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
unname(vapply()) to capitalise each vector element independently while
preserving the original scalar behaviour (no names attribute on output).

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

.Rbuildignore

@@ -3,9 +3,9 @@
 ^\.github$
 ^\.gitea$
 ^README\.Rmd$
+^NEWS\.md$
 ^Makefile$
 ^Dockerfile$
-^LICENSE\.md$
 ^\.claude$
 ^\.playwright-mcp$
 ^civilytics-site\.png$

NEWS.md

@@ -0,0 +1,16 @@
+# civilytics 0.3.2
+
+## New features
+- Added comprehensive test coverage for the `prop_conf` module, including
+  correctness checks against `binom.test()` for Clopper-Pearson intervals and
+  formula-based verification for Wald and Agresti-Coull intervals.
+
+## Bug fixes
+- Removed vendored headshot images (`Knowles_Headshot_2019_good.jpg`,
+  `Knowles_Headshot_2019_prisma.jpg`) from `inst/img/` to prevent personal
+  photos from being distributed with the package. The `plot_jpeg()` example
+  now references a generic placeholder path instead of a specific headshot.
+
+## Internal
+- Renamed `LICENSE.md` to `LICENSE` for R packaging convention compliance so
+  that the LGPL-3 license ships correctly with built tarballs.

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 +110,14 @@ 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]]
+
-  paste(toupper(substring(s, 1,1)), substring(s, 2),
+  # Vectorised over elements of x — each element is capitalised independently.
+  # unname() strips names inherited from the input vector so the output
+  # matches the original scalar behaviour (no names attribute).
+  unname(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

@@ -10,7 +10,8 @@
 #' @importFrom graphics rasterImage
 #' @examples
 #' \dontrun{
-#' img <- system.file("img","Knowles_Headshot_2019_good.jpg",package="civilytics")
+#' # Supply a path to your own JPEG file
+#' img <- "my_photo.jpg"
 #' plot_jpeg(img)
 #' }
 plot_jpeg <- function(path, add=FALSE, upscale = TRUE)
@@ -74,8 +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)
     )
   }
 
@@ -125,7 +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)) {
@@ -145,7 +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$labels) == "caption")
@@ -186,8 +187,8 @@ add_logo_ga <- function(plot_list, logo, nrow = 1, widths = NULL,
   if (!is.null(font_scale) && font_scale != 1) {
     plot_list <- lapply(plot_list, function(p) {
       base_size <- p$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)
       )
     })
   }
@@ -275,9 +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

man/plot_jpeg.Rd

@@ -22,7 +22,8 @@ Plot a jpeg image as a raster
 }
 \examples{
 \dontrun{
-img <- system.file("img","Knowles_Headshot_2019_good.jpg",package="civilytics")
+# Supply a path to your own JPEG file
+img <- "my_photo.jpg"
 plot_jpeg(img)
 }
 }

reprex.r

@@ -0,0 +1,51 @@
+
+
+library(civilytics)
+library(ggplot2)
+library(grid)
+data(mtcars)
+
+ggplot(mtcars, aes(x = hp, y = mpg)) +
+  geom_point() +
+  labs(title = "This is the title", subtitle = "More context.",
+         caption = "JEK made this for you.") +
+  theme_civilytics_dark(font_size = 16)
+
+
+
+(ggplot(mtcars, aes(x = hp, y = mpg)) +
+  geom_point() +
+  labs(title = "This is the title", subtitle = "More context.",
+         caption = "JEK made this for you.") +
+  theme_civilytics_dark(font_size = 16)) |>
+  civilytics_logo(variant = "dark") |>
+  grid::grid.draw()
+
+dev.off()
+
+(ggplot(mtcars, aes(x = hp, y = mpg)) +
+  geom_point() +
+  labs(title = "This is the title", subtitle = "More context.",
+         caption = "JEK made this for you.") +
+  theme_civilytics_dark()) |>
+  civilytics_logo(variant = "dark") |>
+  grid::grid.draw()
+
+dev.off()
+
+(ggplot(mtcars, aes(x = hp, y = mpg)) +
+  geom_point() +
+  labs(title = "This is the title", subtitle = "More context.",
+         caption = "JEK made this for you.") +
+  theme_civilytics_dark(font_size = 14)) |>
+  civilytics_logo(variant = "dark") |>
+  grid::grid.draw()
+
+dev.off()
+(ggplot(mtcars, aes(x = hp, y = mpg)) +
+  geom_point() +
+  labs(title = "This is the title", subtitle = "More context.",
+         caption = "JEK made this for you.") +
+  theme_civilytics_dark(font_size = 16)) |>
+  civilytics_logo(variant = "dark", position = "top-right") |>
+  grid::grid.draw()

