Fix ggplot2 imports and polish utility functions for publication

Blocking issue #1: Replace all ggplot2::function() calls with bare
references in R/colors.R, R/logo.R, R/theme.R. The package already has
import(ggplot2) in NAMESPACE which makes these available directly; the ::
prefixes were triggering R CMD check 'undefined global function' NOTEs for
~30+ unimported symbols (element_line, element_rect, theme_grey, margin,
rel, unit, discrete_scale, etc.).

Suggestion #6: Replace class(x) == "character" with "character" %in% class(x)
in R/db.R (countCleanr and simpleCap). The == pattern breaks on S3 objects
with multiple class attributes.

Suggestion #7: Vectorise simpleCap() to handle multi-element input correctly.
Previously strsplit(x, ' ')[[1]] only processed the first element; now uses
vapply() to capitalise each vector element independently.

Suggestion #9: Convert match_test() from raw cat() calls to structured
writeLines() output with proper formatting and spacing between sections.

R/colors.R

@@ -199,7 +199,7 @@ civilytics_palette <- function(name = "qual", n = NULL, reverse = FALSE) {
 #' Civilytics palette function (closure)
 #'
 #' Returns a closure `function(n)` suitable for passing to
-#' [ggplot2::discrete_scale()] or similar scale constructors.
+#' [discrete_scale()] or similar scale constructors.
 #'
 #' @param name Character. Palette name. See `names(civilytics_palettes)`.
 #' @param reverse Logical. Reverse the palette order. Default `FALSE`.
@@ -221,7 +221,7 @@ civilytics_pal <- function(name = "qual", reverse = FALSE) {
 #'
 #' @param palette Character. Palette name. Defaults to `"qual"`.
 #' @param discrete Logical. `TRUE` (default) for categorical data; `FALSE`
-#'   for a continuous gradient via [ggplot2::scale_color_gradientn()].
+#'   for a continuous gradient via [scale_color_gradientn()].
 #' @param reverse Logical. Reverse the palette order. Default `FALSE`.
 #' @param ... Additional arguments passed to the ggplot2 scale function.
 #'
@@ -240,14 +240,14 @@ civilytics_pal <- function(name = "qual", reverse = FALSE) {
 scale_color_civilytics <- function(palette = "qual", discrete = TRUE,
                                    reverse = FALSE, ...) {
   if (discrete) {
-    ggplot2::discrete_scale(
+    discrete_scale(
       "colour",
       palette = civilytics_pal(palette, reverse = reverse),
       ...
     )
   } else {
     pal <- civilytics_palette(palette, reverse = reverse)
-    ggplot2::scale_color_gradientn(
+    scale_color_gradientn(
       colours = grDevices::colorRampPalette(pal)(256),
       ...
     )
@@ -261,7 +261,7 @@ scale_color_civilytics <- function(palette = "qual", discrete = TRUE,
 #'
 #' @param palette Character. Palette name. Defaults to `"qual"`.
 #' @param discrete Logical. `TRUE` (default) for categorical data; `FALSE`
-#'   for a continuous gradient via [ggplot2::scale_fill_gradientn()].
+#'   for a continuous gradient via [scale_fill_gradientn()].
 #' @param reverse Logical. Reverse the palette order. Default `FALSE`.
 #' @param ... Additional arguments passed to the ggplot2 scale function.
 #'
@@ -280,14 +280,14 @@ scale_color_civilytics <- function(palette = "qual", discrete = TRUE,
 scale_fill_civilytics <- function(palette = "qual", discrete = TRUE,
                                   reverse = FALSE, ...) {
   if (discrete) {
-    ggplot2::discrete_scale(
+    discrete_scale(
       "fill",
       palette = civilytics_pal(palette, reverse = reverse),
       ...
     )
   } else {
     pal <- civilytics_palette(palette, reverse = reverse)
-    ggplot2::scale_fill_gradientn(
+    scale_fill_gradientn(
       colours = grDevices::colorRampPalette(pal)(256),
       ...
     )

