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# Simultaneous confidence intervals for linear contrasts
#
# Author: FrankKonietschke
###############################################################################
multcomp.wrapper <- function(model, hypotheses, alternative, rhs=0, alpha, factorC ) {
type<-""
if (any(factorC== c("Tukey", "Dunnett", "Sequen",
"Williams", "Changepoint", "AVE", "McDermott", "Marcus", "UmbrellaWilliams"))) {
eval(parse(text=paste("type <- mcp(",factorC,"=hypotheses)")))
} else {
eval(parse(text=paste("type <- mcp(",factorC,"=hypotheses)")))
}
glhtObj <- glht(model, linfct = type, rhs=rhs, alternative=alternative)
summaryGLHT <- summary(glhtObj)
pvalues <- summaryGLHT$test$pvalues
estimates <- summaryGLHT$test$coefficients
confint <- confint(glhtObj,level=(1-alpha))$confint
rejected1 <- (pvalues < alpha)
confi <- cbind(confint)
print(cbind(confi,pvalues))
return(list(adjPValues=pvalues,rejected=rejected1,confIntervals= confi,
errorControl = new(Class='ErrorControl',type="FWER",alpha=alpha)))
}
mutoss.multcomp<- function() { return(new(Class="MutossMethod",
label="Multiple Contrast Tests",
errorControl="FWER",
callFunction="multcomp.wrapper",
output=c("adjPValues", "rejected","confIntervals","errorControl"),
info="<h2>Parametric multiple contrast tests and simultaneous confidence intervals</h2>
<p>With this function, it is possible to compute simultaneous tests and confidence intervals for general linear hypotheses in parametric models<p>
<p></p>
<h3>Reference:</h3>
<ul>
<li>Frank Bretz, Alan Genz and Ludwig A. Hothorn \"<i>On the numerical availability of multiple comparison procedures.</i>\" Biometrical Journal, 43(5), 645-656. , 2001.</li>
</ul>",
parameters=list(model=list(type="ANY"),
hypotheses=list(type="ANY"),
alpha=list(type="numeric"),
alternative=list(type="character", label="Alternative", choices=c("two.sided", "less", "greater")),
factorC=list(type="character", label="Factor for Comparison", fromR="FactorVar")
)
)) }
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