tests/testthat/test_propint.R

@@ -1,2 +1,173 @@
-# test prop intervals
+# Tests for proportion confidence interval functions
 
+# --- clopper_pearson ---------------------------------------------------------
+
+test_that("clopper_pearson returns a named numeric vector of length 3", {
+  result <- clopper_pearson(20, 40)
+  expect_type(result, "double")
+  expect_length(result, 3)
+  expect_named(result, c("low", "observed", "high"))
+})
+
+test_that("clopper_pearson observed matches num/den", {
+  result <- clopper_pearson(20, 40)
+  expect_equal(unname(result["observed"]), 20 / 40)
+})
+
+test_that("clopper_pearson matches binom.test in base R", {
+  # The implementation is documented as producing the same results as
+  # binom.test(), which uses the Clopper-Pearson method.
+  for (num in c(0, 1, 5, 20, 39, 40)) {
+    result <- clopper_pearson(num, 40)
+    bt <- binom.test(num, 40)$conf.int
+    expect_equal(unname(result["low"]),     bt[1], tolerance = 1e-10)
+    expect_equal(unname(result["high"]),    bt[2], tolerance = 1e-10)
+  }
+})
+
+test_that("clopper_pearson interval is valid (low <= observed <= high)", {
+  result <- clopper_pearson(5, 10)
+  expect_lte(result["low"],      result["observed"])
+  expect_gte(result["high"],     result["observed"])
+})
+
+test_that("clopper_pearson handles edge cases", {
+  # num = 0: lower bound should be exactly 0
+  zero_result <- clopper_pearson(0, 10)
+  expect_equal(unname(zero_result["low"]),    0, tolerance = 1e-15)
+  expect_gt(unname(zero_result["high"]),      0)
+  # Upper bound should match binom.test exactly
+  bt_zero <- binom.test(0, 10)$conf.int[2]
+  expect_equal(unname(zero_result["high"]),   unname(bt_zero), tolerance = 1e-10)
+
+  # num = den: upper bound should be exactly 1 (observed is at the boundary)
+  full_result <- clopper_pearson(10, 10)
+  expect_equal(unname(full_result["high"]),   1, tolerance = 1e-15)
+  # Lower bound for all-successes case is well below observed (asymmetric interval)
+  bt_full <- binom.test(10, 10)$conf.int
+  expect_equal(unname(full_result["low"]),    unname(bt_full[1]), tolerance = 1e-10)
+})
+
+test_that("clopper_pearson respects conf.level", {
+  wide <- clopper_pearson(20, 40, conf.level = 0.99)
+  narrow <- clopper_pearson(20, 40, conf.level = 0.80)
+
+  # Higher confidence level produces a wider interval
+  expect_gt(unname(wide["high"]) - unname(wide["low"]),
+            unname(narrow["high"]) - unname(narrow["low"]))
+})
+
+
+# --- z_univariate ------------------------------------------------------------
+
+test_that("z_univariate returns a single numeric value", {
+  result <- z_univariate(0.13, 0.11, 2500)
+  expect_type(result, "double")
+  expect_length(result, 1)
+})
+
+test_that("z_univariate equals the formula by hand calculation", {
+  # z = (p_hat - p_0) / sqrt(p_0 * (1 - p_0) / n)
+  unit_prop <- 0.13
+  global_prop <- 0.11
+  unit_denom <- 2500
+
+  expected <- (unit_prop - global_prop) /
+    sqrt((global_prop * (1 - global_prop)) / unit_denom)
+
+  result <- z_univariate(unit_prop, global_prop, unit_denom)
+  expect_equal(result, expected, tolerance = 1e-12)
+})
+
+test_that("z_univariate is zero when proportions are equal", {
+  expect_equal(z_univariate(0.5, 0.5, 100), 0, tolerance = 1e-15)