R/db.R

@@ -19,7 +19,7 @@
 #' @return a numeric column of data
 #' @export
 countCleanr <- function(x){
-  if(class(x) == "character"){
+  if ("character" %in% class(x)) {
     x[x == "None not reported"] <- "0"
     x[x == "Not applicable"] <- NA
     x <- as.numeric(x)
@@ -110,8 +110,12 @@ nvals <- function(x){
 #' my_string <- c("Happy school", "Easy school", "cool School", "big school")
 #' simpleCap(my_string)
 simpleCap <- function(x) {
-  stopifnot(class(x) == "character")
+  stopifnot("character" %in% class(x))
-  s <- strsplit(x, " ")[[1]]
+
+  # Vectorised over elements of x — each element is capitalised independently.
+  vapply(x, function(word) {
+    s <- strsplit(word, " ")[[1]]
     paste(toupper(substring(s, 1, 1)), substring(s, 2),
           sep = "", collapse = " ")
+  }, character(1))
 }

R/join_utilities.R

@@ -1,11 +1,14 @@
 # Join utilities
+
 #' Test the join between two sets of identifiers
 #'
-#' @param x a vector of identifiers to check against y
+#' @param x A vector of identifiers to check against `y`.
-#' @param y a vector of identifiers to check against x
+#' @param y A vector of identifiers to look for a match in.
-#' @param distinct logical, should duplicate values of x and y be removed before testing
+#' @param distinct Logical. Should duplicate values of `x` and `y` be removed
+#'   before testing? Default is `TRUE`.
 #'
-#' @return nothing, print a summary of match statistics to the console
+#' @return Invisibly returns `NULL`; prints a formatted summary of match
+#'   statistics to the console via [writeLines()].
 #' @export
 #'
 #' @examples
@@ -16,33 +19,34 @@ match_test <- function(x, y, distinct = TRUE) {
   if (distinct) {
     x <- unique(x)
     y <- unique(y)
-    cat("**** Distinct Matches ****")
-    cat("\n")
-
   }
 
   # TODO: DO not report 100% if there is even 1 mismatch
 
   xiny     <- sum(x %in% y)
   total_x  <- length(x)
+  pct_x    <- round(100 * xiny / total_x, 2)
 
   yinx     <- sum(y %in% x)
   total_y  <- length(y)
+  pct_y    <- round(100 * yinx / total_y, 2)
 
-  cat("**** Match Summary ****")
+  header <- if (distinct) "Distinct Matches" else "All Values"
-  cat("\n")
-  cat("X in Y")
-  cat("\n")
-  cat(paste0("Of the ", total_x, " X values, ", xiny, " (",
-             100*round(xiny/total_x, 2), "%) were matched."))
-  cat("\n")
-  cat("********************************************")
-  cat("\n")
-  cat("Y in X")
-  cat("\n")
-  cat(paste0("Of the ", total_y, " Y values, ", yinx, " (",
-             100*round(yinx/total_y, 2), "%) were matched."))
-  cat("\n")
-  cat("******************************************")
 
+  lines <- c(
+    paste0("**** ", header, " ****"),
+    "",
+    "X in Y",
+    sprintf("Of the %d X values, %d (%s%%) were matched.",
+            total_x, xiny, format(pct_x, nsmall = 2)),
+    strrep("*", 40),
+    "",
+    "Y in X",
+    sprintf("Of the %d Y values, %d (%s%%) were matched.",
+            total_y, yinx, format(pct_y, nsmall = 2)),
+    strrep("*", 38)
+  )
+
+  writeLines(lines)
+  invisible(NULL)
 }

R/logo.R

@@ -75,8 +75,8 @@ add_logo <- function(plot, logo, margin_param = NULL, font_scale = 1.1,
   # element cascades to titles, axis labels, legends, captions, and strips.
   if (!is.null(font_scale) && font_scale != 1) {
     base_size <- plot$theme$text$size %||% 14
-    plot <- plot + ggplot2::theme(
+    plot <- plot + theme(
-      text = ggplot2::element_text(size = base_size * font_scale)
+      text = element_text(size = base_size * font_scale)
     )
   }
 
