistory(file = "[Link]") #saves all commands you’ve inputed
history([Link] = 46, reverse = FALSE) #displays last 46 commands
SAVE OUTPUT (DISALLOWS YOU TO SEE OUTPUT IN CONSOLE)
sink("MIsession12_9_05.Rlis")
SAVE BOTH COMMANDS AND OUTPUT, AT END OF SESSION:
<Under “File”, Choose “Save to file…”>
CHECK HOW LONG A FUNCTION TAKES
t1 <- [Link]()
<SOME FUNCTION>
t2 <- [Link]()
difftime(t1,t2)
#ALTERNATIVE
[Link](for (i in 1:runs){perm_results[i,] <- matrix(t(permstats[1:2,]),nrow=1) })
EXAMPLES OF HOW FUNCTION IS USED (MEAN IN THIS CASE)
example(mean)
RENAME ALL OBJECTS IN ENVIRONMENT AND GIVE THEM PREFIX
vars <- ls()
for (i in vars){ cat(paste("MDD.",i," <- ",i, sep=""),file="temp")
eval(parse(file="temp"))
cat(paste("remove(",i,")", sep=""),file="temp2")
eval(parse(file="temp2"))}
MAKE USEFUL LISTS
newlist <- list(
comment=matrix(c(
"I created this on 6-3-06.",
"There should be 6 columns and 50 rows." ,
"Make sure that if you want to use the data matrix, you index it with",
"two brackets rather than one, i.e., [[]] rather than [], since the latter",
"just provides another list."), nrow=6,ncol=1),
dimms=c("r","b","g","y","o","p"),
data=red[1:20,])
IMPORTING/EXPORTING
EXPORT DATA INTO A SPECIFIC FOLDER & FORMAT
[Link](dataset, file = "C:/temp/MyData", append = FALSE, quote = TRUE, sep = "&", eol = "\n", na
= "-999", dec = ".", [Link] = FALSE, [Link] = TRUE, qmethod ="double")
SAVE FILES FROM SPSS THAT ARE READABLE IN S-PLUS (IN SPSS LANGUAGE):
##Import directly from an excel file – OR -
##Always save as *.dbf, not text! Make sure to have S-Plus see it is a dbf file (filetype) before importing.
SAVE TRANSLATE OUTFILE='C:\Matts Folder\RESEARCH\S-Plus\attempt3.db4'/TYPE=TAB /FIELDNAMES
/KEEP=nmcode2 sex weeksbf k5 k1 k8 zcd_sad TO zcd_slp f.sad2 TO f.noeat2 /RENAME zcd_sad=zsad.
READ IN A DATA FRAME AND A HEADER FILE:
heads <- [Link]("C:/temp/colnames.study1")
heads2 <- [Link](heads) #the data frame must be a matrix to change col & row #s
dim(heads2) <- c(1,50) #originally, the header file was 10x5
##BUT THE ABOVE SCREWS IT UP… R READS DOWN COLUMN BY COLUMN, SO WE MUST TRANSPOSE 1ST:
heads <- [Link]("C:/temp/colnames.study1")
heads2 <- [Link](t(heads)) #the data frame must be a matrix to change cols & rows
dim(heads2) <- c(1,50)
study1 <- [Link]("C:/temp/[Link]")
names(study1) <- heads2
READ & WRITE TABLES
data1 <- [Link]("C:/temp/[Link]", header = TRUE, sep = "&", dec = ".",[Link] = TRUE,
[Link] = c("NA", " ","999"),colClasses = NA, skip = 0, [Link] = TRUE)
[Link]([Link], file="C:/temp/[Link]") #saves it to read it as a text file
save([Link],file=”C:/temp/[Link]”) #saves it for reading back into R
EXPLORING DATA
MULTI-WAY IF/THEN STATEMENT:
x <- c(1,2,3,4,5)
if (x[1]==2) a <- 3 else if (x[1]==3) a <- 4 else if (x[1]==1) a <- 6 else a <- NA
RUN A SEQUENTIAL NUMBER OF STATISTICS ON MANY VARIABLES:
for (k in 152:171){
[Link] <- lm(scale(dataset[,k]) ~ var1*var2, [Link]=[Link])
print("THIS IS FOR VARIABLE:")
print(names(dataset[k]))
print(summary([Link]))
print(anova([Link]))}
