From 7ac328748988b70024bce4289eac1dc25804cfd2 Mon Sep 17 00:00:00 2001
From: unknown <greenp@GREENP-W7L.landcare.ad.landcareresearch.co.nz>
Date: Fri, 28 Aug 2015 17:40:04 +1200
Subject: [PATCH 1/3] lrtest for factor covariates

---
 R/testLibrary.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/R/testLibrary.R b/R/testLibrary.R
index 8c20836..2a3cb1d 100644
--- a/R/testLibrary.R
+++ b/R/testLibrary.R
@@ -102,7 +102,7 @@ fixeddesc <- function(text, xname) {
     function(fit, sim) {
 
         # test used
-        rval <- if(text=="default") defaultdesc(fit) else text
+        rval <- if(text=="default") defaultdesc(fit, xname) else text
 
         # effect size
         fe <- maybe(fixef)(sim)$value
@@ -122,6 +122,8 @@ fixeddesc <- function(text, xname) {
 # glmer - ztest
 defaulttest <- function(fit, xname) {
 
+    if(is.factor(getData(fit)[[xname]])) return(lrtest(fit, xname))
+
     switch(class(fit)[1],
 
         lm       = ttest(fit, xname),
@@ -132,7 +134,9 @@ defaulttest <- function(fit, xname) {
     )
 }
 
-defaultdesc <- function(fit) {
+defaultdesc <- function(fit, xname) {
+
+    if(is.factor(getData(fit)[[xname]])) return("Likelihood ratio")
 
     switch(class(fit)[1],
 

From d61dbcfbda33f844c6f859f58861551f98d714a0 Mon Sep 17 00:00:00 2001
From: unknown <greenp@GREENP-W7L.landcare.ad.landcareresearch.co.nz>
Date: Fri, 28 Aug 2015 17:40:34 +1200
Subject: [PATCH 2/3] attempt workaround for uncatchable warnings

---
 R/maybe.R | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 59 insertions(+)

diff --git a/R/maybe.R b/R/maybe.R
index e4ee45c..1e7a2af 100644
--- a/R/maybe.R
+++ b/R/maybe.R
@@ -64,6 +64,65 @@ 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()

From 0e05d3772ea5d3e91be15d317b5bd88df5ca8d17 Mon Sep 17 00:00:00 2001
From: unknown <greenp@GREENP-W7L.landcare.ad.landcareresearch.co.nz>
Date: Thu, 8 Oct 2015 12:52:29 +1300
Subject: [PATCH 3/3] Use @frame and $model for getData

---
 R/getData.R                                     | 9 ++++++++-
 tests/testthat/{helper_options.R => test_aaa.R} | 2 +-
 2 files changed, 9 insertions(+), 2 deletions(-)
 rename tests/testthat/{helper_options.R => test_aaa.R} (82%)

diff --git a/R/getData.R b/R/getData.R
index df92e91..27468ae 100644
--- a/R/getData.R
+++ b/R/getData.R
@@ -34,7 +34,14 @@ getData <- function(object) {
     if(!is.null(newData)) return(newData)
 
     #
-    # 2nd choice: Use the `data` argument
+    # 2nd choice: @frame for merMod, $model for lm.
+    #
+
+    if(is(object, "merMod")) return(object@frame)
+    if(is(object, "lm")) return(object$model)
+
+    #
+    # 3rd choice: Use the `data` argument
     #
 
     dataName <- as.character(getCall(object)$data)
diff --git a/tests/testthat/helper_options.R b/tests/testthat/test_aaa.R
similarity index 82%
rename from tests/testthat/helper_options.R
rename to tests/testthat/test_aaa.R
index ce368ff..9bd0dad 100644
--- a/tests/testthat/helper_options.R
+++ b/tests/testthat/test_aaa.R
@@ -11,4 +11,4 @@ helperopts <- simrOptions(nsim=test.nsim, progress=test.progress)
 # Useful to have an example model.
 #
 
-fm1 <- lmer(y ~ x + (1|g), data=example)
+fm1 <- lmer(y ~ x + (1|g), data=simdata)