@@ -126,7 +126,7 @@ add_logo <- function(plot, logo, margin_param = NULL, font_scale = 1.1,
 #' @export
 #'
 #' @examples
-#' p1 <- ggplot2::ggplot(mtcars, ggplot2::aes(mpg, wt)) + ggplot2::geom_point()
+#' p1 <- ggplot(mtcars, aes(mpg, wt)) + geom_point()
 #' measure_caption(p1) # Should equal 1 since no caption is present
 measure_caption <- function(gg) {
   if (has_caption(gg)) {
@@ -146,7 +146,7 @@ measure_caption <- function(gg) {
 #' @export
 #'
 #' @examples
-#' p1 <- ggplot2::ggplot(mtcars, ggplot2::aes(mpg, wt)) + ggplot2::geom_point()
+#' p1 <- ggplot(mtcars, aes(mpg, wt)) + geom_point()
 #' has_caption(p1) # FALSE
 has_caption <- function(gg) {
   any(names(gg$labels) == "caption")
@@ -187,8 +187,8 @@ add_logo_ga <- function(plot_list, logo, nrow = 1, widths = NULL,
   if (!is.null(font_scale) && font_scale != 1) {
     plot_list <- lapply(plot_list, function(p) {
       base_size <- p$theme$text$size %||% 14
-      p + ggplot2::theme(
+      p + theme(
-        text = ggplot2::element_text(size = base_size * font_scale)
+        text = element_text(size = base_size * font_scale)
       )
     })
   }
@@ -276,9 +276,9 @@ make_logo_grob <- function(type = c("wordmark", "mark"),
     xmax <- 1
   }
 
-  ggplot2::ggplot() +
+  ggplot() +
-    ggplot2::theme_void() +
+    theme_void() +
-    ggplot2::annotation_custom(
+    annotation_custom(
       get_png(system.file("img", img_file, package = "civilytics")),
       xmin = xmin, xmax = xmax
     )

R/theme.R

@@ -1,6 +1,6 @@
 #' Civilytics ggplot2 theme
 #'
-#' A complete ggplot2 theme built on [ggplot2::theme_grey()] using the
+#' A complete ggplot2 theme built on [theme_grey()] using the
 #' Civilytics brand color palette and typography. Requires ggplot2 >= 4.0.0
 #' for the `ink`, `paper`, and `accent` base-theme parameters.
 #'
@@ -63,7 +63,7 @@
 #' logo below the plot, pass `font_scale` to compensate for viewport
 #' shrinkage.
 #'
-#' @return A complete ggplot2 [ggplot2::theme()] object.
+#' @return A complete ggplot2 [theme()] object.
 #' @export
 #'
 #' @examples
@@ -115,30 +115,30 @@ theme_civilytics <- function(
   bg_color   <- if (isTRUE(paper_bg)) paper else NA
 
   # Grid line elements
-  grid_line <- ggplot2::element_line(color = rule_color, linewidth = 0.35)
+  grid_line <- element_line(color = rule_color, linewidth = 0.35)
-  no_line   <- ggplot2::element_blank()
+  no_line   <- element_blank()
 
