Fixes for R CMD check

R/date-time-breaks.r

@@ -1,3 +1,8 @@
+# Time breaks
+# Automatically compute sensible axis breaks for time data
+# 
+# @arguments range in seconds
+# @keyword internal
 time_breaks <- function(seconds) {
   days <- seconds / 86400
   if (days > 5) {
@@ -17,6 +22,11 @@ time_breaks <- function(seconds) {
 
 }
 
+# Date breaks
+# Automatically compute sensible axis breaks for date data
+# 
+# @arguments range in days
+# @keyword internal
 date_breaks <- function(days) {
   length <- cut(days, c(0, 10, 56, 365, 730, 5000, Inf), labels=FALSE)
 

R/facet-wrap.r

@@ -98,11 +98,13 @@ FacetWrap <- proto(Facet, {
     axes_h <- grobMatrix(axes_h, nrow, ncol, .$as.table)
     axes_height <- grobRowHeight(axes_h)
 
-    all <- cweave(
-      rweave(gap,    axes_v, gap,    gap), 
-      rweave(labels, panels, axes_h, gap), 
-      rweave(gap,    gap,    gap,    gap)
-    )
+    all <- rweave(
+      cweave(gap,    labels, gap),
+      cweave(axes_v, panels, gap),
+      cweave(gap,    axes_h, gap),
+      cweave(gap,    gap,    gap)
+    )    
+
     margin <- list(theme$panel.margin)
     heights <- interleave(labels_height, panels_height, axes_height, margin)
     heights <- do.call("unit.c", heights)

R/fortify.r

@@ -10,13 +10,13 @@ fortify <- function(model, data, ...) UseMethod("fortify")
 # The following statistics will be added to the data frame:
 # 
 # \itemize{
-#   \item[.hat] Diagonal of the hat matrix
-#   \item[.sigma] Estimate of residual standard deviation when corresponding
-#      observation is dropped from model
-#   \item{.cooksd} Cooks distance, \code{\link{cooks.distance}}
-#   \item{.fitted} Fitted values of model
-#   \item{.resid} Residual
-#  \item{.stdresid} Standardised residuals
+#   \item{.hat}{Diagonal of the hat matrix}
+#   \item{.sigma}{Estimate of residual standard deviation when corresponding
+#      observation is dropped from model}
+#   \item{.cooksd}{Cooks distance, \code{\link{cooks.distance}}}
+#   \item{.fitted}{Fitted values of model}
+#   \item{.resid}{Residuals}
+#  \item{.stdresid}{Standardised residuals}
 # }
 # 
 # If you have missing values in your model data, you may need to refit 
@@ -69,7 +69,7 @@ fortify.lm <- function(model, data = model$model, ...) {
 
   data$.hat <- infl$hat
   data$.sigma <- infl$sigma 
-  data$.cooksd <- cooks.distance(mod)
+  data$.cooksd <- cooks.distance(model)
 
   data$.fitted <- predict(model)
   data$.resid <- resid(model)

R/guides-legend.r

@@ -43,7 +43,8 @@ guide_legends_box <- function(scales, layers, default_mapping, horizontal = FALS
 # @argument list description usage of aesthetics in geoms
 # @keyword internal
 # @value A list of grobs
-# 
+# @alias build_legend
+# @alias build_legend_data
 #X theme_update(legend.background = theme_rect(size = 0.2))
 #X qplot(mpg, wt, data = mtcars)
 #X qplot(mpg, wt, data = mtcars, colour = cyl)
@@ -84,7 +85,7 @@ build_legend <- function(name, mapping, layers, default_mapping, theme) {
   points <- laply(layers, function(l) l$geom$objname == "point")
   width <- max(unlist(llply(legend_data[points], "[[", "size")), 0)
 
-  name <- eval(parse(text = name))    
+  name <- eval(parse(text = name))
   title <- theme_render(
     theme, "legend.title",
     name, x = 0, y = 0.5

