Nothing
summary.fit.bivar<-function(object,level=0.95,...){
x <- object
if (!is.element("fit.bivar", class(x)))
stop("Argument 'x' must be an object of class \"fit.bivar\".")
ci.level <- level
if (ci.level <= 0 || ci.level >= 1)
stop("'ci.level' must be within 0 and 1")
coeff <- x$fixef
lvm<-x$levelmod
vcov <- as.matrix(x$vcov)
coeff <- as.numeric(coeff)
coef.se <- sqrt(diag(vcov))
tval <- coeff/coef.se
tvalci <- qt((1 - ci.level)/2, df=x$studynum-2 , lower.tail = FALSE)
pvalue <- 2 * (1 - pt(abs(tval),df=x$studynum-2))
ci.lb <- coeff - tvalci * coef.se
ci.ub <- coeff + tvalci * coef.se
tabfixed <- cbind(coeff, coef.se, x$studynum-2, tval, pvalue, 1-ci.level, ci.lb, ci.ub)
colnames(tabfixed)<-c("coefficient","standard error", "df", "tval", "p", "alpha", "lower", "upper")
if (is.null(x$mods)){
cat("Fit bivariate model of Reitsma et al.(2005) without covariate.\n")
names(x$fixef)[1:2]<-c("logit_sensitivity","logit_specificity")
}
else if (!is.null(x$bi.both)){
cat("Fit bivariate model of Reitsma et al.(2005) with covariate",x$mf.mods,"that affects both sensitivity and specificity.\n")
for (i in 1:length(lvm)){
names(x$fixef)[i]<-paste0("logit_sensitivity_",lvm[i])
names(x$fixef)[length(lvm)+i]<-paste0("logit_specificity_",lvm[i])
}
}
else if (!is.null(x$bi.sen)){
cat("Fit bivariate model of Reitsma et al.(2005) with covariate",x$mf.mods,"that affects only sensitivity.\n")
names(x$fixef)[1]<-paste0("logit_specificity_",lvm[1])
names(x$fixef)[2]<-paste0("logit_sensitivity_",lvm[1])
for (i in 3:(length(lvm)+1)){
names(x$fixef)[i]<-paste0("logit_sensitivity_",lvm[i-1])
}
}
else if (!is.null(x$bi.spe)){
cat("Fit bivariate model of Reitsma et al.(2005) with covariate",x$mf.mods,"that affects only specificity.\n")
names(x$fixef)[1]<-paste0("logit_sensitivity_",lvm[1])
names(x$fixef)[2]<-paste0("logit_specificity_",lvm[1])
for (i in 3:(length(lvm)+1)){
names(x$fixef)[i]<-paste0("logit_specificity_",lvm[i-1])
}
}
rownames(tabfixed)<-names(x$fixef)
tabvcov<-x$vcov
rownames(tabvcov)<-colnames(tabvcov)<-names(x$fixef)
cat("Fixed-effects coefficients:", "\n", sep = "")
print(tabfixed)
cat("\n")
cat("\n")
cat("Covariance Matrix of Fixed Effect Parameter Estimates: \n")
print(tabvcov)
cat("\n")
}
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