install.packages("car")
library (car)
getwd()
####Get a working directory
##Mean if there is more than one treatment
mean.growth<-tapply(task1$artemia,list(task1$treatment,task1$flow),mean)
mean.growth
##SD
sd.growth<-tapply(task1$artemia,list(task1$treatment,task1$flow),sd)
sd.growth
##Number of Samples (Pop Size)
n.growth<-tapply(task1$artemia,list(task1$treatment,task1$flow),length)
n.growth
##SE
se.growth<-sd.growth/sqrt(n.growth)
se.growth
## To plot the barplot we will need to work out the Mean,Sd,n,Se
barplot(mean.growth,beside=T,legend=F,ylim=c(0,100))
#### Assign limits,arrows,scale and labels
##mids<-barplot(Data to plot,ylim=c(lower Value,Higher Value), xlab = "X Axis Name",
##            ylab = "Y Axis Name")

mids<-barplot(mean.artemia,beside=T,legend=TRUE,ylim=c(0,10), xlab = "Water Velocity",
              ylab = "larvae Abundance")
##arrows(Name of barplot,mean.growth+se.growth,name of barplot,mean.growth-se.growth,code=3,angle=90,length=0.1)
arrows(mids,mean.growth+se.growth,mids,mean.growth-se.growth,code=3,angle=90,length=0.1)
##wilcox.test(response varable ~ Explanatory variable)
##wilcox.test(File$column~File$Column)
with(task1, interaction.plot(treatment,flow,artemia))
with(task1, leveneTest(artemia~treatment*flow))
with(task1, shapiro.test(artemia))
##levene test for homogeneity, <0.05 ... homo, okay
##shapiro test for normality, <0.05 ... not normal, needs transforming
task1$sqrt.abund<-sqrt(task1$artemia)
View(task1)
shapiro.test(task1$sqrt.abund)
##shapiro still <0.05, req transformation ... log
task1$log.abund<-log(task1$artemia)
View(task1)
shapiro.test(task1$log.abund)
##after 2 transformations non parametric equivalent must be used...
## could use KW non Para test (stefan doesnt want to)
## using 2way anova instead
with(task1, aov(sqrt.abund~treatment*flow))
AovSummary<-with(task1, aov(sqrt.abund~treatment*flow))
summary(AovSummary)
TukeyHSD<-TukeyHSD(task1$sqrt.abund~task1$treatment*task1$flow)

posthoc<-TukeyHSD(task1,"task1$sqrt.abund")
plot(posthoc)