Version 2.4-1

pbreheny · Jun 23, 2017 · c9132c4 · c9132c4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: visreg
 Title: Visualization of Regression Models
 Version: 2.4-1
-Date: 2017-06-09
+Date: 2017-06-23
 Author: Patrick Breheny, Woodrow Burchett
 Maintainer: Patrick Breheny <[email protected]>
 Imports: lattice
 Suggests: rgl, MASS, survival, knitr, ggplot2
 Enhances: nlme
 VignetteBuilder: knitr
-Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'randomForest', etc.)
+Description: Provides a convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R ('lm', 'glm', 'coxph', 'rlm', 'gam', 'locfit', 'lmer', 'randomForest', etc.)
 License: GPL-3
 URL: http://pbreheny.github.io/visreg
diff --git a/NEWS b/NEWS
@@ -1,3 +1,15 @@
+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!)
+  * Changed: Default for transformed outcomes now rug=2
+  * Changed: Default color for persp plot
+  * Changed: visreg(fit) no longer plots constant objects
+  * Changed: Appearance of strip names for numeric 'by' variables
+  * Fixed: plot.visreg wasn't plotting gg objects by default
+  * Fixed: Bug in formula parsing w/ complicated interactions
+  * Fixed: Bugs in ggFactorPlot
+  * Fixed: print.cond warning using warning() instead of printing text
+
 2.4-0 (2017-06-09)
   * New: gg=TRUE works for regular plots, not just cross-sectional plots
   * New: gg=TRUE returns a gg object, which can then be manipulated further

diff --git a/R/plot.visreg.R b/R/plot.visreg.R
@@ -1,6 +1,6 @@
-plot.visreg <- function(x, overlay=FALSE, print.cond=FALSE, whitespace=0.2, partial=identical(x$meta$trans, I), band=TRUE, rug=(2*!partial),
-                        strip.names=is.numeric(x$fit[,x$meta$by]), legend=TRUE, line.par=NULL, fill.par=NULL,
-                        points.par=NULL, gg=FALSE, ...) {
+plot.visreg <- function(x, overlay=FALSE, print.cond=FALSE, whitespace=0.2, partial=identical(x$meta$trans, I), band=TRUE,
+                        rug=ifelse(partial, 0, 2), strip.names=is.numeric(x$fit[,x$meta$by]), legend=TRUE, line.par=NULL,
+                        fill.par=NULL, points.par=NULL, gg=FALSE, ...) {
   warn <- FALSE
   if (missing(print.cond)) {
     if (!("by" %in% names(x$meta)) & x$meta$hasInteraction) print.cond <- warn <- TRUE

diff --git a/R/setupX.R b/R/setupX.R
@@ -1,16 +1,24 @@
 setupX <- function(fit, f, name, nn, cond, ...) {
   ## Set up n x p matrix for (conditional) partial residuals
   x <- f[,name]
-	# Get the reference to plot contrasts from `cond` - if not present, fall back on using the mean (numerical) or the first factor
-	xref <- if (is.factor(x)) {
-		if (name %in% names(cond)) {
-			if (cond[[name]] %in% levels(x)) which(levels(x) == cond[[name]]) else xref = type.convert(cond[[name]], na.strings='')
-		} else {
-			1
-		}
-	} else {
-		if (name %in% names(cond)) cond[[name]] else mean(x)
-	}
+  if (is.factor(x)) {
+    xref <- 1
+    if (name %in% names(cond)) {
+      if (cond[[name]] %in% levels(x)) {
+        xref <- which(levels(x) == cond[[name]])
+      } else if (cond[[name]] %in% 1:length(levels(x))) {
+        xref <- cond[[name]]
+      } else {
+        warning(paste0("You have specified a value for ", name, " that is not one of its levels.\n  Using reference level instead."))
+      }
+    }
+  } else {
+    if (name %in% names(cond)) {
+      xref <- cond[[name]]
+    } else {
+      xref <- mean(x)
+    }
+  }
   x <- if (is.factor(x)) factor(c(xref, as.integer(x)), labels=levels(x)) else c(xref, x)
   xdf <- data.frame(x)
   names(xdf) <- name

diff --git a/inst/tests/visreg-contrast.R b/inst/tests/visreg-contrast.R
@@ -1,15 +1,28 @@
-## Tests of contrast plots
-## Real example; overparameterized model
-CO2$Plant <- factor(as.character(CO2$Plant))
-fit <- lm(uptake~.,CO2)
-visreg(fit,"conc",type="contrast")
-visreg(fit,"Plant",type="contrast")
+# Tests of contrast plots
 
