Add methods for multcomp package objects.

Fixes #144
tidyverse · Dec 20, 2011 · 9e50eb6 · 9e50eb6
1 parent b9e2c4a
commit 9e50eb6
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Showing 5 changed files with 145 additions and 2 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,7 +30,8 @@ Suggests:
     maps,
     hexbin,
     gpclib,
-    maptools
+    maptools,
+    multcomp
 Extends:
     sp
 License: GPL-2
@@ -188,3 +189,4 @@ Collate:
     'annotation-map.r'
     'autoplot.r'
     'zzz.r'
+    'fortify-multcomp.r'
diff --git a/NAMESPACE b/NAMESPACE
@@ -252,8 +252,11 @@ S3method(facet_train_layout,null)
 S3method(facet_train_layout,wrap)
 S3method(format,facet)
 S3method(fortify,"NULL")
+S3method(fortify,cld)
+S3method(fortify,confint.glht)
 S3method(fortify,data.frame)
 S3method(fortify,default)
+S3method(fortify,glht)
 S3method(fortify,Line)
 S3method(fortify,Lines)
 S3method(fortify,lm)
@@ -262,6 +265,7 @@ S3method(fortify,Polygon)
 S3method(fortify,Polygons)
 S3method(fortify,SpatialLinesDataFrame)
 S3method(fortify,SpatialPolygons)
+S3method(fortify,summary.glht)
 S3method(ggplot,data.frame)
 S3method(ggplot,default)
 S3method(grid.draw,absoluteGrob)

diff --git a/NEWS b/NEWS
@@ -1,7 +1,7 @@
 ggplot2 0.9.0
 ----------------------------------------------------------------
 
-NEW GEOMS/ANNOTATIONS
+NEW FEATURES
 
 * `geom_map`
 
@@ -11,6 +11,8 @@ NEW GEOMS/ANNOTATIONS
 
 * `annotation_map`
 
+* New fortify methods for objects produced by the `multcomp` package.
+
 MINOR CHANGES
 
 * `geom_text` now supports `fontfamily`, `fontface`, and `lineheight`

diff --git a/R/fortify-multcomp.r b/R/fortify-multcomp.r
@@ -0,0 +1,84 @@
+#' Fortify methods for objects produced by \pkg{multcomp}
+#'
+#' @param model an object of class \code{glht}, \code{confint.glht},
+#'  \code{summary.glht} or \code{\link{cld}}
+#' @param data,... other arguments to the generic ignored in this method.
+#' @name fortify-multcomp
+#' @examples
+#' if (require("multcomp")) {
+#' amod <- aov(breaks ~ wool + tension, data = warpbreaks)
+#' wht <- glht(amod, linfct = mcp(tension = "Tukey"))
+#'
+#' fortify(wht)
+#' ggplot(wht, aes(lhs, estimate)) + geom_point()
+#'
+#' CI <- confint(wht)
+#' fortify(CI)
+#' ggplot(CI, aes(lhs, estimate, ymin = lwr, ymax = upr)) +
+#'    geom_pointrange()
+#'
+#' fortify(summary(wht))
+#' ggplot(mapping = aes(lhs, estimate)) +
+#'    geom_linerange(aes(ymin = lwr, ymax = upr), data = CI) + 
+#'    geom_point(aes(size = p), data = summary(wht)) + 
+#'    scale_size(trans = "reverse")
+#'
+#' cld <- cld(wht)
+#' fortify(cld)
+#' }
+NULL
+
+#' @method fortify glht
+#' @rdname fortify-multcomp
+#' @export
+fortify.glht <- function(model, data, ...) {
+  unrowname(data.frame(
+    lhs = rownames(model$linfct),
+    rhs = model$rhs,
+    estimate = coef(model), 
+    check.names = FALSE, 
+    stringsAsFactors = FALSE))
+}
+
+#' @rdname fortify-multcomp
+#' @method fortify confint.glht
+#' @export
+fortify.confint.glht <- function(model, data, ...) {
+  coef <- model$confint
+  colnames(coef) <- tolower(colnames(coef))
+
+  unrowname(data.frame(
+    lhs = rownames(coef),
+    rhs = model$rhs,
+    coef,
+    check.names = FALSE, 
+    stringsAsFactors = FALSE))
+}
+
+#' @method fortify summary.glht
+#' @rdname fortify-multcomp
+#' @export
+fortify.summary.glht <- function(model, data, ...) {
+  coef <- as.data.frame(
+    model$test[c("coefficients", "sigma", "tstat", "pvalues")])
+  names(coef) <- c("estimate", "se", "t", "p")
+
+  unrowname(data.frame(
+    lhs = rownames(coef),
+    rhs = model$rhs,
+    coef,
+    check.names = FALSE, 
+    stringsAsFactors = FALSE))
+}
+
+
+#' @method fortify cld
+#' @rdname fortify-multcomp
+#' @export
+fortify.cld <- function(model, data, ...) {
+  unrowname(data.frame(
+    lhs = names(model$mcletters$Letters),
+    letters = model$mcletters$Letters,
+    check.names = FALSE, 
+    stringsAsFactors = FALSE))
+}
diff --git a/man/fortify-multcomp.Rd b/man/fortify-multcomp.Rd
@@ -0,0 +1,51 @@
+\name{fortify-multcomp}
+\alias{fortify-multcomp}
+\alias{fortify.cld}
+\alias{fortify.confint.glht}
+\alias{fortify.glht}
+\alias{fortify.summary.glht}
+\title{Fortify methods for objects produced by \pkg{multcomp}}
+\usage{
+  \method{fortify}{glht} (model, data, ...)
+
+  \method{fortify}{confint.glht} (model, data, ...)
+
+  \method{fortify}{summary.glht} (model, data, ...)
+
+  \method{fortify}{cld} (model, data, ...)
+}
+\arguments{
+  \item{model}{an object of class \code{glht},
+  \code{confint.glht}, \code{summary.glht} or
+  \code{\link{cld}}}
+
+  \item{data,...}{other arguments to the generic ignored in
+  this method.}
+}
+\description{
+  Fortify methods for objects produced by \pkg{multcomp}
+}
+\examples{
+if (require("multcomp")) {
+amod <- aov(breaks ~ wool + tension, data = warpbreaks)
+wht <- glht(amod, linfct = mcp(tension = "Tukey"))
+
+fortify(wht)
+ggplot(wht, aes(lhs, estimate)) + geom_point()
+
+CI <- confint(wht)
+fortify(CI)
+ggplot(CI, aes(lhs, estimate, ymin = lwr, ymax = upr)) +
+   geom_pointrange()
+
+fortify(summary(wht))
+ggplot(mapping = aes(lhs, estimate)) +
+   geom_linerange(aes(ymin = lwr, ymax = upr), data = CI) +
+   geom_point(aes(size = p), data = summary(wht)) +
+   scale_size(trans = "reverse")
+
+cld <- cld(wht)
+fortify(cld)
+}
+}
+