+})
+
+test_that("z_univariate sign follows the direction of deviation", {
+  # When unit_prop > global_prop, z should be positive
+  expect_gt(z_univariate(0.2, 0.1, 100), 0)
+
+  # When unit_prop < global_prop, z should be negative
+  expect_lt(z_univariate(0.1, 0.2, 100), 0)
+})
+
+
+# --- waldInterval ------------------------------------------------------------
+
+test_that("waldInterval returns a named numeric vector of length 2", {
+  result <- waldInterval(x = 20, n = 40)
+  expect_type(result, "double")
+  expect_length(result, 2)
+  expect_named(result, c("lwr", "upr"))
+})
+
+test_that("waldInterval matches documented example values", {
+  # The roxygen @examples comment says: waldInterval(x = 20, n = 40)
+  # returns approximately 0.345 and 0.655
+  result <- waldInterval(20, 40)
+
+  p_hat <- 20 / 40                         # 0.5
+  se <- sqrt(p_hat * (1 - p_hat) / 40)      # ~0.0791
+  z_crit <- qnorm(0.975)                    # ~1.96
+
+  expect_equal(unname(result["lwr"]), p_hat - z_crit * se, tolerance = 1e-12)
+  expect_equal(unname(result["upr"]), p_hat + z_crit * se, tolerance = 1e-12)
+})
+
+test_that("waldInterval interval is centered on the sample proportion", {
+  result <- waldInterval(30, 50)
+  midpoint <- (unname(result["lwr"]) + unname(result["upr"])) / 2
+  expect_equal(midpoint, 30 / 50, tolerance = 1e-12)
+})
+
+test_that("waldInterval respects conf.level", {
+  wide <- waldInterval(20, 40, conf.level = 0.99)
+  narrow <- waldInterval(20, 40, conf.level = 0.80)
+
+  expect_gt(unname(wide["upr"]) - unname(wide["lwr"]),
+            unname(narrow["upr"]) - unname(narrow["lwr"]))
+})
+
+
+# --- agresti_coull_interval --------------------------------------------------
+
+test_that("agresti_coull_interval returns a named numeric vector of length 3", {
+  result <- agresti_coull_interval(20, 40)
+  expect_type(result, "double")
+  expect_length(result, 3)
+  expect_named(result, c("low", "observed", "high"))
+})
+
+test_that("agresti_coull_interval observed matches num/den", {
+  result <- agresti_coull_interval(20, 40)
+  expect_equal(unname(result["observed"]), 20 / 40)
+})
+
+test_that("agresti_coull_interval interval is valid (low <= observed <= high)", {
+  result <- agresti_coull_interval(15, 30)
+  expect_lte(result["low"],      result["observed"])
+  expect_gte(result["high"],     result["observed"])
+})
+
+test_that("agresti_coull_interval matches manual formula calculation", {
+  num <- 20
+  den <- 40
+  conf_level <- 0.95
+
+  z <- qnorm(1 - (1 - conf_level) / 2)
+  n_tilde <- den + z^2
+  p_tilde <- (num + z^2 / 2) / n_tilde
+  margin <- z * sqrt(p_tilde * (1 - p_tilde) / n_tilde)
+
+  result <- agresti_coull_interval(num, den, conf.level = conf_level)
+  expect_equal(unname(result["low"]),    p_tilde - margin, tolerance = 1e-12)
+  expect_equal(unname(result["high"]),   p_tilde + margin, tolerance = 1e-12)
+})
+
+test_that("agresti_coull_interval respects conf.level", {
+  wide <- agresti_coull_interval(20, 40, conf.level = 0.99)
+  narrow <- agresti_coull_interval(20, 40, conf.level = 0.80)
+
+  expect_gt(unname(wide["high"]) - unname(wide["low"]),
+            unname(narrow["high"]) - unname(narrow["low"]))
+})