REMOVE CERTAIN VARIABLES FROM A REG EQUATION W/O RETYPING LOTS:
reg1 <- lm(var1 ~ var2+var3+var4+var5+var4*var5))
summary(update(reg1, .~. – var4 – var5-var4*var5))
LOOK AT A LOT OF MEANS AT ONCE
apply(dataset[,c(1,2,26,35,49,65,74)],2,mean) !This gives you the means of each variable (COLUMN)
apply(dataset[,c(9,33,48,61,80)],1,mean) !Gives you each subject’s mean across vars (ROW)
APPLY A FUNCTION BROKEN UP BY SOME FACTOR (E.G., SEAS):
tapply(dataset[,5], dataset$seas, FUN=mean)
DO STATS ON SUBSETS OF DATA
summary(dataset[,c("var1","var2")])
summary(dataset[var1<40,]$var1)
summary(dataset[var1<40,]$var99)
summary(lm(var1~var2+var3, data=dataset[-150,]))
summary(lm(iwt5[iwt5$seas=='w',]$[Link] ~ iwt7$[Link] + [Link], [Link] = [Link]))
summary(lm(var1~var2+var3, subset=(var22 == xor("death", "love")), data=dataset))
pairs(dataset[runif(446)<.10,214:226],labels=[Link](dataset[,214:226]))
MEANS MATRIX
[Link] <- matrix(nrow=3, ncol=4)
ccc <- c("Belly","Poli","Admin")
for(col in 1:4){
switch (col,
"1" = for(i in 1:3) [Link][i,col] <- mean(Read[grp==ccc[i]]),
"2" = for(i in 1:3) [Link][i,col] <- mean(Dance[grp==ccc[i]]),
"3" = for(i in 1:3) [Link][i,col] <- mean(TV[grp==ccc[i]]),
"4" = for(i in 1:3) [Link][i,col] <- mean(Ski[grp==ccc[i]])
)}
[Link] <- aggregate(ximp,by=list(BWData_wn$eventnum),mean, [Link]=TRUE) #much easier
STATISTICS FOR COMBINED ROWS AND COLUMNS OF VARIABLES
meanvc <- vector(length=18)
sdvc <- vector(length=18)
for (i in 1:18){meanvc[i] <- mean([Link](dataset[1:nrow(dataset),c(seq(41+i,131+i,by=18))]))
sdvc[i] <- sd(stack(dataset[1:nrow(dataset),c(seq(41+i,131+i,by=18))])$values)}
ROW MEANS
sympavg <- matrix(0,nrow(zsymptoms),18)
for (i in 1:18){sympavg[,i] <- rowMeans(dataset[1:nrow(dataset),c(seq(i,18*6,by=18))], [Link] =TRUE)}
LAGGED DIFFERENCE SCORES
diff(x, lag=1)
MANAGING DATA SETS
STANDARDIZE A VARIABLE CONDITIONALLY:
x <- vector(length=121)
for(k in 1:121) {
if([Link][k,3]=="a") x[k] <- ([Link][k,4] - mean([Link][var1=="a"]))/stdev([Link][var1=="a"])
else x[k] <- ([Link][k] - mean([Link][var1=="b"]))/ stdev([Link][var1=="b"]) }
REPLACE CERTAIN VALUES WITH ‘NA’:
dataset[5,2] <- NA #replace a single cell with NA
for (k in 3:9){for (i in 1:121){if(dataset[i,k]==5) x[i,k] <- NA else dataset[i,k] <- dataset[i,k]}}
dataset[which(dataset[,3:9]==-999)] <- NA #much easier & faster than looping
[Link] <- [Link](winred[,c(33,64,94,123,152,184)]) #only works for matrices!
[Link][[Link](sumsymp)] <- NA #for every place sumsymp is NA, [Link] is now NA
RECODE DATA
new <- matrix(0,nrow(dataset),6)
new <- ((dataset[,22:27]==1)*1 + (dataset[,22:27]==2)*2 + (dataset[,22:27]==3)*8 +
(dataset[,22:27]==4)*3 + (dataset[,22:27]==5)*4 + (dataset[,22:27]==6)*7 +
(dataset[,22:27]==7)*5 + (dataset[,22:27]==8)*6 + (dataset[,22:27]==9)*9 +
(dataset[,22:27]==10)*7 + (dataset[,22:27]==11)*8 + (dataset[,22:27]==12)*8)
CHECK MISSING VALUES
which([Link](dataset)==TRUE, [Link]=TRUE)) #which subjects have missing data?
dim(which([Link](dataset)==TRUE, [Link]=TRUE) )[1] #how many NAs in dataset?