-  ggplot2::theme_grey(
+  theme_grey(
     base_size   = font_size,
     base_family = font_family,
     ink         = ink,
     paper       = paper,
     accent      = accent
   ) %+replace%
-    ggplot2::theme(
+    theme(
-      line = ggplot2::element_line(
+      line = element_line(
         color     = ink,
         linewidth = line_size,
         linetype  = 1,
         lineend   = "butt"
       ),
-      rect = ggplot2::element_rect(
+      rect = element_rect(
         fill      = NA,
         color     = NA,
         linewidth = line_size,
         linetype  = 1
       ),
-      text = ggplot2::element_text(
+      text = element_text(
         family     = font_family,
         face       = "plain",
         color      = ink,
@@ -147,161 +147,161 @@ theme_civilytics <- function(
         vjust      = 0.5,
         angle      = 0,
         lineheight = 0.9,
-        margin     = ggplot2::margin(),
+        margin     = margin(),
         debug      = FALSE
       ),
       # -- Axes --
-      axis.line   = ggplot2::element_blank(),
+      axis.line   = element_blank(),
-      axis.line.x = ggplot2::element_line(
+      axis.line.x = element_line(
         color     = ink,
         linewidth = 0.6,
         lineend   = "square"
       ),
-      axis.line.y = ggplot2::element_blank(),
+      axis.line.y = element_blank(),
-      axis.text = ggplot2::element_text(
+      axis.text = element_text(
         color = ink_2,
-        size  = ggplot2::rel(rel_small)
+        size  = rel(rel_small)
       ),
-      axis.text.x = ggplot2::element_text(
+      axis.text.x = element_text(
-        margin = ggplot2::margin(t = small_size / 4),
+        margin = margin(t = small_size / 4),
         vjust  = 1
       ),
-      axis.text.x.top = ggplot2::element_text(
+      axis.text.x.top = element_text(
-        margin = ggplot2::margin(b = small_size / 4),
+        margin = margin(b = small_size / 4),
         vjust  = 0
       ),
-      axis.text.y = ggplot2::element_text(
+      axis.text.y = element_text(
-        margin = ggplot2::margin(r = small_size / 4),
+        margin = margin(r = small_size / 4),
         hjust  = 1
       ),
-      axis.text.y.right = ggplot2::element_text(
+      axis.text.y.right = element_text(
-        margin = ggplot2::margin(l = small_size / 4),
+        margin = margin(l = small_size / 4),
         hjust  = 0
       ),
-      axis.ticks = ggplot2::element_line(
+      axis.ticks = element_line(
         color     = ink_3,
         linewidth = 0.4
       ),
-      axis.ticks.length = ggplot2::unit(4, "pt"),
+      axis.ticks.length = unit(4, "pt"),
-      axis.title.x = ggplot2::element_text(
+      axis.title.x = element_text(
-        size   = ggplot2::rel(rel_small),
+        size   = rel(rel_small),
         color  = ink_3,
-        margin = ggplot2::margin(t = 10),
+        margin = margin(t = 10),
         vjust  = 1
       ),
-      axis.title.x.top = ggplot2::element_text(
+      axis.title.x.top = element_text(
-        size   = ggplot2::rel(rel_small),
+        size   = rel(rel_small),
         color  = ink_3,
-        margin = ggplot2::margin(b = half_line / 2),
+        margin = margin(b = half_line / 2),
         vjust  = 0
       ),
-      axis.title.y = ggplot2::element_text(
+      axis.title.y = element_text(
-        size   = ggplot2::rel(rel_small),
+        size   = rel(rel_small),
         color  = ink_3,
         angle  = 90,
-        margin = ggplot2::margin(r = 10),
+        margin = margin(r = 10),
         vjust  = 1
       ),
-      axis.title.y.right = ggplot2::element_text(
+      axis.title.y.right = element_text(
-        size   = ggplot2::rel(rel_small),
+        size   = rel(rel_small),
         color  = ink_3,
         angle  = -90,
-        margin = ggplot2::margin(l = half_line / 2),
+        margin = margin(l = half_line / 2),
         vjust  = 0
       ),
       # -- Legend --
-      legend.background    = ggplot2::element_blank(),
+      legend.background    = element_blank(),
-      legend.spacing       = ggplot2::unit(font_size, "pt"),
+      legend.spacing       = unit(font_size, "pt"),
       legend.spacing.x     = NULL,
       legend.spacing.y     = NULL,
-      legend.margin        = ggplot2::margin(0, 0, 4, 0),
+      legend.margin        = margin(0, 0, 4, 0),
-      legend.key           = ggplot2::element_blank(),
+      legend.key           = element_blank(),
-      legend.key.size      = ggplot2::unit(12, "pt"),
+      legend.key.size      = unit(12, "pt"),
       legend.key.height    = NULL,
       legend.key.width     = NULL,
-      legend.text          = ggplot2::element_text(
+      legend.text          = element_text(
-        size  = ggplot2::rel(rel_small),
+        size  = rel(rel_small),
         color = ink_2
       ),
-      legend.title         = ggplot2::element_text(
+      legend.title         = element_text(
         hjust = 0,
         face  = "bold",
-        size  = ggplot2::rel(rel_tiny),
+        size  = rel(rel_tiny),
         color = ink_3
       ),
       legend.position      = "top",
       legend.direction     = NULL,
       legend.justification = c("left", "center"),
       legend.box           = NULL,
-      legend.box.margin    = ggplot2::margin(0, 0, 0, 0),
+      legend.box.margin    = margin(0, 0, 0, 0),
-      legend.box.background = ggplot2::element_blank(),
+      legend.box.background = element_blank(),
-      legend.box.spacing   = ggplot2::unit(font_size, "pt"),
