Merge pull request #28 from carlbfrederick/master

(lame) examples for all exported functions and package helpfile

NAMESPACE

@@ -45,6 +45,7 @@ importFrom(shiny,reactive)
 importFrom(shiny,reactiveValues)
 importFrom(shiny,renderPlot)
 importFrom(shiny,renderPrint)
+importFrom(shiny,runApp)
 importFrom(shiny,shinyApp)
 importFrom(shiny,sidebarLayout)
 importFrom(shiny,sidebarPanel)

R/merExtract.R

@@ -3,7 +3,19 @@
 #' @description Extracts random effect terms from an lme4 model
 #' @param merMod a merMod object from the lme4 package
 #' @importFrom plyr adply rbind.fill
-#' @return a data frame with random effects from lme4 by group id
+#' @return a data frame with the following columns
+#' \describe{
+#'   \item{groupFctr}{The name of the grouping factor associated with the random effects}
+#'   \item{groupID}{The level of the grouping factor associated with the random effects}
+#'   \item{'term'}{One column per random effect, the name is derived from the merMod}
+#'   \item{'term'_se}{One column per random effect, the name is derived from the merMod}
+#' }
+#' @examples
+#' require(lme4)
+#' m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+#' rfx <- REextract(m2)
+#' #Note the column names
+#' head(rfx)
 #' @export
 REextract <- function(merMod){
   stopifnot(class(merMod) == "lmerMod" | class(merMod) == "glmerMod")
@@ -53,6 +65,11 @@ REextract <- function(merMod){
 #' }
 #' @details Use the Gelman sim technique to build empirical Bayes estimates.
 #'  Uses the sim function in the arm package
+#' @examples
+#' require(lme4)
+#' m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+#' re2 <- REsim(m2, 25)
+#' head(re2)
 #' @export
 REsim <- function(merMod, n.sims = 200, oddsRatio = FALSE){
   stopifnot(class(merMod) == "lmerMod" | class(merMod) == "glmerMod")
@@ -97,6 +114,11 @@ REsim <- function(merMod, n.sims = 200, oddsRatio = FALSE){
 #' }
 #' @details Use the Gelman sim technique to build fixed effect estimates and
 #' confidence intervals. Uses the sim function in the arm package
+#' @examples
+#' require(lme4)
+#' m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+#' fe2 <- FEsim(m2, 25)
+#' head(fe2)
 #' @export
 FEsim <- function(merMod, n.sims = 200, oddsRatio=FALSE){
   stopifnot(class(merMod) == "lmerMod" | class(merMod) == "glmerMod")
@@ -125,6 +147,10 @@ FEsim <- function(merMod, n.sims = 200, oddsRatio=FALSE){
 #' response variable standard deviations?
 #' @import lme4
 #' @return a numeric which represents the RMSE
+#' @examples
+#' require(lme4)
+#' m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+#' RMSE.merMod(m2)
 #' @export
 RMSE.merMod <- function(merMod, scale = FALSE){
   stopifnot(class(merMod) == "lmerMod")

R/merTools-package.r

@@ -1,4 +1,40 @@
-#' merTools.
+#' merTools: Provides methods for extracting and exploring results from merMod
+#' objects in the lme4 package.
+#'
+#' The merTools package contains convenience tools for extracting useful
+#' information from and exploring the implications of merMod objects created by
+#' the lme4 package.  These convenience functions are especially useful for
+#' merMod objects that take a long time to estimate due to their complexity or
+#' because they are estimated on very large samples.
+#'
+#' See the vignettes for usage examples
+#'
+#' @section merMod extraction/utility functions:
+#'
+#' \itemize{
+#'   \item \code{\link{fastdisp}}
+#'   \item \code{\link{superFactor}}
+#'   \item \code{\link{REextract}}
+#'   \item \code{\link{REsim}}
+#'   \item \code{\link{FEsim}}
+#'   \item \code{\link{RMSE.merMod}}
+#'   \item \code{\link{thetaExtract}}
+#'   \item \code{\link{REquantile}}
+#' }
+#'
+#' @section merMod exploration functions:
+#'
+#' \itemize{
+#'   \item \code{\link{plotREsim}}
+#'   \item \code{\link{plotFEsim}}
+#'   \item \code{\link{draw}}
+#'   \item \code{\link{wiggle}}
+#'   \item \code{\link{subBoot}}
+#'   \item \code{\link{predictInterval}}
+#'   \item \code{\link{expectedRank}}
+#'   \item \code{\link{REimpact}}
+#'   \item \code{\link{shinyMer}}
+#' }
 #'
 #' @name merTools
 #' @docType package

