#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#        REVISION
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#Two-WAY ANALYSIS OF VARIANCE 
#      WITH REPLICATES
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#DATA SET
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
poisons.df
attach(poisons.df)
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#DIAGNOSTIC PLOTS
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 par(mfrow=c(3,2))
 plot.design(poisons.df)
 plot.design(poisons.df,fun=median)
 plot.factor(poisons.df)
 attach(poisons.df)
 interaction.plot(treatment,poison,surv.time)
 interaction.plot(treatment,poison,surv.time,fun=median)

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#ANOVA TABLE
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 poisons.aov_aov(surv.time~poison*treatment,poisons.df)
 summary(poisons.aov)
                   
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#ESTIMATED COEFFICIENTS
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 summary.lm(poisons.aov)
model.tables(poisons.aov)


#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#RESIDUALS
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  par(mfrow=c(1,2))
  hist(resid(poisons.aov))
  qqnorm(resid(poisons.aov))

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#TRANSFORMATIONS
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  par(mfrow=c(1,1))
  plot(fitted(poisons.aov),resid(poisons.aov))
 poisons.aovt_aov(1/surv.time~poison*treatment,poisons.df)
 summary(poisons.aovt)

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#MULTIPLE COMPARISONS
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 mca.poisons_multicomp(poisons.aovt,focus="poison")
 plot(mca.poisons)
 mca.poisons