Version 2.5-0; html vignette

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: visreg
 Title: Visualization of Regression Models
-Version: 2.4-1
-Date: 2017-06-23
+Version: 2.5-0
+Date: 2018-02-26
 Author: Patrick Breheny, Woodrow Burchett
 Maintainer: Patrick Breheny <[email protected]>
 Imports: lattice

NAMESPACE

@@ -5,4 +5,5 @@ import("grDevices")
 export(visreg, visreg2d, visregList)
 S3method(plot, visreg)
 S3method(plot, visregList)
+S3method(plot, visreg2d)
 S3method(subset, visreg)

NEWS

@@ -1,3 +1,15 @@
+2.5-0 (2018-02-26)
+  * New: Overlay now works for gg plots
+  * New: gg option for visreg2d
+  * New: Improved support for betareg models
+  * New: Support for polr models
+  * Changed: visreg2d now split into calculation and plotting functions
+  * Changed: vignette now HTML instead of PDF
+  * Fixed: Formula parser now handles nested parentheses
+  * Fixed: Multi-reponse models with missing residuals() methods
+  * Fixed: Rugs now work with gg plots
+  * Fixed: Formula parsing for strata() in coxph models
+
 2.4-1 (2017-06-23)
   * New: Can now specify reference level for contrast plots by including x
     variable in 'cond' list (thank you GitHub@jealie for implementing this!)
@@ -21,7 +33,7 @@
     control/options
   * New: Added option to use ggplot2 instead of lattice to produce multi-panel
     plots
-  * New: Support for glmmADMB models.
+  * New: Support for glmmADMB models
   * Documentation: Added quick-start vignette
   * Fixed: Bug in which user options were not being passed to axis() when
     the horizontal axis was a factor

man/plot.visreg2d.Rd

@@ -0,0 +1,88 @@
+\name{plot.visreg2d}
+\alias{plot.visreg2d}
+\title{Visualization of regression functions for two variables}
+\description{Plot method for visualizing how two variables interact to
+  affect the response in regression models.}
+\usage{
+\method{plot}{visreg2d}(x, plot.type=c("image","persp","rgl", "gg"),
+xlab, ylab, zlab, color, print.cond=FALSE, whitespace=0.2, ...)
+}
+\arguments{
+  \item{x}{
+    A \code{\link{visreg2d}} object.
+  }
+  \item{plot.type}{
+    The style of plot to be produced.  The following three options are
+    supported:
+    \itemize{
+      \item \code{'image'}, a filled contour plot.
+      \item \code{'gg'}, a filled contour plot using \code{ggplot2}.
+      \item \code{'persp'}, a 3 dimensional perspective plot.
+      \item \code{'rgl'}, a version of the perspective plot that can be
+      rotated. Note: requires the rgl package to use.
+    }
+  }
+  \item{xlab}{
+    Axis label for x variable}
+  \item{ylab}{
+    Axis label for y variable}
+  \item{zlab}{
+    Axis label for outcome}
+  \item{color}{
+    For {\code{plot.type='persp'}} or {\code{plot.type='rgl'}}, the
+    color of the surface.  For {\code{plot.type='image'}} or
+    {\code{plot.type='gg'}}, a vector of colors used to establish a
+    color palette.}
+  \item{print.cond}{
+    If \code{print.cond==TRUE}, the explanatory variable values
+    conditioned on in a conditional plot are printed to the console
+    (default: \code{FALSE}). If \code{print.cond==TRUE} and
+    \code{type=="contrast"}, the conditions will still be printed, but
+    they have no bearing on the plot unless interactions are present.
+  }
+  \item{whitespace}{
+    When \code{xvar} or \code{yvar} is a factor, whitespace determines
+    the amount of space in between the factors.  Default is 0.2, meaning
+    that 20 percent of the axis is whitespace.
+  }
+  \item{\dots}{
+    Graphical parameters can be passed to the function to customize the
+    plots.
+  }
+}
+\references{
+  \itemize{
+    \item \url{http://pbreheny.github.io/visreg}
+    \item Breheny, P. and Burchett, W. (2017), Visualizing regression
+    models using visreg.
+    \url{https://journal.r-project.org/archive/2017/RJ-2017-046/index.html}
+  }
+}
+\author{
+  Patrick Breheny and Woodrow Burchett
+}
+\seealso{
+  \url{http://pbreheny.github.io/visreg/surface.html}
+  \code{\link{visreg}}
+}
+\examples{
+fit <- lm(Ozone ~ Solar.R + Wind + Temp + I(Wind^2) + I(Temp^2) +
+I(Wind*Temp)+I(Wind*Temp^2) + I(Temp*Wind^2) + I(Temp^2*Wind^2),
+data=airquality)
+
+visreg2d(fit, x="Wind", y="Temp", plot.type="image")
+visreg2d(fit, x="Wind", y="Temp", plot.type="image",
+         color=c("purple", "green", "red"))
+visreg2d(fit, x="Wind", y="Temp", plot.type="persp")
+
+## Requires the rgl package
+\dontrun{
+visreg2d(fit,x="Wind",y="Temp",plot.type="rgl")
+}
+
+## Requires the ggplot2 package
+\dontrun{
+visreg2d(fit, x="Wind", y="Temp", plot.type="gg")
+}
+
+}

