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# kensyn Package. Knowledge synthesis in Agriculture : from experimental network to meta-analyisis.
# Others. Network of experiments: Wheat varieties with different crop managements
# Francois Piraux (Arvalis) 2017-11-01
# R version 3.1.3
library(lme4) # version 1.1-10
library(emmeans)
library(car) # version 2.0-25
# required : pbkrtest, lmerTest, multcompView
# loading data
DF <- wheat_var_itk
DF$variete <- factor(DF$variete, levels=unique(DF$variete))
DF$experimentation <- as.factor(DF$experimentation)
str(DF)
summary(DF)
table(DF$variete, DF$conduite)
## fiting the model
options(contrasts=c("contr.sum","contr.poly"))
res.lmer <- lmer(rendement ~ conduite*variete + (1|experimentation) + (1|experimentation:conduite) + (1|experimentation:variete), data=DF, na.action=na.exclude)
res.lmer
## validation of the model
plot(fitted(res.lmer),residuals(res.lmer), abline(h=0))
hist(residuals(res.lmer))
## anova type III
Anova(res.lmer, test="F", type="III")
# ajusted mean and contrasts
# mean per crop management
itk.lsm <- emmeans(res.lmer, ~ conduite)
itk.lsm
confint(contrast(itk.lsm, method="tukey"))
# mean per variety
variete.lsm <- emmeans(res.lmer, ~ variete)
variete.lsm
# mean per variety per crop management
intera.lsm <- emmeans(res.lmer, ~ variete|conduite)
intera.lsm
# end of file
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