SUBSET DATA:
[Link] <- dataset[seas=="spring" | seas=="summer",] #only for spring & summer
dataset.subset2 <- dataset[var5 != NA,] #only non-missing on var5
dataset.subset2 <- dataset[dataset[,5] != NA,] #same thing
dataset3 <- dataset[,-c(5:20)] #all columns except 5:20
dataset4 <- dataset[,c(1,4,23)] #only columns 1,4, &23
[Link](categ2, daysbf, CONSV)[categ2!="other" & categ2 != "nosit",]
LOOK AT TWO COLUMNS OF DATA NEXT TO EACH OTHER:
dataset[,c(18,34)] #look at two columns side by side
cbind(var1, var3, var67) #if dataset is attached
dataset2 <- edit(dataset) #open in excel-like spreadsheet, saved in dataset2
[Link](dataset) #an alternative; opens in script editor windor
ORDER/SORT A DATASET
cbind(order(dataset$var1),dataset[order(dataset$var1),]) #1st column is original row#, 2nd is its value
a <- c(1,2,3,4,5,6,6,5,4,3,2)
b <- c(5,4,3,2,1,2,3,4,5,6,7)
c <- cbind(a,b)
c[order(a),]
RENAME 5th COLUMN IN DATA SET
names(dataset)[5] <- 'newname'
REARRANGE A SET OF COLUMNS
newdataset <- dataset[,c(1:13,seq(14,48,by=2),seq(15,49,by=2))]
USE [Link] NOT CBIND IF WANT TO USE VARIABLE NAMES FOR SOMETHING
dataset <- [Link](dataset[,],y[,])
CHANGE CLASS ATTRIBUTES IN A DATA SET
for (i in 1:dim(x)[2]){
if (class(x[,i])=="factor") class(x[,i]) <- "character" else class(x[,i]) <- class(x[,i])}
CHECK IF THERE ARE ANY REPEAT #S IN A VECTOR
dim([Link](vect))
dim([Link](unique(vect)))
LOOK AT THE ROW OF DATA THAT FITS SOME CRITERIA:
dataset[dataset$FAMNO==52444,]
MAKE “DATA1, DATA2, DATA3” BY LOOPING
for (i in 1:5) {
cat(paste("newz",i, sep=""),"<- data[(i*5000-4999):(i*5000),]",file="temp")
eval(parse(file="temp"))}
RETURNS “TRUE” IF ALL VALUES ARE REAL, “FALSE” IF 1+ MISSING
all([Link](x)==FALSE)
if (all([Link](y)==FALSE)==TRUE) k <- 5 else k <- 5-1 # k=5 if no missing in y, k=4 ow
TAKE THE POSITION OF AN ELEMENT AND USE IT AS A VARIABLE
a <- dataset[1:nrow(dataset),28:33]
set2 <- matrix(0,nrow(dataset),6)
for (i in 1:dim(a)[1]){set2[i,1:length(which(a[i,]==1))] <- which(a[i,]==1)}
GIVE VARIABLES IN DATA FRAME ALTERED NAMES FROM ANOTHER DATA SET
winsymp <- [Link](winsymp)
names(winsymp) <- paste("S",names(dataset[,42:149]),sep="")
RESHAPE DATA SET FROM “WIDE” TO “LONG” FORMAT
BWData <- reshape(Dataset, idvar=c("FAMNO","ID"),
varying=list(names(Dataset)[4:9],names(Dataset)[10:15],names(Dataset)[16:21],names(Dataset)[22:27],na
mes(Dataset)[28:33], names(Dataset)[h[1:6]], names(Dataset)[h[7:12]], names(Dataset)[h[13:18]],
names(Dataset)[h[19:24]], names(Dataset)[h[25:30]]), direction="long")
FUNCTIONS
SWITCH
for(i in c(-1:3,9,11)) print(switch(i, 1,2,3,4,5,6,7,8,99,10,"this is eleven"))
switch("a","a"=1,"cc"=2,"d"=3)
WRITE A FUNCTION WITH SET DEFAULTS
[Link] <- function(x, file="C:/temp/[Link]"){
pdf(file, horizontal=FALSE, height=5, pointsize=10)
for(k in 1:dim(x)[[2]]) {
hist(x[, k], main = paste("Histogram of" , names(x[k])), xlab = names(x[k]))} [Link]() }
FACTOR ANALYSIS WITH BINARY DATA; (POLYCOR LIBRARY)
library(polycor)
#change numeric 0/1’s to factor scores (binary data, to run polychoric corr)
[Link] <- matrix([Link](score),nrow=5000,ncol=40,byrow=F)
[Link] <- hetcor([Link][,1:10],ML=FALSE)$correlations
