Tidy up lintr issues

.lintr

@@ -2,5 +2,4 @@ linters: linters_with_defaults(
     pipe_consistency_linter(pipe = "auto"),
     object_name_linter(styles = "snake_case", regexes = c("na\\.value"))
   )
-exclude: "^#| fig.alt = "
 encoding: "UTF-8"

R/colour_table.R

@@ -9,7 +9,7 @@
 
 colour_table <- function(pal) {
 
-  `%>%` <- dplyr::`%>%`
+  `%>%` <- dplyr::`%>%` # nolint: object_name_linter.
 
   tibble::enframe(pal) %>%
     dplyr::mutate(example = "") %>%

R/data.R

@@ -1,14 +1,12 @@
-# nolint: start
 #' @title Scottish Government colours and palettes
 #'
 #' @description
-#' * \code{sg_colour_values} is a vector containing colour names and their corresponding
-#' hex codes.
+#' * \code{sg_colour_values} is a vector containing colour names and their
+#'  corresponding hex codes.
 #' * \code{sg_colour_palettes} is a list grouping colours into palettes.
 #'
-#' @source \href{https://designsystem.gov.scot/guidance/charts/data-visualisation-colour-palettes}{Scottish Government Design System}
+#' @source \href{https://designsystem.gov.scot/guidance/charts/data-visualisation-colour-palettes}{Scottish Government Design System} # nolint: line_length_linter.
 #' @md
-# nolint: end
 
 "sg_colour_values"
 
@@ -19,12 +17,12 @@
 #' @title Social Security Scotland colours and palettes
 #'
 #' @description
-#' * \code{sss_colour_values} is a vector containing colour names and their corresponding
-#' hex codes.
+#' * \code{sss_colour_values} is a vector containing colour names and their
+#'  corresponding hex codes.
 #' * \code{sss_colour_palettes} is a list grouping colours into palettes.
 #'
-#' @source Contact the \href{mailto:[email protected]}{Social Security Scotland Statistics mailbox}
-#' with any queries about these colours and palettes.
+#' @source Contact the \href{mailto:[email protected]}{Social Security Scotland Statistics mailbox} # nolint: line_length_linter.
+#'  with any queries about these colours and palettes.
 #'
 #' @md
 
@@ -34,17 +32,15 @@
 "sss_colour_palettes"
 
 
-# nolint start
 #' @title Government Analysis Function colours and palettes
 #'
 #' @description
-#' * \code{af_colour_values} is a vector containing colour names and their corresponding
-#' hex codes.
+#' * \code{af_colour_values} is a vector containing colour names and their
+#'  corresponding hex codes.
 #' * \code{af_colour_palettes} is a list grouping colours into palettes.
 #'
-#' @source \href{https://analysisfunction.civilservice.gov.uk/policy-store/data-visualisation-colours-in-charts/}{Government Analysis Function Colours Guidance}
+#' @source \href{https://analysisfunction.civilservice.gov.uk/policy-store/data-visualisation-colours-in-charts/}{Government Analysis Function Colours Guidance} # nolint: line_length_linter.
 #' @md
-# nolint end
 
 "af_colour_values"
 

data-raw/af_colours.R

@@ -1,6 +1,5 @@
-# Government Analysis Function (AF) colours and palettes
-# Source: https://analysisfunction.civilservice.gov.uk/policy-store/
-#   data-visualisation-colours-in-charts/
+#' Government Analysis Function (AF) colours and palettes
+#' Source: https://analysisfunction.civilservice.gov.uk/policy-store/data-visualisation-colours-in-charts/ # nolint: line_length_linter.
 
 af_colour_values <- c(
   `dark-blue`    = "#12436D",

data-raw/sg_colours.R

@@ -1,6 +1,5 @@
-# Scottish Government (SG) Design System colours and palettes ----
-# Source: https://designsystem.gov.scot/guidance/
-#   charts/data-visualisation-colour-palettes
+#' Scottish Government (SG) Design System colours and palettes
+#' Source: https://designsystem.gov.scot/guidance/charts/data-visualisation-colour-palettes # nolint: line_length_linter.
 