R/labels.r

@@ -14,6 +14,7 @@ update_labels <- function(p, labels) {
 
   for(name in names(labels)) {
     scale <- p$scales$get_scales(name)$clone()
+    p$scales$add(scale)
     scale$name <- labels[[name]]
   }
 

R/plot.r

@@ -1,14 +1,11 @@
 # Create a new plot
 # Create a new ggplot plot
 # 
-# @alias package-ggplot
 # @seealso \url{http://had.co.nz/ggplot2}
-# @seealso ggplot.data.frame
+# @alias ggplot.default
 # @keyword hplot
 ggplot <- function(data = NULL, ...) UseMethod("ggplot")
 
-# Catch all plotting method
-# 
 ggplot.default <- function(data, mapping = aes(), ...) {
   if (is.null(data)) {
     ggplot.data.frame(data, mapping, ...)
@@ -24,6 +21,7 @@ ggplot.default <- function(data, mapping = aes(), ...) {
 # @arguments default data frame
 # @arguments default list of aesthetic mappings (these can be colour, size, shape, line type -- see individual geom functions for more details)
 # @seealso \url{http://had.co.nz/ggplot2}
+# @alias package-ggplot
 # @keyword hplot
 ggplot.data.frame <- function(data, mapping=aes(), ..., environment = globalenv()) {
   if (!missing(mapping) && !inherits(mapping, "uneval")) stop("Mapping should be created with aes or aes_string")

R/scale-date.r

@@ -10,7 +10,6 @@
 #
 #   * threshold for displaying first/last tick mark outside the data: if the last date point is > threshold * interval (default to 0.9)
 
-TransDate <- Trans$new("date", "as.numeric", "to_date")
 ScaleDate <- proto(ScaleContinuous,{
   .major_seq <- NULL
   .minor_seq <- NULL

R/scale-datetime.r

@@ -1,5 +1,8 @@
+# To time
+# Turn numeric vector into POSIXct vector
+# 
+# @keyword internal
 to_time <- function(x) structure(x, class = c("POSIXt", "POSIXct"))
-TransDatetime <- Trans$new("datetime", "as.numeric", "to_time")
 
 ScaleDatetime <- proto(ScaleDate, {
   .major_seq <- NULL

R/stat-smooth-methods.r

@@ -4,7 +4,7 @@
 # @keywords internal
 # @alias predictdf.default
 # @alias predictdf.glm
-predictdf <- function(model, ...) UseMethod("predictdf")
+predictdf <- function(model, xseq, se, level) UseMethod("predictdf")
 
 predictdf.default <- function(model, xseq, se, level) {
   pred <- stats::predict(model, data.frame(x = xseq), se = se)

R/theme-defaults.r

@@ -58,6 +58,7 @@ theme_bw <- function(base_size = 12) {
 
     legend.background = theme_rect(colour=NA), 
     legend.key =        theme_rect(colour = "grey80"),
+    legend.key.size =   unit(1.2, "lines"),
     legend.text =       theme_text(size = base_size * 0.8),
     legend.title =      theme_text(size = base_size * 0.8, face = "bold", hjust = 0),
     legend.position =   "right",

R/trans-.r

@@ -112,4 +112,7 @@ TransLogit <- ProbabilityTrans$new("logis")
 TransPow10 <- Trans$new("pow10",function(x) 10^x, "log10", function(x) log10(x))
 TransProbit <- ProbabilityTrans$new("norm")
 TransReverse <- Trans$new("reverse", function(x) -x, function(x) -x, function(x) bquote(.(-x)))
-TransSqrt <- Trans$new("sqrt", "sqrt", function(x) x^2, function(x) x^2)
+TransSqrt <- Trans$new("sqrt", "sqrt", function(x) x^2, function(x) x^2)
+
+TransDate <- Trans$new("date", "as.numeric", "to_date")
+TransDatetime <- Trans$new("datetime", "as.numeric", "to_time")