## ------------------------------------------------------------------------ HABITAT <- factor(c('Mixed','Gipps.Manna','Gipps.Manna', 'Gipps.Manna','Mixed','Mixed','Mixed','Mixed')) GST <- c(3.4, 3.4, 8.4, 3.0, 5.6, 8.1, 8.3, 4.6) EYR <- c(0.0, 9.2, 3.8, 5.0, 5.6, 4.1, 7.1, 5.3) ## ---- results='markup'--------------------------------------------------- MACNALLY <- data.frame(HABITAT, GST, EYR) MACNALLY ## ---- results='markup'--------------------------------------------------- row.names(MACNALLY) <- c('Reedy Lake', 'Pearcedale', 'Warneet', 'Cranbourne', 'Lysterfield', 'Red Hill', 'Devilbend', 'Olinda') MACNALLY ## ---- results='markup'--------------------------------------------------- download.file('http://www.flutterbys.com.au/stats/downloads/data/macnally.csv', '~/macnally.csv') ## ---- results='markup'--------------------------------------------------- getwd() ## ---- results='markup'--------------------------------------------------- getwd() ## ---- results='markup', eval=FALSE--------------------------------------- ## #Go to a subdirectory of the current directory ## setwd('data') ## #Go to the parent directory ## setwd('..') ## #Go to a sibling directory ## setwd('../data') ## ---- results='markup', eval=TRUE, tidy=FALSE---------------------------- MACNALLY <- read.csv( '/home/murray/Work/SUYR/downloads/data/macnally.csv', header=T, row.names=1, strip.white=TRUE) MACNALLY ## ---- results='markup'--------------------------------------------------- MACNALLY <- read.csv('../data/macnally.csv', header=T, row.names=1, strip.white=TRUE) getwd() #to see the current working directory MACNALLY summary(MACNALLY) str(MACNALLY) glimpse(MACNALLY) MACNALLY[1:10,1:5] MACNALLY$GST ## ---- results='markup'--------------------------------------------------- MACNALLY <- read.table('../data/macnally.txt', header=T, row.names=1, sep='\t', strip.white=TRUE) MACNALLY ## ---- results='markup', eval=FALSE--------------------------------------- ## write.table(MACNALLY, '../data/macnally.csv', ## quote=FALSE, row.names=TRUE, sep=',') ## ---- results='markup'--------------------------------------------------- library(XLConnect) wb=loadWorkbook("../data/macnally.xlsx") macnally=readWorksheet(wb,sheet="Sheet1",header=TRUE) head(macnally) ##OR library(gdata) macnally<- read.xls('../data/macnally.xlsx',sheet='Sheet1',header=TRUE) head(macnally) ## ---- results='markup'--------------------------------------------------- library(XLConnect) wb=loadWorkbook("../data/macnally1.xlsx", create=TRUE) createSheet(wb, name='MacNally') writeWorksheet(wb, macnally, sheet='MacNally') saveWorkbook(wb) ## ---- results='markup', eval=FALSE--------------------------------------- ## save(MACNALLY, file='../data/macnally.RData') ## ---- results='markup', eval=FALSE--------------------------------------- ## #calculate the mean GST ## meanGST <- mean(MACNALLY$GST) ## #display the mean GST ## meanGST ## #save the MACNALLY data frame as well as the mean GST object ## save(MACNALLY, meanGST, file='macnallystats.RData') ## ---- results='markup', eval=FALSE--------------------------------------- ## load(file='../data/macnally.RData') ## ---- results='markup', eval=TRUE---------------------------------------- dump('MACNALLY','') ## ---- results='markup', eval=FALSE--------------------------------------- ## dump('MACNALLY','') ## ---- results='markup'--------------------------------------------------- DATA <- data.frame(LOCATION=gl(3,2,6, paste('Location',1:3)), TREATMENT = gl(2,3,6, LETTERS[1:2]), Y=rnorm(6,10,2) ) DATA ## ------------------------------------------------------------------------ HABITAT <- factor(c('Mixed','Gipps.Manna','Gipps.Manna','Gipps.Manna','Mixed', 'Mixed','Mixed','Mixed')) GST <- c(3.4, 3.4, 8.4, 3.0, 5.6, 8.1, 8.3, 4.6) EYR <- c(0.0, 9.2, 3.8, 5.0, 5.6, 4.1, 7.1, 5.3) MACNALLY <- data.frame(HABITAT, GST, EYR) ## ---- results='markup'--------------------------------------------------- ls() ## ---- results='markup'--------------------------------------------------- str(DATA) ## ---- results='markup'--------------------------------------------------- LOCATION DATA$LOCATION ## ---- results='markup'--------------------------------------------------- with(DATA, LOCATION) ## ---- results='markup', eval=FALSE--------------------------------------- ## MACNALLY[rows,columns] ## ---- results='markup', eval=FALSE--------------------------------------- ## MACNALLY[rows,columns] ## ---- results='markup'--------------------------------------------------- MACNALLY[5,2] ## ---- results='markup'--------------------------------------------------- MACNALLY[5,] MACNALLY[,2] ## ---- results='markup'--------------------------------------------------- MACNALLY[1:5,] ## ---- results='markup'--------------------------------------------------- MACNALLY[,c(1,3)] ## ---- results='markup'--------------------------------------------------- MACNALLY[,c('GST','EYR')] ## ---- results='markup'--------------------------------------------------- MACNALLY[MACNALLY$GST>3,] ## ---- results='markup'--------------------------------------------------- MACNALLY[MACNALLY$GST>3 & MACNALLY$HABITAT=='Mixed',] ## ---- results='markup', echo=FALSE--------------------------------------- str(subset.data.frame) ## ---- results='markup'--------------------------------------------------- subset(MACNALLY, select=c(1,3)) ## ---- results='markup'--------------------------------------------------- subset(MACNALLY, select=c(GST,EYR)) #OR subset(MACNALLY, select=GST:EYR) ## ---- results='markup'--------------------------------------------------- subset(MACNALLY, select=-GST) ## ---- results='markup'--------------------------------------------------- subset(MACNALLY, GST>3) ## ---- results='markup'--------------------------------------------------- subset(MACNALLY, GST>3 & HABITAT=='Mixed') ## ---- results='markup', tidy=FALSE--------------------------------------- subset(MACNALLY, GST>3 & HABITAT=='Mixed', select=c(HABITAT,EYR)) ## ---- results='markup', tidy=FALSE--------------------------------------- subset(MACNALLY, HABITAT %in% c('Mixed','Gipps.Manna')) ## ---- results='markup', eval=TRUE, tidy=FALSE---------------------------- MACNALLY <- read.csv('../data/macnally.csv', header=T, row.names=1, strip.white=TRUE) MACNALLY ## ---- results='markup', tidy=TRUE---------------------------------------- library(plyr) ddply(MACNALLY, ~HABITAT, summarize, GST=mean(GST)) ## ---- results='markup', tidy=TRUE---------------------------------------- library(plyr) ddply(MACNALLY, ~HABITAT, numcolwise(mean)) ## ---- results='markup', tidy=TRUE---------------------------------------- library(plyr) meansd <- function(x) { data.frame(Mean=numcolwise(mean)(x), SD=numcolwise(sd)(x)) } ddply(MACNALLY, ~HABITAT,meansd) ## ---- results='markup', tidy=TRUE---------------------------------------- library(plyr) ddply(MACNALLY, ~HABITAT,function(x) { data.frame(Mean=numcolwise(mean)(x), SD=numcolwise(sd)(x)) })