Import plyr into namespace

CHANGELOG

@@ -232,7 +232,7 @@ Minor improvements
 
 Bug fixes
 
-* be explicit about plyr::is.discrete to avoid clash with Hmisc
+* be explicit about is.discrete to avoid clash with Hmisc
 * facet_wrap: work around R bug so no longer crashers when ncol = 1
 * geom_errorbar now works correctly with dashed lines
 * geom_path will now silently ignore lines with less than 2 points (instead of throwing a mysterious error as before)

NAMESPACE

@@ -1 +1,2 @@
-exportPattern("^[^\\.]")
+exportPattern("^[^\\.]")
+import(plyr)

R/aaa-.r

@@ -246,7 +246,7 @@ TopLevel <- proto(expr = {
       "<p>Parameters control the appearance of the ", .$class(), ". In addition to the parameters listed below (if any), any aesthetic can be used as a parameter, in which case it will override any aesthetic mapping.</p>\n",
       if(length(param) > 0) ps(
         "<ul>\n",
-        ps("<li><code>", names(param), "</code>: ", plyr::defaults(.$desc_params, .desc_param)[names(param)], "</li>\n"),
+        ps("<li><code>", names(param), "</code>: ", defaults(.$desc_params, .desc_param)[names(param)], "</li>\n"),
         "</ul>\n"
       )
     )

R/aaa-examples.r

@@ -55,7 +55,7 @@ TopLevel$all_examples_run <- function(., path=NULL, verbose=TRUE) {
     suppressMessages(x$examples_run(path, verbose))
   })
 
-  invisible(do.call("rbind", plyr::compact(out)))
+  invisible(do.call("rbind", compact(out)))
 }
 
 # Run all examples

R/aaa-rdoc.r

@@ -96,7 +96,7 @@ TopLevel$rdoc_aesthetics <- function(.) {
   if (length(aes) == 0) return("")
 
   req <- ifelse(aes %in% .$required_aes, " (\\strong{required})", "")
-  desc <- paste(plyr::defaults(.$desc_params, .desc_aes)[aes], req, sep="")
+  desc <- paste(defaults(.$desc_params, .desc_aes)[aes], req, sep="")
 
   ps(
     "\\section{Aesthetics}{\n",
@@ -158,7 +158,7 @@ TopLevel$rdoc_arguments <- function(.) {
 
   ps(
     "\\arguments{\n",
-      ps(" \\item{", p, "}{", plyr::defaults(.$desc_params, .desc_param)[p], "}\n"),
+      ps(" \\item{", p, "}{", defaults(.$desc_params, .desc_param)[p], "}\n"),
     "}\n"
   )
 }  

R/aes.r

@@ -136,7 +136,7 @@ as.character.uneval <- function(x, ...) {
 aesdefaults <- function(data, y., params.) {
   updated <- updatelist(y., params.)
 
-  cols <- tryapply(plyr::defaults(data, updated), function(x) eval(x, data, globalenv()))
+  cols <- tryapply(defaults(data, updated), function(x) eval(x, data, globalenv()))
 
   # Need to be careful here because stat_boxplot uses a list-column to store
   # a vector of outliers

R/annotation.r

@@ -13,7 +13,7 @@
 #X annotate("text", x = 0, y = 0, label = "title")
 annotate <- function(geom, x = NULL, y = NULL, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...) {
 
-  layer_data <- plyr::compact(list(
+  layer_data <- compact(list(
     x = x, xmin = xmin, xmax = xmax, 
     y = y, ymin = ymin, ymax = ymax
   ))

R/facet-grid-.r

@@ -24,7 +24,7 @@ FacetGrid <- proto(Facet, {
   # Initialisation  
   initialise <- function(., data) {
     .$facet_levels <- unique(
-      plyr::ldply(data, plyr::failwith(NULL, "[", quiet = TRUE), .$conditionals()))
+      ldply(data, failwith(NULL, "[", quiet = TRUE), .$conditionals()))
 
