#' Formats for Bayesian Binomial Test
# Show
#' @keywords internal
#' @export
#' @rdname dfba_binomial_method
#' @param object An object of class \code{\linkS4class{dfba_binomial_out}}
setMethod("show", "dfba_binomial_out", function(object) {
cat("Prior and Posterior Beta Shape Parameters:","\n")
cat("========================\n")
cat(" ", "Prior Beta Shape Parameters","\n")
cat(" ", sprintf("%-10s", "a0"), "\t", "b0", "\n")
cat(" ", sprintf("%-10g", object$a0), "\t", object$b0, "\n")
cat(" ", "Posterior Beta Shape Parameters:"," ","\n")
cat(" ", sprintf("%-10s", "a_post"), "\t", "b_post", "\n")
cat(" ", sprintf("%-10g", object$a_post), "\t", object$b_post, "\n")
cat("Estimates of the Binomial Population Rate Parameter", "\n")
cat("========================\n")
cat(" ", "Posterior Mean", "\n")
cat(" ", object$phimean, "\n")
cat(" ", "Posterior Median", "\n")
cat(" ", object$phimedian, "\n")
cat(" ", "Posterior Mode", "\n")
cat(" ", object$phimode, "\n")
cat(" ", paste0(round(object$prob_interval*100), "% Equal-tail interval limits:"), "\n")
cat(" ",
sprintf("%-12s", "Lower Limit"),
"\t",
"Upper Limit",
"\n")
cat(" ",
sprintf("%-12g",
object$eti_lower),
"\t",
object$eti_upper,
"\n")
cat(" ", paste0(round(object$prob_interval*100), "% Highest-density interval limits:"), "\n")
cat(" ",
sprintf("%-12s",
"Lower Limit"),
"\t",
"Upper Limit",
"\n")
cat(" ",
ifelse(is.na(object$hdi_lower),
sprintf("%-12s", "NA*"),
sprintf("%-12g", object$hdi_lower)
),
"\t",
ifelse(is.na(object$hdi_upper),
"NA*",
object$hdi_upper),
"\n\n",
ifelse(is.na(object$hdi_lower), "Note: this beta distribution has no defined highest-density interval\n
", "\n"))
})
# Plot
#' @export
#' @rdname dfba_binomial_method
#' @param x An object of class \code{\linkS4class{dfba_binomial_out}}
#' @param plot.prior Show prior distribution (default = TRUE)
setMethod("plot",
signature("dfba_binomial_out"),
function(x,
plot.prior=TRUE){
x.data<-seq(0, 1, 1/1000)
y.predata<-dbeta(x.data, x$a0, x$b0)
y.postdata<-dbeta(x.data, x$a_post, x$b_post)
xlab <- "phi"
ylab <- "Probability Density"
if (plot.prior==FALSE){
plot(x.data,
y.postdata,
type="l",
xlab=xlab,
ylab=ylab)
} else {
plot(x.data,
y.postdata,
type="l",
xlab=xlab,
ylab=ylab,
main=expression("--"~"Prior"~ - "Posterior"))
lines(x.data,
y.predata,
lty=2)
}
})
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