tests/testthat/test_utils.R

@@ -65,7 +65,193 @@ test_that("na_sum quiet=TRUE suppresses the message", {
 })
 
 
+context("Test Utilities - Postcode Lookup")
+
+# --- postcode_lookup -------------------------------------------------------
+
+# Build a lookup that mirrors the internal implementation:
+# state.name + "District of Columbia" + "Puerto Rico"
+map_name <- c(state.name, "District of Columbia", "Puerto Rico")
+map_abb  <- c(state.abb, "DC", "PR")
+
+lookup_ref <- function(x) {
+  map_abb[match(as.character(x), map_name)]
+}
+
+
+test_that("postcode_lookup returns correct abbreviations for known states", {
+  expect_equal(postcode_lookup("Montana"),   lookup_ref("Montana"))
+  expect_equal(postcode_lookup("Texas"),      lookup_ref("Texas"))
+  expect_equal(postcode_lookup("New York"),   lookup_ref("New York"))
+  expect_equal(postcode_lookup("California"), lookup_ref("California"))
+})
+
+
+test_that("postcode_lookup handles DC and Puerto Rico", {
+  # These are not in state.name/state.abb but should still resolve.
+  expect_equal(postcode_lookup("District of Columbia"), "DC")
+  expect_equal(postcode_lookup("Puerto Rico"),          "PR")
+})
+
+
+test_that("postcode_lookup is vectorized", {
+  states <- c("Montana", "Texas", "California", "Florida")
+  result <- postcode_lookup(states)
+  expected <- lookup_ref(states)
+  expect_equal(result, expected)
+  expect_length(result, length(states))
+})
+
+
+test_that("postcode_lookup returns NA for unknown state names", {
+  # match() returns NA when there is no match; the function propagates it.
+  result <- postcode_lookup("Atlantis")
+  expect_true(is.na(unname(result)))
+})
+
+
+test_that("postcode_lookup matches all built-in states", {
+  # Every entry in state.name should resolve to a valid abbreviation.
+  results <- postcode_lookup(state.name)
+  expected <- lookup_ref(state.name)
+  expect_equal(results, expected)
+  expect_false(any(is.na(results)))
+})
+
+
+context("Test Utilities - Race Short Names")
+
+# --- race_short_names -------------------------------------------------------
+
+# A reference implementation mirroring the function logic for cross-checking.
+race_ref <- function(x) {
+  x <- as.character(x)
+  x[x %in% c("Black", "Black Or African American", "Black or African American",
+             "African American")] <- "black"
+  x[x %in% c("Hispanic", "Hispanic Or Latino", "Hispanic or Latino")] <- "hisp_lat"
+  x[x %in% c("White", "white", "White and Not Hispanic")] <- "white"
+  x[x %in% c("Asian", "Asian American")] <- "asian"
+  x[x %in% c("Two Or More Races", "Two or More Races")] <- "two_or_more"
+  x[x %in% c("Native Hawaiian Or Other Pacific Islander",
+             "Native Hawaiian or Other Pacific Islander",
+             "Native Hawaiian Pacific Islander")] <- "native_haw"
+  x[x %in% c("American Indian", "American Indian Or Alaska Native",
+             "American Indian or Alaska Native", "American Indian or Native Alaskan")] <- "amind"
+  x[x %in% c("Not Reported")] <- "other"
+  x
+}
+
+
+test_that("race_short_names returns character vector of same length", {
+  input <- c("Black", "Hispanic Or Latino", "White")
+  result <- race_short_names(input)
+  expect_type(result, "character")
+  expect_length(result, length(input))
+})
+
+
