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#############################################################################
## Copyright (c) 2010-2022 Rune Haubo Bojesen Christensen
##
## This file is part of the ordinal package for R (*ordinal*)
##
## *ordinal* is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 2 of the License, or
## (at your option) any later version.
##
## *ordinal* is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## A copy of the GNU General Public License is available at
## <https://www.r-project.org/Licenses/> and/or
## <http://www.gnu.org/licenses/>.
#############################################################################
## This file contains:
## Implementation of of nominal_test.clm() and scale_test.clm() for
## automatic testing of nominal and scale effects in clm()s. These
## functions work in a fashion similar to add1().
nominal_test <- function(object, ...) {
UseMethod("nominal_test")
}
scale_test <- function(object, ...) {
UseMethod("scale_test")
}
nominal_test.clm <-
function(object, scope, trace=FALSE, ...)
### Test nominal effects for all (or selected) terms in location
### and scale formulas.
{
## get scope: vector of terms names which to add to nominal:
termsnm <- attr(object$terms, "term.labels")
if(!is.null(object$S.terms))
termsnm <- union(termsnm, attr(object$S.terms, "term.labels"))
if(!missing(scope) && !is.null(scope)) {
if(!is.character(scope))
scope <- attr(terms(update.formula(object, scope)),
"term.labels")
if(!all(match(scope, termsnm, 0L) > 0L))
stop("scope is not a subset of term labels")
} else {
scope <- termsnm
}
if(!is.null(object$nom.terms)) {
scope <- scope[!scope %in% attr(object$nom.terms,
"term.labels")]
}
if(!length(scope))
message("\nno additional terms to add to nominal\n")
env <- environment(formula(object))
## get list of (updated) nominal formulas:
nomforms <- if(!is.null(object$call$nominal))
lapply(scope, function(tm) {
update.formula(old=formula(object$nom.terms),
new=as.formula(paste("~. + ", tm)))
}) else lapply(scope, function(tm) {
as.formula(paste("~", tm), env=env) })
ns <- length(scope)
## results matrix:
ans <- matrix(nrow = ns + 1L, ncol = 3L,
dimnames = list(c("<none>", scope),
c("df", "logLik", "AIC")))
ans[1L, ] <- c(object$edf, object$logLik, AIC(object))
n0 <- nobs(object)
## for all terms in scope:
i <- 1
for(i in seq(ns)) {
if(trace) {
cat("trying +", scope[i], "\n", sep = " ")
utils::flush.console()
}
## update and fit model with nominal effect added:
nfit <- try(update(object, nominal=nomforms[[i]],
convergence="silent"), silent=TRUE)
## model may not be identifiable or converge:
if(!inherits(nfit, "try-error") &&
### NOTE: non-negative convergence codes indicate that the likelihood
### is correctly determined:
nfit$convergence$code >= 0) {
ans[i + 1L, ] <- c(nfit$edf, nfit$logLik, AIC(nfit))
nnew <- nobs(nfit)
if(all(is.finite(c(n0, nnew))) && nnew != n0)
stop("number of rows in use has changed: remove missing values?")
}
}
dfs <- ans[, 1L] - ans[1L, 1L]
dfs[1L] <- NA
aod <- data.frame(Df = dfs, logLik = ans[, 2L], AIC = ans[, 3L])
rownames(aod) <- rownames(ans)
## compute likelihood ratio statistic and p-values:
LR <- 2*(ans[, 2L] - ans[1L, 2L])
LR[1L] <- NA
nas <- !is.na(LR)
P <- LR
P[nas] <- pchisq(LR[nas], dfs[nas], lower.tail = FALSE)
aod[, c("LRT", "Pr(>Chi)")] <- list(LR, P)
head <- c("Tests of nominal effects",
paste("\nformula:", Deparse(formula(object$terms))))
if(!is.null(object$call$scale))
head <- c(head, paste("scale: ",
Deparse(formula(object$S.terms))))
if(!is.null(object$call$nominal))
head <- c(head, paste("nominal:",
Deparse(formula(object$nom.terms))))
class(aod) <- c("anova", "data.frame")
attr(aod, "heading") <- head
aod
}
scale_test.clm <-
function(object, scope, trace=FALSE, ...)
### Test scale effects for all (or selected) terms in formula
{
## get scope: vector of terms names which to add to scale:
termsnm <- attr(object$terms, "term.labels")
if(!missing(scope) && !is.null(scope)) {
if(!is.character(scope))
scope <- attr(terms(update.formula(object, scope)),
"term.labels")
if(!all(match(scope, termsnm, 0L) > 0L))
stop("scope is not a subset of term labels")
} else {
scope <- termsnm
}
## if(!is.null(object$nom.terms)) {
## scope <- scope[!scope %in% attr(object$nom.terms,
## "term.labels")]
## }
if(!is.null(object$S.terms)) {
scope <- scope[!scope %in% attr(object$S.terms,
"term.labels")]
}
if(!length(scope))
message("\nno relevant terms to add to scale\n")
env <- environment(formula(object))
## get list of (updated) scale formulas:
scaleforms <-
if(!is.null(object$call$scale))
lapply(scope, function(tm) {
update.formula(old=formula(object$S.terms),
new=as.formula(paste("~. + ", tm)))
})
else
lapply(scope, function(tm) as.formula(paste("~", tm), env=env))
ns <- length(scope)
## results matrix:
ans <- matrix(nrow = ns + 1L, ncol = 3L,
dimnames = list(c("<none>", scope),
c("df", "logLik", "AIC")))
ans[1L, ] <- c(object$edf, object$logLik, AIC(object))
n0 <- nobs(object)
## for all terms in scope:
for(i in seq(ns)) {
if(trace) {
cat("trying +", scope[i], "\n", sep = " ")
utils::flush.console()
}
## update and fit model with scale effect added:
nfit <- try(update(object, scale=scaleforms[[i]]), silent=TRUE)
## model may not be identifiable or converge:
if(!inherits(nfit, "try-error") &&
nfit$convergence$code >= 0) {
ans[i + 1L, ] <- c(nfit$edf, nfit$logLik, AIC(nfit))
nnew <- nobs(nfit)
if (all(is.finite(c(n0, nnew))) && nnew != n0)
stop("number of rows in use has changed: remove missing values?")
}
}
dfs <- ans[, 1L] - ans[1L, 1L]
dfs[1L] <- NA
aod <- data.frame(Df = dfs, logLik = ans[, 2L], AIC = ans[, 3L])
rownames(aod) <- rownames(ans)
## compute likelihood ratio statistic and p-values:
LR <- 2*(ans[, 2L] - ans[1L, 2L])
LR[1L] <- NA
nas <- !is.na(LR)
P <- LR
P[nas] <- pchisq(LR[nas], dfs[nas], lower.tail = FALSE)
aod[, c("LRT", "Pr(>Chi)")] <- list(LR, P)
head <- c("Tests of scale effects",
paste("\nformula:", Deparse(formula(object$terms))))
if(!is.null(object$call$scale))
head <- c(head, paste("scale: ",
Deparse(formula(object$S.terms))))
if(!is.null(object$call$nominal))
head <- c(head, paste("nominal:",
Deparse(formula(object$nom.terms))))
class(aod) <- c("anova", "data.frame")
attr(aod, "heading") <- head
aod
}
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