Applying post-fit procedures on spaMM results
Packages implementing post-fit procedures define helper functions that may handle a limited range of classes of fit results. This documentation topic gives further directions to apply some post-fit procedures that handle objects of class HLfit. For other procedures, spaMM results may or may not be handled correctly by default. In such cases, diagnosing a failure in a debugging session may suggest a simple solution (such as providing the coef. argument to multcomp::glht).
For multiple comparison procedures by multcomp::glht, one has to explicitly give the argument coef.=fixef.HLfit (see Examples; fixef.HLfit is the spaMM method for the generic function fixef);
For DHARMa plots, see plot.HLfit;
For using RLRsim::RLRTSim(), see get_RLRTSim_args.
if (requireNamespace("multcomp", quietly = TRUE)) {
library(multcomp)
set.seed(123)
irisr <- cbind(iris,id=sample(4,replace=TRUE,size=nrow(iris)))
irisfit <- fitme(Petal.Length~ Species +(1|id), data=irisr, family=Gamma(log))
summary(glht(irisfit,mcp("Species" = "Tukey"), coef.=fixef.HLfit))
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