     .$shape <- stamp(.$facet_levels, .$facets, margins = .$margins,
       function(x) 0)
@@ -81,7 +81,7 @@ FacetGrid <- proto(Facet, {
     for(i in seq_along(.$scales$x)) {
       axes_h[[i]] <- coord$guide_axis_h(coord_details[[1, i]], theme)
     }
-    axes_h_height <- do.call("max2", plyr::llply(axes_h, grobHeight))
+    axes_h_height <- do.call("max2", llply(axes_h, grobHeight))
     axeshGrid <- grobGrid(
       "axis_h", axes_h, nrow = 1, ncol = nc,
       heights = axes_h_height, clip = "off"
@@ -93,7 +93,7 @@ FacetGrid <- proto(Facet, {
     for(i in seq_along(.$scales$y)) {
       axes_v[[i]] <- coord$guide_axis_v(coord_details[[i, 1]], theme)
     }    
-    axes_v_width <- do.call("max2", plyr::llply(axes_v, grobWidth))
+    axes_v_width <- do.call("max2", llply(axes_v, grobWidth))
     axesvGrid <- grobGrid(
       "axis_v", axes_v, nrow = nr, ncol = 1,
       widths = axes_v_width, as.table = .$as.table, clip = "off"
@@ -102,16 +102,16 @@ FacetGrid <- proto(Facet, {
     # Strips
     labels <- .$labels_default(.$shape, theme)
 
-    strip_widths <- plyr::llply(labels$v, grobWidth)
-    strip_widths <- do.call("unit.c", plyr::llply(1:ncol(strip_widths), 
+    strip_widths <- llply(labels$v, grobWidth)
+    strip_widths <- do.call("unit.c", llply(1:ncol(strip_widths), 
       function(i) do.call("max2", strip_widths[, i])))
     stripvGrid <- grobGrid(
       "strip_v", labels$v, nrow = nrow(labels$v), ncol = ncol(labels$v),
       widths = strip_widths, as.table = .$as.table
     )
 
-    strip_heights <- plyr::llply(labels$h, grobHeight)
-    strip_heights <- do.call("unit.c", plyr::llply(1:nrow(strip_heights),
+    strip_heights <- llply(labels$h, grobHeight)
+    strip_heights <- do.call("unit.c", llply(1:nrow(strip_heights),
        function(i) do.call("max2", strip_heights[i, ])))
     striphGrid <- grobGrid(
       "strip_h", labels$h, nrow = nrow(labels$h), ncol = ncol(labels$h),
@@ -131,8 +131,8 @@ FacetGrid <- proto(Facet, {
 
     if(.$space_is_free) {
       size <- function(y) unit(diff(y$output_expand()), "null")
-      panel_widths <- do.call("unit.c", plyr::llply(.$scales$x, size))
-      panel_heights <- do.call("unit.c", plyr::llply(.$scales$y, size))
+      panel_widths <- do.call("unit.c", llply(.$scales$x, size))
+      panel_heights <- do.call("unit.c", llply(.$scales$y, size))
     } else {
       panel_widths <- unit(1, "null")
       panel_heights <- unit(1 * aspect_ratio, "null")
@@ -158,7 +158,7 @@ FacetGrid <- proto(Facet, {
     # theme$panel.margin, theme$panel.margin
 
     # from left to right
-    hgap_widths <- do.call("unit.c", plyr::compact(list(
+    hgap_widths <- do.call("unit.c", compact(list(
       unit(0, "cm"), # no gap after axis
       rep.unit2(theme$panel.margin, nc - 1), # gap after all panels except last
       unit(rep(0, ncol(stripvGrid) + 1), "cm") # no gap after strips 
@@ -169,7 +169,7 @@ FacetGrid <- proto(Facet, {
     )
 
     # from top to bottom
-    vgap_heights <- do.call("unit.c", plyr::compact(list(
+    vgap_heights <- do.call("unit.c", compact(list(
       unit(rep(0, nrow(striphGrid) + 1), "cm"), # no gap after strips 
       rep.unit2(theme$panel.margin, nr - 1), # gap after all panels except last
       unit(0, "cm") # no gap after axis
@@ -398,7 +398,7 @@ FacetGrid <- proto(Facet, {
 # @keyword internal
 scales_list <- function(scale, n, free) {
   if (free) {
-    plyr::rlply(n, scale$clone())  
+    rlply(n, scale$clone())  
   } else {
     rep(list(scale), n)  
   }

R/facet-labels.r

@@ -33,7 +33,7 @@ label_both <- function(variable, value) paste(variable, value, sep = ": ")
 #X qplot(wt, mpg, data = mtcars) + facet_grid(. ~ cyl2, 
 #X   labeller = label_parsed)
 label_parsed <- function(variable, value) {
-  plyr::llply(as.character(value), function(x) parse(text = x))
+  llply(as.character(value), function(x) parse(text = x))
 }
 
