confint.default and AIC/BIC for S4 objects

git-svn-id: https://svn.r-project.org/R/trunk@88801 00db46b3-68df-0310-9c12-caf00c1e9a41

Author: pd

doc/NEWS.Rd

@@ -16,6 +16,14 @@
 
   \subsection{NEW FEATURES}{
     \itemize{
+      \item \code{AIC.default} and \code{BIC.default} now checks whether 
+      the \code{methods} namespace is loaded rather than \code{stats4}. It
+      still uses \code{stats4::logLik} and \code{stats4::nobs}, but packages
+      no longer need to load \code{stats4} explicitly.
+
+      \item \code{confint.default} now also works on S4 objects, as long as they
+      have \code{coef()} and \code{vcov()} generics.
+
       \item \code{binomial(identity)} and \code{quasibinomial(identity)} now work
       without having to quote the argument.
 

src/library/stats/R/AIC.R

@@ -29,7 +29,7 @@ AIC.logLik <- function(object, ..., k = 2)
 AIC.default <- function(object, ..., k = 2)
 {
     ## AIC for various fitted objects --- any for which there's a logLik() method:
-    ll <- if(isNamespaceLoaded("stats4")) stats4::logLik else logLik
+    ll <- if(isNamespaceLoaded("methods")) stats4::logLik else logLik
     if(!missing(...)) {# several objects: produce data.frame
 	lls <- lapply(list(object, ...), ll)
         vals <- vapply(lls,
@@ -62,8 +62,8 @@ BIC.logLik <- function(object, ...)
 
 BIC.default <- function(object, ...)
 {
-    ll   <- if(isNamespaceLoaded("stats4")) stats4::logLik else logLik
-    Nobs <- if(isNamespaceLoaded("stats4")) stats4::nobs   else nobs
+    ll   <- if(isNamespaceLoaded("methods")) stats4::logLik else logLik
+    Nobs <- if(isNamespaceLoaded("methods")) stats4::nobs   else nobs
     if(!missing(...)) {# several objects: produce data.frame
         lls <- lapply(list(object, ...), ll)
         vals <- vapply(lls,

src/library/stats/R/confint.R

@@ -156,17 +156,23 @@ confint.profile.nls <-
 
 confint.default <- function (object, parm, level = 0.95, ...)
 {
+    if(isNamespaceLoaded("methods")) {
+        coef <- stats4::coef
+        vcov <- stats4::vcov
+    }
     cf <- coef(object)
     pnames <- names(cf)
     if(missing(parm)) parm <- pnames
     else if(is.numeric(parm)) parm <- pnames[parm]
+    parm_num <- match(parm, pnames) # in case names are missing from vcov
     a <- (1 - level)/2
     a <- c(a, 1 - a)
     pct <- .format_perc(a, 3)
     fac <- qnorm(a)
     ci <- array(NA, dim = c(length(parm), 2L),
 		dimnames = list(parm, pct))
-    ses <- sqrt(diag(vcov(object)))[parm]
+    ses <- sqrt(diag(vcov(object)))[parm_num]
     ci[] <- cf[parm] + ses %o% fac
     ci
 }
+

src/library/stats/man/confint.Rd

@@ -15,7 +15,7 @@
 \description{
   Computes confidence intervals for one or more parameters in a fitted
   model.  There is a default and a method for objects inheriting from class
-  \code{"\link{lm}"}.
+  \code{"\link{lm}"} and several other classes.
 }
 \usage{
 confint(object, parm, level = 0.95, \dots)
@@ -40,10 +40,13 @@ confint(object, parm, level = 0.95, \dots)
   1 - (1-level)/2 in \% (by default 2.5\% and 97.5\%).
 }
 \details{
-  \code{confint} is a generic function.  The default method assumes
-  normality, and needs suitable \code{\link{coef}} and
+  \code{confint} is a generic function.  The default method is based on
+  inverting the Wald test, assuming approximate
+  normality of the estimator. It needs suitable \code{\link{coef}} and
   \code{\link{vcov}} methods to be available.  The default method can be
-  called directly for comparison with other methods.
+  called directly for comparison with other methods. It also works for 
+  fitted models in the S4 class system, provided that the \pkg{methods}
+  namespace is loaded.
 
   For objects of class \code{"lm"} the direct formulae based on \eqn{t}
   values are used.