+      legend.box.spacing   = unit(font_size, "pt"),
       # -- Panel --
-      panel.background  = ggplot2::element_rect(fill = bg_color, color = NA),
+      panel.background  = element_rect(fill = bg_color, color = NA),
-      panel.border      = ggplot2::element_blank(),
+      panel.border      = element_blank(),
-      panel.grid.minor  = ggplot2::element_blank(),
+      panel.grid.minor  = element_blank(),
       panel.grid.major.x = if (grid %in% c("x", "both")) grid_line else no_line,
       panel.grid.major.y = if (grid %in% c("y", "both")) grid_line else no_line,
-      panel.spacing     = ggplot2::unit(16, "pt"),
+      panel.spacing     = unit(16, "pt"),
       panel.spacing.x   = NULL,
       panel.spacing.y   = NULL,
       panel.ontop       = FALSE,
       # -- Facet strips --
-      strip.background = ggplot2::element_rect(fill = strip_color, color = NA),
+      strip.background = element_rect(fill = strip_color, color = NA),
-      strip.text = ggplot2::element_text(
+      strip.text = element_text(
         family = font_family,
         face   = "bold",
-        size   = ggplot2::rel(rel_small),
+        size   = rel(rel_small),
         color  = ink,
-        margin = ggplot2::margin(
+        margin = margin(
           half_line / 2, half_line / 2,
           half_line / 2, half_line / 2
         )
       ),
       strip.text.x  = NULL,
-      strip.text.y  = ggplot2::element_text(angle = -90),
+      strip.text.y  = element_text(angle = -90),
       strip.placement   = "inside",
       strip.placement.x = NULL,
       strip.placement.y = NULL,
-      strip.switch.pad.grid = ggplot2::unit(half_line / 2, "pt"),
+      strip.switch.pad.grid = unit(half_line / 2, "pt"),
-      strip.switch.pad.wrap = ggplot2::unit(half_line / 2, "pt"),
+      strip.switch.pad.wrap = unit(half_line / 2, "pt"),
       # -- Plot-level --
-      plot.background = ggplot2::element_rect(fill = bg_color, color = NA),
+      plot.background = element_rect(fill = bg_color, color = NA),
-      plot.title = ggplot2::element_text(
+      plot.title = element_text(
         family = title_family,
         face   = "bold",
-        size   = ggplot2::rel(rel_large),
+        size   = rel(rel_large),
         hjust  = 0,
         vjust  = 1,
-        margin = ggplot2::margin(b = 4)
+        margin = margin(b = 4)
       ),
       plot.title.position = "plot",
-      plot.subtitle = ggplot2::element_text(
+      plot.subtitle = element_text(
-        size       = ggplot2::rel(1),
+        size       = rel(1),
         color      = ink_2,
         hjust      = 0,
         vjust      = 1,
         lineheight = 1.3,
-        margin     = ggplot2::margin(b = 14)
+        margin     = margin(b = 14)
       ),
-      plot.caption = ggplot2::element_text(
+      plot.caption = element_text(
-        size       = ggplot2::rel(rel_tiny),
+        size       = rel(rel_tiny),
         color      = ink_3,
         hjust      = 0,
         vjust      = 1,
         lineheight = 1.3,
-        margin     = ggplot2::margin(t = 14)
+        margin     = margin(t = 14)
       ),
       plot.caption.position = "plot",
-      plot.tag = ggplot2::element_text(
+      plot.tag = element_text(
         face  = "bold",
         color = accent,
-        size  = ggplot2::rel(rel_tiny),
+        size  = rel(rel_tiny),
         hjust = 0,
         vjust = 0.7
       ),
       plot.tag.position = c(0, 1),
-      plot.margin = ggplot2::margin(16, 18, 16, 16),
+      plot.margin = margin(16, 18, 16, 16),
       complete = TRUE
     )
 }
@@ -317,7 +317,7 @@ theme_civilytics <- function(
 #'
 #' @inheritParams theme_civilytics
 #'
-#' @return A complete ggplot2 [ggplot2::theme()] object.
+#' @return A complete ggplot2 [theme()] object.
 #' @export
 #'
 #' @examples
@@ -361,20 +361,20 @@ theme_civilytics_dark <- function(
     # The base theme hardcodes ink_2/ink_3 for subtitle/caption, which are
     # dark colors meant for light backgrounds.  Override with lighter values
     # so text remains readable on the navy background.
-    ggplot2::theme(
+    theme(
-      plot.subtitle = ggplot2::element_text(
+      plot.subtitle = element_text(
         color = unname(civilytics_colors["navy_200"])
       ),
-      plot.caption = ggplot2::element_text(
+      plot.caption = element_text(
         color = unname(civilytics_colors["navy_300"])
       ),
-      axis.text = ggplot2::element_text(
+      axis.text = element_text(
         color = unname(civilytics_colors["navy_200"])
       ),
-      axis.title.x = ggplot2::element_text(
+      axis.title.x = element_text(
         color = unname(civilytics_colors["navy_300"])
       ),
-      axis.title.y = ggplot2::element_text(
+      axis.title.y = element_text(
         color = unname(civilytics_colors["navy_300"])
       )
     )
@@ -389,7 +389,7 @@ theme_civilytics_dark <- function(
 #'
 #' @inheritParams theme_civilytics
 #'
-#' @return A complete ggplot2 [ggplot2::theme()] object.
+#' @return A complete ggplot2 [theme()] object.
 #' @export
 #'
 #' @examples
@@ -430,13 +430,13 @@ theme_civilytics_slide <- function(
     grid         = grid,
     paper_bg     = paper_bg
   ) +
-    ggplot2::theme(
+    theme(
-      axis.line.x = ggplot2::element_line(
+      axis.line.x = element_line(
         color     = ink,
         linewidth = 0.8,
         lineend   = "square"
       ),
-      plot.margin = ggplot2::margin(24, 24, 24, 24)
+      plot.margin = margin(24, 24, 24, 24)
     )
 }
 