man/visreg2d.Rd

@@ -6,11 +6,8 @@ A function used to visualize how two variables interact to affect the
 response in regression models.
 }
 \usage{
-visreg2d(fit, xvar, yvar, type=c("conditional", "contrast", "effect"),
-trans=I, scale=c("linear", "response"),
-plot.type=c("image", "persp", "rgl"), nn=ifelse(plot.type=="persp", 49,
-99), 
-cond=list(), print.cond=FALSE, whitespace=0.2, ...)
+visreg2d(fit, xvar, yvar, type=c("conditional", "contrast"), trans=I,
+scale=c("linear", "response"), nn=99, cond=list(), plot=TRUE, ...)
 }
 \arguments{
   \item{fit}{
@@ -51,16 +48,6 @@ cond=list(), print.cond=FALSE, whitespace=0.2, ...)
     function will be applied so that the model is plotted on the scale
     of the original response.
   }
-  \item{plot.type}{
-    The style of plot to be produced.  The following three options are
-    supported:
-    \itemize{
-      \item \code{'image'}, a filled contour plot.
-      \item \code{'persp'}, a 3 dimensional perspective plot.
-      \item \code{'rgl'}, a version of the perspective plot that can be
-      rotated. Note: requires the rgl package to use.
-    }
-  }
   \item{nn}{
     Resolution of the three dimensional plot.  Higher values will
     results in a smoother looking plot.
@@ -73,27 +60,22 @@ cond=list(), print.cond=FALSE, whitespace=0.2, ...)
     can be overridden by specifying their values using \code{cond} (see
     examples).
   }
-  \item{print.cond}{
-    If \code{print.cond==TRUE}, the explanatory variable values
-    conditioned on in a conditional plot are printed to the console
-    (default: \code{FALSE}). If \code{print.cond==TRUE} and
-    \code{type=="contrast"}, the conditions will still be printed, but
-    they have no bearing on the plot unless interactions are present.
-  }
-  \item{whitespace}{
-    When \code{xvar} or \code{yvar} is a factor, whitespace determines
-    the amount of space in between the factors.  Default is 0.2, meaning
-    that 20 percent of the axis is whitespace.
+  \item{plot}{
+    Send the calculations to \code{\link{plot.visreg2d}}, producing a
+    plot?  Default is TRUE.
   }
   \item{\dots}{
-    Graphical parameters can be passed to the function to customize the
-    plots.
+    Graphical parameters (e.g., \code{ylab}) can be passed to the
+    function to customize the plots.
   }
 }
 \value{
-  In addition to providing plots, the \code{visreg2d} function also
-  invisibly returns the x, y, and Z values used in the creation of its
-  plots.
+  A \code{visreg2d} object consisting of:
+  \item{x}{Values of \code{xvar} to be plotted}
+  \item{y}{Values of \code{yvar} to be plotted}
+  \item{z}{Values of outcome to be plotted}
+  \item{meta}{Meta-information needed to construct plots, such as the
+    name of the x and y variables.}  
 }
 \references{
   \itemize{
@@ -115,12 +97,17 @@ fit <- lm(Ozone ~ Solar.R + Wind + Temp + I(Wind^2) + I(Temp^2) +
 I(Wind*Temp)+I(Wind*Temp^2) + I(Temp*Wind^2) + I(Temp^2*Wind^2),
 data=airquality)
 
-visreg2d(fit,x="Wind",y="Temp",plot.type="image")
-visreg2d(fit,x="Wind",y="Temp",plot.type="persp")
+visreg2d(fit, x="Wind", y="Temp", plot.type="image")
+visreg2d(fit, x="Wind", y="Temp", plot.type="persp")
 
 ## Requires the rgl package
 \dontrun{
-visreg2d(fit,x="Wind",y="Temp",plot.type="rgl")
+visreg2d(fit, x="Wind", y="Temp", plot.type="rgl")
+}
+
+## Requires the ggplot2 package
+\dontrun{
+visreg2d(fit, x="Wind", y="Temp", plot.type="gg")
 }
 
 }