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#' Print methods for the different object types
#'
#' Printing \code{pim}, \code{pim.environment}, \code{pim.formula} and
#' \code{pim.poset} objects.
#'
#' @param x the object
#' @param digits an integer that defines the number of digits printed
#' @param n number of observations shown by \code{print}
#' @param show.vcov a logical value indicating whether the variance-
#' covariance matrix should be shown or not. Defaults to \code{FALSE}
#' @param ... arguments passed to other methods. Currently ignored
#'
#' @return invisible NULL
#' @include pim-class.R pim.environment-class.R pim.formula-class.R pim.poset-class.R
#'
#' @examples
#' data(FEVData)
#' Model <- pim(FEV~ Smoke*Sex , data=FEVData)
#' print(Model)
#' print(penv(Model))
#' # You get the drift
#'
#' @importFrom utils head
#' @export
setGeneric('print')
#------------------------
# print method for pim
#------------------------
print.pim <- function(x, digits = max(3L, getOption("digits") - 3L),
show.vcov = FALSE, ...){
orig <- paste(deparse(x@formula@orig))
coefs <- coef(x)
vc <- vcov(x)
cat('\nProbabilistic Index Model:\nFormula: ',orig,
"\nType: ", x@model,
"\nLink: ", x@link,
"\n\n")
if (length(coefs)) {
cat("Coefficients:\n")
print.default(format(coefs, digits = digits), print.gap = 2L,
quote = FALSE)
}
else cat("No coefficients\n")
cat("\n")
if(show.vcov){
cat("VCOV matrix:\n")
print.default(format(vc, digits = digits), print.gap = 2L,
quote=FALSE)
}
invisible(NULL)
}
# show method for pim
setMethod('show',
'pim',
function(object){print(object, show.vcov = FALSE)})
#' @rdname print
# print method for pim
setMethod('print',
'pim',
print.pim)
#------------------------
# print method for pim.environment
#------------------------
print.pim.environment <- function(x, digits = max(3L, getOption("digits") - 3L), n = 6L, ...){
no <- nobs(x)
nc <- length(classes(x))
complete <- is.complete(x)
ww <- if(complete) "with" else "without"
cat('\nPIM environment with',no,
'observations of',nc,'variables.\n\n')
print(head(as.data.frame(x), n = n))
if(n<no) cat("(Only first",n,"observations shown.)\n")
cat("\n",ww,"poset\n")
if(complete)
print(t(poset(x))[,seq_len(n)])
if(n<no) cat("(Only first",n,"columns shown.)\n")
invisible(NULL)
}
# show method for pim.environment
setMethod('show',
'pim.environment',
function(object){print(object)})
#' @rdname print
# print method for pim.environment
setMethod('print',
'pim.environment',
print.pim.environment)
#------------------------
# print method for pim.poset
#------------------------
print.pim.poset <- function(x, digits = max(3L, getOption("digits") - 3L), n = 6L, ...){
no <- nobs(x)
cat('\nPIM poset for',no,
'observations.\n','comparison:',compare(x),'\n\n')
print(t(poset(x))[,seq_len(n)])
if(n<no) cat("(Only first",n,"columns shown.)\n")
invisible(NULL)
}
# show method for pim.poset
setMethod('show',
'pim.poset',
function(object){print(object)})
#' @rdname print
# print method for pim.poset
setMethod('print',
'pim.poset',
print.pim.poset)
#------------------------
# print method for pim.formula
#------------------------
print.pim.formula <- function(x, digits = max(3L, getOption("digits") - 3L), ...){
intercept <- has.intercept(x)
ww <- if(intercept) 'with' else 'without'
cat('\nPIM formula',ww,'intercept:\n')
print(x@orig)
cat('\nLeft hand side:',deparse(lhs(x)))
}
# show method for pim.formula
setMethod('show',
'pim.formula',
function(object){print(object)})
#' @rdname print
# print method for pim.formula
setMethod('print',
'pim.formula',
print.pim.formula)
#------------------------
# print method for pim.summary
#------------------------
print.pim.summary <- function(x, digits = max(3L, getOption("digits") - 3L),...){
orig <- paste(deparse(formula(x@formula)))
cat("pim.summary of following model : \n", orig)
cat("\nType: ", model(x),
"\nLink: ", link(x),"\n\n")
Tab <- cbind(
Estimate = coef(x),
"Std. Error" = x@se,
"z value" = x@zval,
"Pr(>|z|)" = x@pr
)
cat("\n")
printCoefmat(Tab, digits = digits)
if(length(x@h0) == 1){
cat("\nNull hypothesis: b =",x@h0,"\n")
} else {
thenames <- rownames(Tab)
cat("\nNull hypotheses:\n")
for(i in seq_along(x@h0)){
cat(" b_",thenames[i]," = ",x@h0[i],"\n", sep="")
}
cat("\n")
}
}
setMethod("show",
"pim.summary",
function(object){
print.pim.summary(object)
})
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