update examples vignette (LRT for random effects)

pitakakariki · Oct 12, 2015 · b1f454b · b1f454b
1 parent 6c19bad
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Showing 2 changed files with 4 additions and 61 deletions.
diff --git a/R/maybe.R b/R/maybe.R
@@ -64,65 +64,6 @@ maybe <- function(f) {
     }
 }
 
-maybe2 <- function(f) {
-
-    cfw <- "(converted from warning)"
-
-    function(...) {
-
-        opts <- options(warn=2)
-        on.exit(options(opts))
-
-        returnValue <- NULL
-        warningValue <- NULL
-        warningTag <- NULL
-        errorValue <- NULL
-        errorTag <- NULL
-
-        returnValue <- tryCatch(
-
-            withCallingHandlers(eval.parent(f(...)),
-
-                error=function(e) {
-
-                    if(str_detect(e$message, cfw)) {
-
-                        # get rid of conversions junk
-                        msg <- e$message
-                        msg <- substring(msg, 24+str_locate(msg, cfw)[1,1])
-                        msg <- str_trim(msg)
-
-                        warningValue <<- append(warningValue, msg)
-                        wtag <- if(is.null(e$tag)) "" else e$tag
-                        warningTag <<- append(warningTag, wtag)
-                        message(msg)
-                        print(computeRestarts())
-                        invokeRestart("muffleWarning")
-
-                    } else {
-
-                        errorValue <<- e$message
-                        errorTag <<- if(is.null(e$tag)) "" else e$tag
-                        return(NULL)
-                    }
-                }
-            )
-        )
-
-        rval <- list()
-        class(rval) <- "Maybe"
-
-        rval["value"] <- list(returnValue) # nb returnValue might be NULL
-        rval["warning"] <- list(warningValue)
-        rval["warningtag"] <- list(warningTag)
-        rval["error"] <- list(errorValue)
-        rval["errortag"] <- list(errorTag)
-
-        return(rval)
-    }
-}
-
-
 list2maybe <- function(x) {
 
     rval <- list()

diff --git a/vignettes/examples.Rmd b/vignettes/examples.Rmd
@@ -136,7 +136,7 @@ fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
 doTest(fm1, compare( ~ Days + (1 | Subject)))
 ```
 
-The LRT is fast but only approximate. You can also use `compare` with a slower but more accurate parametric bootstrap test from the `pbkrtest` package.
+The LRT is fast but only approximate. In fact, when testing random effects, the test is conservative[^1] because the null hypothesis is at a boundary of the parameter space. This means that you will underestimate power if you use the LRT. For more accurate results you can use `compare` with a parametric bootstrap test from the `pbkrtest` package. These can be quite slow, so you may want to use the LRT to exploring designs, and then double check with the parametric bootstrap.
 
 ```{r, eval=FALSE}
 doTest(fm1, compare( ~ Days + (1 | Subject), "pb"))
@@ -146,4 +146,6 @@ Note that the shortcut `rcompare` saves you from retyping the fixed effect speci
 
 ```{r, eval=FALSE}
 doTest(fm1, rcompare( ~ (1 | Subject), "pb"))
-```
+```
+
+[^1]: See, e.g., Pinheiro, J.C., Bates D.M. (2000) _Mixed-Effects Models in S and S-PLUS_, Springer, New York (p84).