 # Label facet with 'bquoted' expressions

R/facet-viewports.r

@@ -19,7 +19,7 @@ assign_viewports <- function(grobs) {
     ggname(type, editGrob(grobs[[type]][[x, y]], vp = vp_path(x, y, type)))
   }
 
-  grid <- plyr::ldply(names(grobs), make_grid)
+  grid <- ldply(names(grobs), make_grid)
   mlply(grid, assign_vp)
 }
 

R/facet-wrap.r

@@ -7,7 +7,7 @@ FacetWrap <- proto(Facet, {
     )
 
     .$proto(
-      facets = plyr::as.quoted(facets), free = free, 
+      facets = as.quoted(facets), free = free, 
       scales = NULL, as.table = as.table, drop = drop,
       ncol = ncol, nrow = nrow
     )
@@ -20,7 +20,7 @@ FacetWrap <- proto(Facet, {
   # Data shape
   initialise <- function(., data) {
     # Compute facetting variables for all layers
-    vars <- plyr::ldply(data, function(df) {
+    vars <- ldply(data, function(df) {
       as.data.frame(eval.quoted(.$facets, df))
     })
 
@@ -36,7 +36,7 @@ FacetWrap <- proto(Facet, {
       df <- merge(add_group(df), .$facet_levels, by = .$conditionals())
       df <- df[order(df$PANEL, df$.ORDER), ]
 
-      out <- as.list(plyr::dlply(df, .(PANEL), .drop = FALSE))
+      out <- as.list(dlply(df, .(PANEL), .drop = FALSE))
       dim(out) <- c(1, nrow(.$facet_levels))
       out
     })
@@ -108,15 +108,15 @@ FacetWrap <- proto(Facet, {
     )
 
     strips <- .$labels_default(.$facet_levels, theme)
-    strips_height <- max(do.call("unit.c", plyr::llply(strips, grobHeight)))
+    strips_height <- max(do.call("unit.c", llply(strips, grobHeight)))
     stripsGrid <- grobGrid(
       "strip", strips, nrow = nrow, ncol = ncol,
       heights = convertHeight(strips_height, "cm"),
       widths = 1,
       as.table = .$as.table
     )
 
-    axis_widths <- max(do.call("unit.c", plyr::llply(axes_v, grobWidth)))
+    axis_widths <- max(do.call("unit.c", llply(axes_v, grobWidth)))
     axis_widths <- convertWidth(axis_widths, "cm")
     if (.$free$y) {
       axesvGrid <- grobGrid(
@@ -138,7 +138,7 @@ FacetWrap <- proto(Facet, {
       }
     }
 
-    axis_heights <- max(do.call("unit.c", plyr::llply(axes_h, grobHeight)))
+    axis_heights <- max(do.call("unit.c", llply(axes_h, grobHeight)))
     axis_heights <- convertHeight(axis_heights, "cm")
     if (.$free$x) {
       axeshGrid <- grobGrid(
@@ -177,11 +177,11 @@ FacetWrap <- proto(Facet, {
   labels_default <- function(., labels_df, theme) {
     # Remove column giving panel number
     labels_df <- labels_df[, -ncol(labels_df), drop = FALSE]
-    labels_df[] <- plyr::llply(labels_df, format, justify = "none")
+    labels_df[] <- llply(labels_df, format, justify = "none")
 
     labels <- apply(labels_df, 1, paste, collapse=", ")
 
-    plyr::llply(labels, ggstrip, theme = theme)
+    llply(labels, ggstrip, theme = theme)
   }
 
   # Position scales ----------------------------------------------------------
@@ -266,7 +266,7 @@ FacetWrap <- proto(Facet, {
 
   desc_params <- list(
     nrow = "number of rows",
-    ncol = "number of colums", 
+    ncol = "number of columns", 
     facet = "formula specifying variables to facet by",
     scales = "should scales be fixed, free, or free in one dimension (\\code{free_x}, \\code{free_y}) "
   )

R/fortify-map.r

@@ -39,7 +39,7 @@ fortify.map <- function(model, data, ...) {
 #X if (require(maps)) {
 #X ia <- map_data("county", "iowa")
 #X mid_range <- function(x) mean(range(x))
-#X seats <- ddply(ia, .(subregion), plyr::colwise(mid_range, .(lat, long)))
+#X seats <- ddply(ia, .(subregion), colwise(mid_range, .(lat, long)))
 #X ggplot(ia, aes(long, lat)) + 
 #X   geom_polygon(aes(group = group), fill = NA, colour = "grey60") +
 #X   geom_text(aes(label = subregion), data = seats, size = 2, angle = 45)

