From 3ef5743afec8117ad1f9e62e5f1628d377dcaaeb Mon Sep 17 00:00:00 2001
From: Ben Bolker <bbolker@gmail.com>
Date: Tue, 5 Feb 2019 09:28:45 -0500
Subject: [PATCH] various cleanup, version bump

---
 DESCRIPTION                |  2 +-
 R/glmmTMB_tidiers.R        |  3 ++-
 R/lme4_tidiers.R           | 14 +++++++-------
 inst/NEWS.Rd               | 16 +++++++++++++++-
 man/augment.ranef.mer.Rd   | 12 ++++++------
 tests/testthat/test-lme4.R |  1 +
 6 files changed, 32 insertions(+), 16 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 678ad39..01a4f7e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: broom.mixed
 Type: Package
 Title: Tidying Methods for Mixed Models
-Version: 0.2.3.9000
+Version: 0.2.4
 Authors@R: c(
     person("Ben", "Bolker", email = "bolker@mcmaster.ca",
         role = c("aut", "cre"),
diff --git a/R/glmmTMB_tidiers.R b/R/glmmTMB_tidiers.R
index 657e295..06525e0 100644
--- a/R/glmmTMB_tidiers.R
+++ b/R/glmmTMB_tidiers.R
@@ -87,7 +87,8 @@ tidy.glmmTMB <- function(x, effects = c("ran_pars", "fixed"),
   ##   - avoid (as.)data.frame
 
   ## R CMD check false positives
-  term <- estimate <- .id <- level <- std.error <- . <- NULL
+  condsd <- condval <- grp <- grpvar <-
+        term <- estimate <- .id <- level <- std.error <- . <- NULL
 
   drop.missing <- function(x) x[vapply(x,length,numeric(1))>0]
   ss <- stats::coef(summary(x))
diff --git a/R/lme4_tidiers.R b/R/lme4_tidiers.R
index befe347..cecb269 100644
--- a/R/lme4_tidiers.R
+++ b/R/lme4_tidiers.R
@@ -342,7 +342,7 @@ augment.merMod <- function(x, data = stats::model.frame(x), newdata, ...) {
   if (missing(newdata)) {
     newdata <- NULL
   }
-  ret <- augment_columns(x, data, newdata, se.fit = NULL, ...)
+  ret <- suppressMessages(augment_columns(x, data, newdata, se.fit = NULL, ...))
 
   # add predictions with no random effects (population means)
   predictions <- stats::predict(x, re.form = NA)
@@ -420,12 +420,12 @@ glance.merMod <- function(x, ...) {
 ##'          geom_vline(xintercept=0,lty=2)+
 ##'          geom_point()+facet_wrap(~variable,scale="free_x")
 ##'       ## emphasize extreme values
-##'       aa2 <- aa  %>% group_by(grp,level) %>%
-##'             mutate(keep=any(estimate/std.error>2))
-##'        ## Update caterpillar plot with extreme levels highlighted
-##'        ##  (highlight all groups with *either* extreme intercept *or*
-##'        ##   extreme slope)
-##'       ggplot(aa2,aes(estimate,level,xmin=lb,xmax=ub,colour=factor(keep)))+
+##'       aa2 <- group_by(aa,grp,level)
+##'       aa3 <- mutate(aa2, keep=any(estimate/std.error>2))
+##'       ## Update caterpillar plot with extreme levels highlighted
+##'       ##  (highlight all groups with *either* extreme intercept *or*
+##'       ##   extreme slope)
+##'       ggplot(aa3, aes(estimate,level,xmin=lb,xmax=ub,colour=factor(keep)))+
 ##'          geom_errorbarh(height=0)+
 ##'          geom_vline(xintercept=0,lty=2)+
 ##'          geom_point()+facet_wrap(~variable,scale="free_x")+
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 12d5660..efd7293 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -4,6 +4,20 @@
 \title{broom.mixed News}
 \encoding{UTF-8}
 
+\section{CHANGES IN VERSION 0.2.4}{
+  \subsection{NEW FEATURES}{
+     \itemize{
+	\item \code{gls} tidier gets confint (GH #49)
+	}
+  }
+  \subsection{BUG FIXES}{
+     \itemize{
+        \item misc fixes for \code{lme4} tidiers (confint for ran_vals, profile conf intervals fixed)
+	\item ran_vals works for \code{glmmTMB}
+     }
+   }
+}
+	
 \section{CHANGES IN VERSION 0.2.3}{
   \subsection{BUG FIXES}{
     \itemize{
@@ -12,7 +26,7 @@
       \item component argument works for random effects in glmmTMB (GH #33: @strengejacke)
     }
   }
-  \subsection{NEW FIXES}{
+  \subsection{NEW FEATURES}{
     \itemize{
       \item \code{brmsfit} and \code{rstanarm} methods allow
       \code{conf.method="HPDinterval"}
diff --git a/man/augment.ranef.mer.Rd b/man/augment.ranef.mer.Rd
index 0c63752..e2ab8ed 100644
--- a/man/augment.ranef.mer.Rd
+++ b/man/augment.ranef.mer.Rd
@@ -37,12 +37,12 @@ if (require("lme4")) {
          geom_vline(xintercept=0,lty=2)+
          geom_point()+facet_wrap(~variable,scale="free_x")
       ## emphasize extreme values
-      aa2 <- aa  \%>\% group_by(grp,level) \%>\%
-            mutate(keep=any(estimate/std.error>2))
-       ## Update caterpillar plot with extreme levels highlighted
-       ##  (highlight all groups with *either* extreme intercept *or*
-       ##   extreme slope)
-      ggplot(aa2,aes(estimate,level,xmin=lb,xmax=ub,colour=factor(keep)))+
+      aa2 <- group_by(aa,grp,level)
+      aa3 <- mutate(aa2, keep=any(estimate/std.error>2))
+      ## Update caterpillar plot with extreme levels highlighted
+      ##  (highlight all groups with *either* extreme intercept *or*
+      ##   extreme slope)
+      ggplot(aa3, aes(estimate,level,xmin=lb,xmax=ub,colour=factor(keep)))+
          geom_errorbarh(height=0)+
          geom_vline(xintercept=0,lty=2)+
          geom_point()+facet_wrap(~variable,scale="free_x")+
diff --git a/tests/testthat/test-lme4.R b/tests/testthat/test-lme4.R
index 0aeb35e..f8a639a 100644
--- a/tests/testthat/test-lme4.R
+++ b/tests/testthat/test-lme4.R
@@ -203,3 +203,4 @@ if (require(lmerTest, quietly = TRUE)) {
   })
   detach("package:lmerTest")
 }
+