man/FEsim.Rd

@@ -31,4 +31,10 @@ Simulate fixed effects from merMod
 Use the Gelman sim technique to build fixed effect estimates and
 confidence intervals. Uses the sim function in the arm package
 }
+\examples{
+require(lme4)
+m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+fe2 <- FEsim(m2, 25)
+head(fe2)
+}
 

man/REextract.Rd

@@ -10,9 +10,22 @@ REextract(merMod)
 \item{merMod}{a merMod object from the lme4 package}
 }
 \value{
-a data frame with random effects from lme4 by group id
+a data frame with the following columns
+\describe{
+  \item{groupFctr}{The name of the grouping factor associated with the random effects}
+  \item{groupID}{The level of the grouping factor associated with the random effects}
+  \item{'term'}{One column per random effect, the name is derived from the merMod}
+  \item{'term'_se}{One column per random effect, the name is derived from the merMod}
+}
 }
 \description{
 Extracts random effect terms from an lme4 model
 }
+\examples{
+require(lme4)
+m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+rfx <- REextract(m2)
+#Note the column names
+head(rfx)
+}
 

man/REsim.Rd

@@ -33,4 +33,10 @@ Simulate random effects from merMod
 Use the Gelman sim technique to build empirical Bayes estimates.
  Uses the sim function in the arm package
 }
+\examples{
+require(lme4)
+m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+re2 <- REsim(m2, 25)
+head(re2)
+}
 

man/RMSE.merMod.Rd

@@ -18,4 +18,9 @@ a numeric which represents the RMSE
 \description{
 Extract the Root Mean Squared Error for a lmerMod object
 }
+\examples{
+require(lme4)
+m2 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy)
+RMSE.merMod(m2)
+}
 

man/merTools.Rd

@@ -4,8 +4,46 @@
 \name{merTools}
 \alias{merTools}
 \alias{merTools-package}
-\title{merTools.}
+\title{merTools: Provides methods for extracting and exploring results from merMod
+objects in the lme4 package.}
 \description{
-merTools.
+The merTools package contains convenience tools for extracting useful
+information from and exploring the implications of merMod objects created by
+the lme4 package.  These convenience functions are especially useful for
+merMod objects that take a long time to estimate due to their complexity or
+because they are estimated on very large samples.
+}
+\details{
+See the vignettes for usage examples
+}
+\section{merMod extraction/utility functions}{
+
+
+\itemize{
+  \item \code{\link{fastdisp}}
+  \item \code{\link{superFactor}}
+  \item \code{\link{REextract}}
+  \item \code{\link{REsim}}
+  \item \code{\link{FEsim}}
+  \item \code{\link{RMSE.merMod}}
+  \item \code{\link{thetaExtract}}
+  \item \code{\link{REquantile}}
+}
+}
+
+\section{merMod exploration functions}{
+
+
+\itemize{
+  \item \code{\link{plotREsim}}
+  \item \code{\link{plotFEsim}}
+  \item \code{\link{draw}}
+  \item \code{\link{wiggle}}
+  \item \code{\link{subBoot}}
+  \item \code{\link{predictInterval}}
+  \item \code{\link{expectedRank}}
+  \item \code{\link{REimpact}}
+  \item \code{\link{shinyMer}}
+}
 }