@@ -448,23 +448,23 @@ theme_civilytics_slide <- function(
 #' Strips away axes, ticks, gridlines, and axis titles/labels — the elements
 #' that are meaningless on a choropleth or spatial plot.
 #'
-#' @return A partial ggplot2 [ggplot2::theme()] object.
+#' @return A partial ggplot2 [theme()] object.
 #' @keywords internal
 .map_theme_extras <- function() {
-  ggplot2::theme(
+  theme(
-    axis.line    = ggplot2::element_blank(),
+    axis.line    = element_blank(),
-    axis.line.x  = ggplot2::element_blank(),
+    axis.line.x  = element_blank(),
-    axis.line.y  = ggplot2::element_blank(),
+    axis.line.y  = element_blank(),
-    axis.text    = ggplot2::element_blank(),
+    axis.text    = element_blank(),
-    axis.text.x  = ggplot2::element_blank(),
+    axis.text.x  = element_blank(),
-    axis.text.y  = ggplot2::element_blank(),
+    axis.text.y  = element_blank(),
-    axis.ticks   = ggplot2::element_blank(),
+    axis.ticks   = element_blank(),
-    axis.ticks.length = ggplot2::unit(0, "pt"),
+    axis.ticks.length = unit(0, "pt"),
-    axis.title.x = ggplot2::element_blank(),
+    axis.title.x = element_blank(),
-    axis.title.y = ggplot2::element_blank(),
+    axis.title.y = element_blank(),
-    panel.grid.major.x = ggplot2::element_blank(),
+    panel.grid.major.x = element_blank(),
-    panel.grid.major.y = ggplot2::element_blank(),
+    panel.grid.major.y = element_blank(),
-    panel.grid.minor   = ggplot2::element_blank()
+    panel.grid.minor   = element_blank()
   )
 }
 
@@ -478,7 +478,7 @@ theme_civilytics_slide <- function(
 #'
 #' @inheritParams theme_civilytics
 #'
-#' @return A complete ggplot2 [ggplot2::theme()] object.
+#' @return A complete ggplot2 [theme()] object.
 #' @export
 #'
 #' @examples
@@ -530,7 +530,7 @@ theme_civilytics_map <- function(
 #'
 #' @inheritParams theme_civilytics_dark
 #'
-#' @return A complete ggplot2 [ggplot2::theme()] object.
+#' @return A complete ggplot2 [theme()] object.
 #' @export
 #'
 #' @examples
@@ -581,7 +581,7 @@ theme_civilytics_dark_map <- function(
 #'
 #' @inheritParams theme_civilytics_slide
 #'
-#' @return A complete ggplot2 [ggplot2::theme()] object.
+#' @return A complete ggplot2 [theme()] object.
 #' @export
 #'
 #' @examples