+test_that("race_short_names maps all known categories correctly", {
+  # One representative from each category group.
+  input <- c(
+    "Black Or African American",
+    "Hispanic or Latino",
+    "White and Not Hispanic",
+    "Asian American",
+    "Two or More Races",
+    "Native Hawaiian or Other Pacific Islander",
+    "American Indian or Alaska Native",
+    "Not Reported"
+  )
+
+  expected <- c(
+    "black", "hisp_lat", "white", "asian",
+    "two_or_more", "native_haw", "amind", "other"
+  )
+
+  result <- race_short_names(input)
+  expect_equal(result, expected)
+})
+
+
+test_that("race_short_names coerces factors to character", {
+  input_factor <- factor(c("Black", "White", "Asian"))
+  result <- race_short_names(input_factor)
+  expect_type(result, "character")
+  expect_equal(result, c("black", "white", "asian"))
+})
+
+
+test_that("race_short_names passes through unrecognized values unchanged", {
+  input <- c("Black", "Some Other Category", "White")
+  result <- race_short_names(input)
+  # Unrecognized category should be returned as-is (lowercased by as.character).
+  expect_equal(result[2], "Some Other Category")
+})
+
+
+test_that("race_short_names handles empty input", {
+  result <- race_short_names(character(0))
+  expect_length(result, 0)
+  expect_type(result, "character")
+})
+
+
+test_that("race_short_names matches reference implementation across all categories",
+{
+  # Exhaustive check: feed every variant string the function handles.
+  all_variants <- c(
+    "Black", "Black Or African American", "Black or African American", "African American",
+    "Hispanic", "Hispanic Or Latino", "Hispanic or Latino",
+    "White", "white", "White and Not Hispanic",
+    "Asian", "Asian American",
+    "Two Or More Races", "Two or More Races",
+    "Native Hawaiian Or Other Pacific Islander",
+    "Native Hawaiian or Other Pacific Islander",
+    "Native Hawaiian Pacific Islander",
+    "American Indian", "American Indian Or Alaska Native",
+    "American Indian or Alaska Native", "American Indian or Native Alaskan",
+    "Not Reported"
+  )
+
+  expect_equal(race_short_names(all_variants), race_ref(all_variants))
+})
+
+
+context("Test Utilities - Get FIPS")
+
+# --- get_fips ---------------------------------------------------------------
+
+
+test_that("get_fips errors gracefully when tidycensus is not installed", {
+  # When tidycensus is absent, the function should stop with an informative message.
+  if (!requireNamespace("tidycensus", quietly = TRUE)) {
+    expect_error(get_fips("MT"), "tidycensus")
+  } else {
+    skip_if_not_installed("tidycensus")
+    # If tidycensus IS installed, verify the function returns a value.
+    result <- get_fips("MT")
+    expect_type(result, "character")
+    expect_gt(length(result), 0)
+  }
+})
+
+
+test_that("get_fips returns a FIPS code for a valid state abbreviation", {
+  skip_if_not_installed("tidycensus")
+  result <- get_fips("MT")
+  # Montana's FIPS state code is "30"
+  expect_equal(result, "30")
+})
+
+
+test_that("get_stabbr returns a valid abbreviation", {
+  skip_if_not_installed("tidycensus")
+  result <- get_fips("CA")
+  # California's FIPS state code is "06"
+  expect_equal(result, "06")
+})
+
+
 context("Test Utilities - Pretty Count")
 
 
-