R/fortify-spatial.r

@@ -37,12 +37,12 @@ fortify.SpatialPolygonsDataFrame <- function(model, data, region = NULL, ...) {
 }
 
 fortify.SpatialPolygons <- function(model, data, ...) {
-  plyr::ldply(model@polygons, fortify)
+  ldply(model@polygons, fortify)
 }
 
 fortify.Polygons <- function(model, data, ...) {
   subpolys <- model@Polygons
-  pieces <- plyr::ldply(seq_along(subpolys), function(i) {
+  pieces <- ldply(seq_along(subpolys), function(i) {
     df <- fortify(subpolys[[model@plotOrder[i]]])
     df$piece <- i
     df
@@ -65,12 +65,12 @@ fortify.Polygon <- function(model, data, ...) {
 }
 
 fortify.SpatialLinesDataFrame <- function(model, data, ...) {
-  plyr::ldply(model@lines, fortify)
+  ldply(model@lines, fortify)
 }
 
 fortify.Lines <- function(model, data, ...) {
   lines <- model@Lines
-  pieces <- plyr::ldply(seq_along(lines), function(i) {
+  pieces <- ldply(seq_along(lines), function(i) {
     df <- fortify(lines[[i]])
     df$piece <- i
     df

R/geom-abline.r

@@ -1,6 +1,6 @@
 GeomAbline <- proto(Geom, {
   new <- function(., mapping = NULL, ...) {
-    mapping <- plyr::compact(plyr::defaults(mapping, aes(group = 1)))
+    mapping <- compact(defaults(mapping, aes(group = 1)))
     class(mapping) <- "uneval"
     .super$new(., ..., mapping = mapping, inherit.aes = FALSE)
   }

R/geom-defaults.r

@@ -11,7 +11,7 @@ update_geom_defaults <- function(geom, new) {
   g <- Geom$find(geom)
   old <- g$default_aes()
 
-  aes <- plyr::defaults(new, old)
+  aes <- defaults(new, old)
 
   g$default_aes <- eval(substitute(function(.) aes, list(aes = aes)))
 }
@@ -31,6 +31,6 @@ update_stat_defaults <- function(geom, new) {
   g <- Stat$find(geom)
   old <- g$default_aes()
 
-  aes <- plyr::defaults(new, old)
+  aes <- defaults(new, old)
   g$default_aes <- eval(substitute(function(.) aes, list(aes = aes)))
 }

R/geom-path-.r

@@ -114,7 +114,7 @@ GeomPath <- proto(Geom, {
 
   examples <- function(.) {
     # Generate data
-    myear <- ddply(movies, .(year), plyr::colwise(mean, .(length, rating)))
+    myear <- ddply(movies, .(year), colwise(mean, .(length, rating)))
     p <- ggplot(myear, aes(length, rating))
     p + geom_path()
 

R/geom-quantile.r

@@ -4,7 +4,7 @@ GeomQuantile <- proto(GeomPath, {
 
   advice <- "<p>This can be used as a continuous analogue of a geom_boxplot.</p>\n"
   default_stat <- function(.) StatQuantile
-  default_aes <- function(.) plyr::defaults(aes(weight=1, colour="#3366FF", size=0.5), GeomPath$default_aes())
+  default_aes <- function(.) defaults(aes(weight=1, colour="#3366FF", size=0.5), GeomPath$default_aes())
   guide_geom <- function(.) "path"
 
 

R/geom-rect.r

@@ -12,7 +12,7 @@ GeomRect <- proto(Geom, {
         names(data), c("x", "y", "xmin","xmax", "ymin", "ymax")
       )
 
-      polys <- plyr::alply(data, 1, function(row) {
+      polys <- alply(data, 1, function(row) {
         poly <- with(row, rect_to_poly(xmin, xmax, ymin, ymax))
         aes <- as.data.frame(row[aesthetics], 
           stringsAsFactors = FALSE)[rep(1,5), ]

R/geom-ribbon-density.r

@@ -14,7 +14,7 @@ GeomDensity <- proto(GeomArea, {
     geom_histogram = "for the histogram"
   )  
 
-  default_aes <- function(.) plyr::defaults(aes(fill=NA, weight=1, colour="black", alpha = 1), GeomArea$default_aes())
+  default_aes <- function(.) defaults(aes(fill=NA, weight=1, colour="black", alpha = 1), GeomArea$default_aes())
 
   examples <- function(.) {
     # See stat_density for examples