change anova() header names (#528)

lme4 · Jun 28, 2019 · 98d8c8a · 98d8c8a
1 parent ab85cad
commit 98d8c8a
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Showing 6 changed files with 26 additions and 15 deletions.
diff --git a/R/lmer.R b/R/lmer.R
@@ -538,10 +538,10 @@ anovaLmer <- function(object, ..., refit = TRUE, model.names=NULL) {
         ## devs <- sapply(mods, deviance)
         llks <- lapply(mods, logLik)
         ## Order models by increasing degrees of freedom:
-        ii <- order(Df <- vapply(llks, attr, FUN.VALUE=numeric(1), "df"))
+        ii <- order(npar <- vapply(llks, attr, FUN.VALUE=numeric(1), "df"))
         mods <- mods[ii]
         llks <- llks[ii]
-        Df   <- Df  [ii]
+        npar   <- npar  [ii]
         calls <- lapply(mods, getCall)
         data <- lapply(calls, `[[`, "data")
         if(!all(vapply(data, identical, NA, data[[1]])))
@@ -554,14 +554,16 @@ anovaLmer <- function(object, ..., refit = TRUE, model.names=NULL) {
             header <- c(header, paste("Subset:", abbrDeparse(subset[[1]])))
         llk <- unlist(llks)
         chisq <- 2 * pmax(0, c(NA, diff(llk)))
-        dfChisq <- c(NA, diff(Df))
-        val <- data.frame(Df = Df,
+        dfChisq <- c(NA, diff(npar))
+        val <- data.frame(npar = npar,
+                          ## afraid to swap in vapply here; wondering
+                          ##   why .sapply was needed in the first place ...
                           AIC = .sapply(llks, AIC), # FIXME? vapply()
                           BIC = .sapply(llks, BIC), #  "       "
                           logLik = llk,
                           deviance = -2*llk,
                           Chisq = chisq,
-                          "Chi Df" = dfChisq,
+                          Df = dfChisq,
                           "Pr(>Chisq)" = pchisq(chisq, dfChisq, lower.tail = FALSE),
                           row.names = names(mods), check.names = FALSE)
         class(val) <- c("anova", class(val))
@@ -594,8 +596,8 @@ anovaLmer <- function(object, ..., refit = TRUE, model.names=NULL) {
         table <- data.frame(df, ss, ms, f)
         dimnames(table) <-
             list(nmeffects,
-                 ## c("Df", "Sum Sq", "Mean Sq", "Denom", "F value", "Pr(>F)"))
-                 c("Df", "Sum Sq", "Mean Sq", "F value"))
+                 ## c("npar", "Sum Sq", "Mean Sq", "Denom", "F value", "Pr(>F)"))
+                 c("npar", "Sum Sq", "Mean Sq", "F value"))
         if ("(Intercept)" %in% nmeffects)
             table <- table[-match("(Intercept)", nmeffects), ]
         structure(table, heading = "Analysis of Variance Table",
@@ -832,7 +834,7 @@ drop1.merMod <- function(object, scope, scale = 0, test = c("none", "Chisq", "us
     } else {
         dfs <- ans[1L, 1L] - ans[, 1L]
         dfs[1L] <- NA
-        aod <- data.frame(Df = dfs, AIC = ans[,2])
+        aod <- data.frame(npar = dfs, AIC = ans[,2])
         if(test == "Chisq") {
             ## reconstruct deviance from AIC (ugh)
             dev <- ans[, 2L] - k*ans[, 1L]

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -20,6 +20,11 @@
       \item In \code{isSingular(x, tol)}, the default tolerance (\code{tol}) has
       been increased from 1e-5 to \code{1e-4}, the default of
       \code{check.conv.singular} in \code{g?lmerControl()}.
+
+      \item for clarity and consistency with base R methods,
+      changes in some column names of \code{anova()} output:
+      "Df" becomes "npar", "Chi Df" becomes "Df" (GH #528)
+
     }
   }
   \subsection{BUG FIXES}{

diff --git a/tests/glmer-1.R b/tests/glmer-1.R
@@ -219,8 +219,8 @@ stopifnot(isTRUE(chkFixed(m0, true.coef = c(1,2))),
 
 stopifnot(all.equal(a01$Chisq[2], 554.334056, tolerance=1e-5),
 	  all.equal(a01$logLik, c(-1073.77193, -796.604902), tolerance=1e-6),
-          a01$ Df == 3:4,
-	  a01$`Chi Df`[2] == 1)
+          a01$ npar == 3:4,
+	  na.omit(a01$ Df) == 1)
 
 if(lme4:::testLevel() > 1) {
     nsim <- 10
@@ -233,8 +233,8 @@ if(lme4:::testLevel() > 1) {
                     m0 <- glmer(y~x + (1|f),           family="poisson", data=dd)
                     m1 <- glmer(y~x + (1|f) + (1|obs), family="poisson", data=dd)
                     a01 <- anova(m0, m1)
-                    stopifnot(a01$ Df == 3:4,
-                              a01$`Chi Df`[2] == 1)
+                    stopifnot(a01$ npar == 3:4,
+                              a01$ Df == 1)
                     list(chk0 = chkFixed(m0, true.coef = c(1,2)),
                          chk1 = chkFixed(m1, true.coef = c(1,2)),
                          chisq= a01$Chisq[2],

diff --git a/tests/lmer-1.Rout.save b/tests/lmer-1.Rout.save
@@ -87,7 +87,7 @@ Data: sleepstudy
 Models:
 fm2: Reaction ~ Days + (1 | Subject) + (0 + Days | Subject)
 fm1: Reaction ~ Days + (Days | Subject)
-    Df  AIC  BIC logLik deviance Chisq Chi Df Pr(>Chisq)
+    npar  AIC  BIC logLik deviance Chisq Df Pr(>Chisq)
 fm2  5 1762 1778   -876     1752                        
 fm1  6 1764 1783   -876     1752  0.06      1        0.8
 > 

diff --git a/tests/testthat/test-methods.R b/tests/testthat/test-methods.R
@@ -72,7 +72,11 @@ test_that("summary", {
 
 context("anova")
 test_that("lmer", {
-    expect_that(suppressMessages(anova(fm0,fm1)), is_a("anova"))
+    aa <- suppressMessages(anova(fm0,fm1))
+    expect_that(aa, is_a("anova"))
+    expect_equal(names(aa),
+                 c("npar", "AIC", "BIC", "logLik", "deviance", "Chisq", "Df", 
+                   "Pr(>Chisq)"))
     expect_warning(do.call(anova,list(fm0,fm1)), "assigning generic names")
     ##
     dat <- data.frame(y = 1:5,

diff --git a/tests/testthat/test-rank.R b/tests/testthat/test-rank.R
@@ -43,7 +43,7 @@ test_that("lmerRank", {
     ## should work:
     expect_is(fm2 <- lmer( z ~ ab + (1|r), data=d2), "lmerMod")
     expect_equal(logLik(fm), logLik(fm2))
-    expect_equal(sum(anova(fm)[, "Df"]), anova(fm2)[, "Df"])
+    expect_equal(sum(anova(fm)[, "npar"]), anova(fm2)[, "npar"])
     expect_equal(sum(anova(fm)[, "Sum Sq"]), anova(fm2)[, "Sum Sq"])
 })