#' Method to get the names of ill-defined parameters
#'
#' The method for generalised nonlinear regression fits as obtained
#' with [mkinfit] and [mmkin] checks if the degradation parameters
#' pass the Wald test (in degradation kinetics often simply called t-test) for
#' significant difference from zero. For this test, the parameterisation
#' without parameter transformations is used.
#'
#' The method for hierarchical model fits, also known as nonlinear
#' mixed-effects model fits as obtained with [saem] and [mhmkin]
#' checks if any of the confidence intervals for the random
#' effects expressed as standard deviations include zero, and if
#' the confidence intervals for the error model parameters include
#' zero.
#'
#' @param object The object to investigate
#' @param x The object to be printed
#' @param conf.level The confidence level for checking p values
#' @param \dots For potential future extensions
#' @param random For hierarchical fits, should random effects be tested?
#' @param errmod For hierarchical fits, should error model parameters be
#' tested?
#' @param slopes For hierarchical [saem] fits using saemix as backend,
#' should slope parameters in the covariate model(starting with 'beta_') be
#' tested?
#' @return For [mkinfit] or [saem] objects, a character vector of parameter
#' names. For [mmkin] or [mhmkin] objects, a matrix like object of class
#' 'illparms.mmkin' or 'illparms.mhmkin'.
#' @note All return objects have printing methods. For the single fits, printing
#' does not output anything in the case no ill-defined parameters are found.
#' @export
illparms <- function(object, ...)
{
UseMethod("illparms", object)
}
#' @rdname illparms
#' @export
#' @examples
#' fit <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE)
#' illparms(fit)
illparms.mkinfit <- function(object, conf.level = 0.95, ...) {
p_values <- suppressWarnings(summary(object)$bpar[, "Pr(>t)"])
na <- is.na(p_values)
failed <- p_values > 1 - conf.level
ret <- names(parms(object))[na | failed]
class(ret) <- "illparms.mkinfit"
return(ret)
}
#' @rdname illparms
#' @export
print.illparms.mkinfit <- function(x, ...) {
class(x) <- NULL
if (length(x) > 0) {
print(as.character(x))
}
}
#' @rdname illparms
#' @export
#' @examples
#' \dontrun{
#' fits <- mmkin(
#' c("SFO", "FOMC"),
#' list("FOCUS A" = FOCUS_2006_A,
#' "FOCUS C" = FOCUS_2006_C),
#' quiet = TRUE)
#' illparms(fits)
#' }
illparms.mmkin <- function(object, conf.level = 0.95, ...) {
result <- lapply(object,
function(fit) {
if (inherits(fit, "try-error")) return("E")
ill <- illparms(fit, conf.level = conf.level)
if (length(ill) > 0) {
return(paste(ill, collapse = ", "))
} else {
return("")
}
})
result <- unlist(result)
dim(result) <- dim(object)
dimnames(result) <- dimnames(object)
class(result) <- "illparms.mmkin"
return(result)
}
#' @rdname illparms
#' @export
print.illparms.mmkin <- function(x, ...) {
class(x) <- NULL
print(x, quote = FALSE)
}
#' @rdname illparms
#' @export
illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, slopes = TRUE, ...) {
if (inherits(object$so, "try-error")) {
ill_parms <- NA
} else {
ints <- intervals(object, conf.level = conf.level)
ill_parms <- character(0)
if (random) {
ill_parms_random_i <- which(ints$random[, "lower"] < 0)
ill_parms_random <- rownames(ints$random)[ill_parms_random_i]
ill_parms <- c(ill_parms, ill_parms_random)
}
if (errmod) {
ill_parms_errmod_i <- which(ints$errmod[, "lower"] < 0 & ints$errmod[, "upper"] > 0)
ill_parms_errmod <- rownames(ints$errmod)[ill_parms_errmod_i]
ill_parms <- c(ill_parms, ill_parms_errmod)
}
if (slopes) {
if (is.null(object$so)) stop("Slope testing is only implemented for the saemix backend")
slope_names <- grep("^beta_", object$so@model@name.fixed, value = TRUE)
ci <- object$so@results@conf.int
rownames(ci) <- ci$name
slope_ci <- ci[slope_names, ]
ill_parms_slopes <- slope_ci[, "lower"] < 0 & slope_ci[, "upper"] > 0
ill_parms <- c(ill_parms, slope_names[ill_parms_slopes])
}
}
class(ill_parms) <- "illparms.saem.mmkin"
return(ill_parms)
}
#' @rdname illparms
#' @export
print.illparms.saem.mmkin <- print.illparms.mkinfit
#' @rdname illparms
#' @export
illparms.mhmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) {
if (inherits(object[[1]], "saem.mmkin")) {
check_failed <- function(x) if (inherits(x$so, "try-error")) TRUE else FALSE
}
result <- lapply(object,
function(fit) {
if (check_failed(fit)) {
return("E")
} else {
if (!is.null(fit$FIM_failed) &&
"random effects and error model parameters" %in% fit$FIM_failed) {
return("NA")
} else {
ill <- illparms(fit, conf.level = conf.level, random = random, errmod = errmod)
if (length(ill) > 0) {
return(paste(ill, collapse = ", "))
} else {
return("")
}
}
}
})
result <- unlist(result)
dim(result) <- dim(object)
dimnames(result) <- dimnames(object)
class(result) <- "illparms.mhmkin"
return(result)
}
#' @rdname illparms
#' @export
print.illparms.mhmkin <- function(x, ...) {
class(x) <- NULL
print(x, quote = FALSE)
}
