14-poissonLMM.R

dev.off() # Reset previous graphical pars
# New GLM, updated from the first by estimating with REML
GLM2 <- update(GLM, .~., method = "REML")
# Plot side by side, beta with respective SEs
plot(coef(GLM2), xlab = "Fixed Effects", ylab = expression(beta), axes = F,
     pch = 16, col = "black", ylim = c(-.9,2.2))
stdErrors <- coef(summary(GLM2))[,2]
segments(x0 = 1:6, x1 = 1:6, y0 = coef(GLM2) - stdErrors, y1 = coef(GLM2) + stdErrors,
         col = "black")
axis(2)
abline(h = 0, col = "grey", lty = 2)
axis(1, at = 1:6,
     labels = c("Intercept", "Rack", "Nutrient (Treated)","AMD (Unclipped)","Status (PP)",
                "Status (Transplant)"), cex.axis = .7)
# LMM
points(1:6 + .1, fixef(finalModel), pch = 16, col = "red")
stdErrorsLMM <- coef(summary(finalModel))[,2]
segments(x0 = 1:6 + .1, x1 = 1:6 + .1, y0 = fixef(finalModel) - stdErrorsLMM,
         y1 = fixef(finalModel) + stdErrorsLMM, col = "red")
# Legend
legend("topright", legend = c("GLM","LMM"), text.col = c("black","red"), bty = "n")