deviance actually returns deviance;

update NEWS; adjust hatvalues for S3 compatibility
lme4 · Jul 21, 2014 · 5ac6f57 · 5ac6f57
1 parent 9e1b3ef
commit 5ac6f57
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diff --git a/R/lmer.R b/R/lmer.R
@@ -562,6 +562,9 @@ coef.merMod <- coefMer
 ##' @importFrom stats deviance
 ##' @S3method deviance merMod
 deviance.merMod <- function(object, REML = NULL, ...) {
+    if (isGLMM(object)) {
+        return(sum(residuals(object,type="deviance")^2))
+    }
     if (isREML(object) && is.null(REML)) {
         warning("deviance() is deprecated for REML fits; use REMLcrit for the REML criterion or deviance(.,REML=FALSE) for deviance calculated at the REML fit")
         return(devCritFun(object, REML=TRUE))
@@ -1338,10 +1341,10 @@ residuals.glmResp <- function(object, type = c("deviance", "pearson",
 }
 
 ## influence values (new feature); not yet exported
-hatvalues.merMod <- function(object, ...) {
+hatvalues.merMod <- function(model, ...) {
     ## prior weights, W ^ {1/2} :
-    sqrtW <- Diagonal(x = sqrt(weights(object, type = "prior")))
-    with(getME(object, c("L", "Lambdat", "Zt", "RX", "X", "RZX")), {
+    sqrtW <- Diagonal(x = sqrt(weights(model, type = "prior")))
+    with(getME(model, c("L", "Lambdat", "Zt", "RX", "X", "RZX")), {
         ## CL:= right factor of the random-effects component of the hat matrix (64)
         CL <- solve(L, solve(L, Lambdat %*% Zt %*% sqrtW,
                              system = "P"), system = "L")

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -3,6 +3,28 @@
 \name{NEWS}
 \title{lme4 News}
 \encoding{UTF-8}
+\section{CHANGES IN VERSION 1.1-8}{
+  \subsection{NEW FEATURES}{
+    \itemize{
+      \item \code{getME} gains a \code{"Tlist"} option
+      (returns a vector of template matrices from which the blocks of 
+      \code{Lambda} are generated)
+      \item \code{hatvalues} method returns the diagonal of the hat matrix
+
+    }
+  }
+  \subsection{USER-VISIBLE CHANGES}{
+    \itemize{
+      \item \code{deviance()} now returns the deviance, rather than half the
+      negative log-likelihood, for GLMMs (there is no difference for
+      LMMs)
+      \item convergence warning and diagnostic test issues are now
+      reported in \code{print} and \code{summary} methods
+
+    }
+  }
+}  
+
 \section{CHANGES IN VERSION 1.1-7}{
   \subsection{NEW FEATURES}{
     \itemize{

diff --git a/inst/tests/test-glmer.R b/inst/tests/test-glmer.R
@@ -51,7 +51,8 @@ test_that("glmer", {
     expect_equal(c(VarCorr(gm1)[[1]]),                  0.41245527438386, tolerance=6e-4)
 ### expect_that(family(gm1),                            equals(binomial()))
 ### ?? binomial() has an 'initialize' component ... and the order is different
-    expect_equal(deviance(gm1),                         184.052674598026, tolerance=1e-5)
+    expect_equal(deviance(gm1),                         73.47428, tolerance=1e-5)
+    ## was -2L = 184.05267459802
     expect_equal(sigma(gm1),                            1)
     expect_equal(extractAIC(gm1),                       c(5, 194.052674598026), tolerance=1e-5)