+# Basic functionality
 ozone <- airquality[complete.cases(airquality),]
 ozone$Heat <- cut(ozone$Temp,3,labels=c("Cool","Mild","Hot"))
 fit <- lm(Ozone ~ Wind*Heat,data=ozone)
 visreg(fit,"Wind", type="contrast", by="Heat",layout=c(3,1))
-visreg(fit,"Wind", type="contrast", cond=list(Heat="Mild"))
+visreg(fit,"Wind", type="contrast", cond=list(Heat="Cool"), print.cond=FALSE)
+visreg(fit,"Wind", type="contrast", cond=list(Heat="Hot"), print.cond=FALSE)
+fit <- lm(Ozone ~ Wind + Heat,data=ozone)
+visreg(fit, "Wind", type="contrast", cond=list(Heat="Cool"))
+visreg(fit, "Wind", type="contrast", cond=list(Heat="Hot"))
+visreg(fit, "Wind", type="contrast", cond=list(Wind=5))
+visreg(fit, "Wind", type="contrast", cond=list(Wind=20))
+visreg(fit, "Heat", type="contrast")
+visreg(fit, "Heat", type="contrast", cond=list(Heat="Hot"))
+visreg(fit, "Heat", type="contrast", cond=list(Heat=3))
+visreg(fit, "Heat", type="contrast", cond=list(Heat=10))
+
+# Real example; overparameterized model
+CO2$Plant <- factor(as.character(CO2$Plant))
+fit <- lm(uptake~.,CO2)
+visreg(fit,"conc",type="contrast")
+visreg(fit,"Plant",type="contrast")
+
 
 ## Toy example
 x1 <- rep(1:10,2)

diff --git a/man/plot.visreg.Rd b/man/plot.visreg.Rd
@@ -12,8 +12,9 @@ accepts a \code{visreg} or \code{visregList} object as calculated by
 \usage{
 \method{plot}{visreg}(x, overlay=FALSE, print.cond=FALSE,
 whitespace=0.2, partial=identical(x$meta$trans, I), band=TRUE,
-rug=!partial, strip.names=is.numeric(x$fit[,x$meta$by]), legend=TRUE,
-line.par=NULL, fill.par=NULL, points.par=NULL, gg=FALSE, ...)
+rug=ifelse(partial, 0, 2), strip.names=is.numeric(x$fit[,x$meta$by]),
+legend=TRUE, line.par=NULL, fill.par=NULL, points.par=NULL, gg=FALSE,
+...)
 }
 \arguments{
 
@@ -121,7 +122,7 @@ line.par=NULL, fill.par=NULL, points.par=NULL, gg=FALSE, ...)
   Patrick Breheny and Woodrow Burchett
 }
 \seealso{
-  \code{\url{http://pbreheny.github.io/visreg/options.html}}
+  \url{http://pbreheny.github.io/visreg/options.html}
   \code{\link{visreg}}
   \code{\link{visreg2d}}
   \code{\link{visreg-faq}}

diff --git a/man/visreg.Rd b/man/visreg.Rd
@@ -156,7 +156,7 @@ cond=list(), jitter=FALSE, collapse=FALSE, plot=TRUE, ...)
   Patrick Breheny and Woodrow Burchett
 }
 \seealso{
-  \code{\url{http://pbreheny.github.io/visreg}}
+  \url{http://pbreheny.github.io/visreg}
   \code{\link{plot.visreg}}
   \code{\link{visreg2d}}
   \code{\link{visreg-faq}}

diff --git a/man/visreg2d.Rd b/man/visreg2d.Rd
@@ -7,8 +7,9 @@ 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),
+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, ...)
 }
 \arguments{
@@ -106,7 +107,7 @@ cond=list(), print.cond=FALSE, whitespace=0.2, ...)
   Patrick Breheny and Woodrow Burchett
 }
 \seealso{
-  \code{\url{http://pbreheny.github.io/visreg/surface.html}}
+  \url{http://pbreheny.github.io/visreg/surface.html}
   \code{\link{visreg}}
 }
 \examples{