rm(list = ls(all = TRUE))
install.packages("ggplot2")
library("ggplot2", lib.loc="~/R/win-library/3.1")
# 
library("ggplot2", lib.loc="~/R/win-library/3.1")
setwd("TYPE FILE LOCATION HERE")
#
LandH <- read.table(file = "TYPE NAME OF TEXT FILE HERE", header = TRUE, dec = ".")
LandH
LandH$Dil<-LandH$Di

LandH$fTr <- factor(LandH$Treatment)
LandH$fTr

M1 <- lm(LandH$Gr~LandH$Dil +LandH$Treatment +LandH$Dil :LandH$Treatment )
M2 <- lm(LandH$Gr~LandH$Dil +LandH$Treatment )

summary(M1)

op<-par(mfrow=c(2,2))
plot(M1)
par(op)

M2 <- lm(LandH$Gr~LandH$Dil +LandH$Treatment )
summary(M2)
anova(M1,M2)

Lgr<- LandH[LandH$fTr=="gr",]
mgr <- lm(Lgr$Gr~Lgr$Dil  )
summary(mgr)

a<-predict(mgr, interval="confidence")
Lvi<- LandH[LandH$fTr=="vi",]
mvi <- lm(Lvi$Gr~Lvi$Dil  )
summary(mvi)

plot(y=LandH$Gr, x=LandH$Dil,pch=rep(c(1,20),each=12) ,
     xlab="Dilution (percentage natural water)",
     ylab="App growth rate",main= "a Modified Grazing experiment")

abline(mgr,lty=1)
abline(mvi,lty=2)

a<-predict(mgr, interval="confidence")
b<-predict(mvi, interval="confidence")

# is not the nicest graph 
lines(Lgr$Dil, a[,2], lty=2)
lines(Lgr$Dil, a[,3], lty=2)
lines(Lvi$Dil, b[,2], lty=3)
lines(Lvi$Dil, b[,3], lty=3)

legend.txt<- c("Grazing","Viral lysis")
legend("topright",legend = legend.txt,pch=c(1,20),lty=c(1:2))

# a more professional looking graph of the experiment

library("ggplot2", lib.loc="~/R/win-library/3.1")
qplot(LandH$Dil,LandH$Gr,color=LandH$fTr,shape=LandH$fTr,
      geom=c("point","smooth"),method=lm, formula=y~x,
      xlab="Dilution (percentage natural water)",ylab="App growth rate",
      main= "a Modified Grazing experiment")