factanal(covmat = [Link], factors=1,lower=.05, start=[Link], nstart=100)
VIEW & IMPUTE MISSING VALUES (NORM LIBRARY)
library(norm) #use “norm” only if all vars normal; if not, use “mix” or “cat”
a <- [Link]([Link](data_wn))
summary(a); a$nmis; a$r
cat("Total subject missing:"); cat(" ", sum([Link](rownames(a$r)[2:length(rownames(a$r))])),"\n")
cat("Total values missing:"); cat(" ", sum(a$nmis),"\n")
thetahat <- [Link](a) #use expectation maximization (EM) algorithm
rngseed(599829)
ximp <- [Link](a,thetahat,data_wn)
GRAPHING
PLOT LEVERAGES WITH TEXT:
[Link] <- lm(var1~var2+var3)
x <- [Link]([Link])
plot(hat(x), type="n", ylab="Leverages")
text(hat(x), labels=[Link](SUBNUM))
LINEPLOT OF MEANS MATRIX
matplot(1:4,t([Link]),type="l",axes=F)
par(lwd=5)
axis(1,1:4,c("Read","Dance","TV","Ski"))
axis(2)
legend(3.5,9,c("Belly","Poli","Admin"),lty=1:3,ncol=1)
ADD NEW POINTS ONTO EXISTING GRAPH
matplot(x, y, pch=19,type="b",main="Change in Var",xlab="Degree",ylab="Var",ylim=c(-.1,.6))
matpoints(x, y2, pch=22,type="b",col=”red”)
INCLUDE TEXT AS POINTS ON A GRAPH:
plot(x,y, type="n", xlab="scaled after", ylab="scaled before")
text(x,y, [Link](subnum))
matplot(abs(mean1[1]-mean1[2:7]), type="c", lty=2, ylim=c(0,.05),col=1)
text(1:6,abs(mean1[1]-mean1[2:7]), "HELLO", font=4, col=1) #”HELLO” at each point of graph
MAKE MATLINES HAVE RANDOM COLORS (ALL 657 OF THEM)
cool <- c(colors())
for (i in 2:10) {
cat("matlines(abs(",paste("mean",i,"[1]-", sep=""),paste("mean",i,"[8:13]", sep=""),"),
pch=19,type='b',col= sample(cool, 1, replace = FALSE))",file="temp")
eval(parse(file="temp"))}
SEE FUNCTION “PAR” FOR TONS OF GRAPHING PARAMETERS
?par
demo(plotmath) #gives you how to get many symbols in R
example(points) # gives lots of symbols
SAVE ALL GRAPHING OBJECTS YOU MAKE UNTIL USE “[Link]” CMD
pdf("C:/temp/[Link]", horizontal=FALSE, height=5, pointsize=10)
matplot(cor(data1[,c(1,8:13)])[2:7,1])
[Link]()
[Link](file="C:/Matts Folder/[Link]", device=pdf) #or more simply, just this
?device #see all the possible devices
CHANGE THE AXIS TICK MARK LABELS TO DEFAULT FOR Y AND A:F FOR X
matplot(1:6, x[c(1:6)], type="b", ylim=c(.75,.9), [Link]=.85,lwd=3, pch=19,xlim=c(.5,6),axes=FALSE)
axis(1,labels=c("a","b","c","d","e","f"))
axis(2)
MORE CONTROL OVER YOUR LABEL LOCATIONS
mtext("X", side=2, padj=-1,adj=.83) #PADJ
FIND THE X & Y LIMITS ON YOUR GRAPH, FOR USE IN PLACING ITEMS IN GRAPH
lim <- par("usr")
text(lim[1]+(.46*(lim[2]-lim[1])),lim[3]+(.93*(lim[4]-lim[3])),"Death", adj=1)
text(lim[1]+(.5*(lim[2]-lim[1])),lim[3]+(.93*(lim[4]-lim[3])),"vs", adj=0.5)
text(lim[1]+(.54*(lim[2]-lim[1])),lim[3]+(.93*(lim[4]-lim[3])),"Failure", adj=0)
QQ PLOT
pdf("C:/temp/[Link]", horizontal=FALSE, height=5, pointsize=10)
for (k in 1:10){qqplot(liab[,k],rnorm(10000))}
[Link]()
PLOT WITH GREEK CHARACTERS, HATS, ETC
?plotmath
#placed on same line
text(7,.3,substitute(paste(hat(eta)^2,"=",x,sep=""), list(x=effectsizes[1,1])),adj=0)
#ALTERNATIVE
text(-.5,-.5, expression(bold(M[1])*":"*hat(MPG)))
MOVE TO ONE PARTICULAR FIGURE IN MULTIPLE FIGURE ENVIRONMENT
par(mfg=c(2,1)) #goes to figure in row 2, col 1
text(5,.1,"hi") #places “hi” there
