Nothing
getSummary.mclogit <- function(obj,
alpha=.05,
rearrange=NULL,
...){
smry <- summary(obj)
N <- obj$N
coef <- smry$coefficients
varPar <- smry$varPar
lower.cf <- qnorm(p=alpha/2,mean=coef[,1],sd=coef[,2])
upper.cf <- qnorm(p=1-alpha/2,mean=coef[,1],sd=coef[,2])
coef <- cbind(coef,lower.cf,upper.cf)
colnames(coef) <- c("est","se","stat","p","lwr","upr")
if(length(varPar)){
se.log.varPar <- varPar[,1]*varPar[,2]
lower.log.varPar <- qnorm(p=alpha/2,mean=log(varPar[,1]),sd=se.log.varPar[2])
upper.log.varPar <- qnorm(p=1-alpha/2,mean=log(varPar[,1]),sd=se.log.varPar[2])
varPar <- cbind(varPar,exp(lower.log.varPar),exp(upper.log.varPar))
colnames(varPar) <- c("est","se","stat","p","lwr","upr")
rownames(varPar) <- paste("Var(",rownames(varPar),")",sep="")
}
if(length(rearrange)){
coef.grps <- lapply(rearrange,function(ii){
if(is.character(ii) && !all(ii %in% rownames(coef)))
stop("coefficient(s) ",dQuote(unname(ii[!(ii %in% rownames(coef))]))," do not exist")
structure(coef[ii,],
dimnames=list(names(ii),dimnames(coef)[[2]])
)
})
grp.titles <- names(rearrange)
coef.grps <- do.call(memisc::collect,coef.grps)
coef <- array(NA,dim=c(
dim(coef.grps)[1] + NROW(varPar),
dim(coef.grps)[2],
dim(coef.grps)[3]
))
coef[seq(dim(coef.grps)[1]),,] <- coef.grps
if(length(varPar))
coef[dim(coef.grps)[1]+seq(nrow(varPar)),,1] <- varPar
dimnames(coef) <- list(
c(dimnames(coef.grps)[[1]],rownames(varPar)),
dimnames(coef.grps)[[2]],
grp.titles
)
}
else {
.coef <- coef
coef <- matrix(NA,nrow=nrow(.coef)+NROW(varPar),ncol=ncol(.coef))
coef[seq(nrow(.coef)),] <- .coef
if(length(varPar))
coef[nrow(.coef)+seq(nrow(varPar)),] <- varPar
rownames(coef) <- c(rownames(.coef),rownames(varPar))
colnames(coef) <- colnames(.coef)
}
phi <- smry$phi
LR <- smry$null.deviance - smry$deviance
df <- obj$model.df
deviance <- deviance(obj)
if(df > 0){
p <- pchisq(LR,df,lower.tail=FALSE)
L0.pwr <- exp(-smry$null.deviance/N)
LM.pwr <- exp(-smry$deviance/N)
McFadden <- 1- smry$deviance/smry$null.deviance
Cox.Snell <- 1 - exp(-LR/N)
Nagelkerke <- Cox.Snell/(1-L0.pwr)
}
else {
LR <- NA
df <- NA
p <- NA
McFadden <- NA
Cox.Snell <- NA
Nagelkerke <- NA
}
ll <- obj$ll
AIC <- AIC(obj)
BIC <- AIC(obj,k=log(N))
sumstat <- c(
phi = phi,
LR = LR,
df = df,
#p = p,
logLik = ll,
deviance = deviance,
McFadden = McFadden,
Cox.Snell = Cox.Snell,
Nagelkerke = Nagelkerke,
AIC = AIC,
BIC = BIC,
N = N
)
list(call=obj$call,
coef=coef,
contrasts = obj$contrasts,
xlevels = obj$xlevels,
sumstat=sumstat)
}
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