library(readr)
DarwinCornData <- read_csv("C:/Users/a84dcs/Desktop/DarwinCornData.csv")
View(DarwinCornData)
# Fixed effect model - Inference to 4 pots only
PotModelFixed<-lm(Height~Pot*Pollination, data=DarwinCornData)
plot(PotModelFixed)
hist(resid(PotModelFixed))
# Comment on the assumptions
anova(PotModelFixed)
#--------------------------------------------
# Mixed effect model - Inference to population of pots
# Use results of fixed effect model
Fpot<-51.352/7.449   #MSPollination / MSPot*Pollination 
prF <- 1-pf(Fpot,1,3)
prF    # Compare to fixed effect result
#--------------------------------------------
# Use lmer to run mixed effect model
library("lme4", lib.loc="~/R/win-library/3.3")
PotModelMixed<-lmer(Height~Pollination + (1 | Pot), data=DarwinCornData)
plot(PotModelMixed)
hist(resid(PotModelMixed))
#Comment on assumptions
#Compare to diagnostics for fixed model
summary(PotModelMixed)   #Note the residual variance
anova(PotModelMixed, type= 1)
# Note MSPollination
# Calculate MSPollination / MSresidual 
# Compare your calculation to anova F value
# Calculate prF, using 1 and 3 df
# Compare F and prF for Pollination for:
# Fixed effect model
# Mixed effect model from fixed effect SS
# Mixed effect model from mixed effect (lmer) model
#------------------------------------------------
# Now do the analysis using Pairs instead of Pots