 sg_colour_values <- c(
   `dark-blue` = "#002d54",

data-raw/sss_colours.R

@@ -1,4 +1,4 @@
-# Social Security Scotland (SSS) colours and palettes ----
+#' Social Security Scotland (SSS) colours and palettes
 
 sss_colour_values <- c(
   `navy` = "#201751",

vignettes/articles/cookbook/_annotations.Rmd

@@ -11,9 +11,7 @@ ann_data <- gapminder |>
   filter(country %in% c("United Kingdom", "China"))
 ```
 
-```{r annotations-1}
-#| fig.alt = "A multiple line chart  using sgplot theme and main2 palette with lines labelled."
-
+```{r annotations-1, fig.alt = "A multiple line chart using sgplot theme and main2 palette with lines labelled."}
 ann_data |>
   ggplot() +
   geom_line(aes(x = year, y = lifeExp, colour = country), linewidth = 1) +
@@ -45,9 +43,7 @@ However, this makes the code difficult to reuse as values are hard coded and not
 
 One way to automate this is to create a supplementary data frame with desired co-ordinates of the labels (see `ann_labs` in the example below). `nudge` arguments can be used to displace text to improve the positioning.
 
-```{r annotations-2}
-#| fig.alt = "A multiple line chart  using sgplot theme and main2 palette with lines labelled."
-
+```{r annotations-2, fig.alt = "A multiple line chart using sgplot theme and main2 palette with lines labelled."}
 ann_labs <- ann_data |>
   group_by(country) |>
   filter(year == max(year)) |>
@@ -80,9 +76,7 @@ ann_data |>
 
 Annotations may also be used to add value labels to a bar chart. Note that `geom_text()` is used here as a background is not required.
 
-```{r annotations-3}
-#| fig.alt = "A bar chart with white text labels at the end of each bar."
-
+```{r annotations-3, fig.alt = "A bar chart with white text labels at the end of each bar."}
 ggplot(bar_data, aes(x = reorder(country, -pop), y = pop)) +
   geom_col(fill = sg_colour_values["dark-blue"]) +
   geom_text(aes(label = format(pop, big.mark = ",")),

vignettes/articles/cookbook/_chart-types.Rmd

@@ -2,9 +2,7 @@
 
 ### Line chart with one line
 
-```{r line-charts-1}
-#| fig.alt = "A line chart using sgplot theme and dark blue colour."
-
+```{r line-charts-1, fig.alt = "A line chart using sgplot theme and dark blue colour."}
 gapminder |>
   filter(country == "United Kingdom") |>
   ggplot(aes(x = year, y = lifeExp)) +
@@ -25,9 +23,7 @@ gapminder |>
 
 ### Line chart with multiple lines
 
-```{r line-charts-2, fig.height = 5}
-#| fig.alt = "A multiple line chart using sgplot theme and main colour palette."
-
+```{r line-charts-2, fig.height = 5, fig.alt = "A multiple line chart using sgplot theme and main colour palette."}
 gapminder |>
   filter(country %in% c("United Kingdom", "China")) |>
   ggplot(aes(x = year, y = lifeExp, colour = country)) +
@@ -60,9 +56,7 @@ bar_data <-
   slice_max(order_by = pop, n = 5)
 ```
 
-```{r bar-chart-1}
-#| fig.alt = "A bar chart using sgplot theme and dark blue colour."
-
+```{r bar-chart-1, fig.alt = "A bar chart using sgplot theme and dark blue colour."}
 ggplot(bar_data, aes(x = reorder(country, -pop), y = pop)) +
   geom_col(fill = sg_colour_values["dark-blue"]) +
   theme_sg() +
@@ -82,9 +76,7 @@ ggplot(bar_data, aes(x = reorder(country, -pop), y = pop)) +
 
 A bar chart can sometimes look better with horizontal bars. This can also be a good option if your bar labels are long and difficult to display horizontally on the x-axis. To produce a horizontal bar chart, swap the variables defined for x and y in `aes()` and make a few tweaks to `theme_sg()`; draw grid lines for the x-axis only by setting the `grid` argument, and draw an axis line for the y-axis only by setting the `axis` argument.
 
-```{r bar-chart-2}
-#| fig.alt = "A horizontal bar chart using sgplot theme and dark blue colour."
-
+```{r bar-chart-2, fig.alt = "A horizontal bar chart using sgplot theme and dark blue colour."}
 ggplot(bar_data, aes(x = pop, y = reorder(country, pop))) +
   geom_col(fill = sg_colour_values["dark-blue"]) +
   theme_sg(grid = "x", axis = "y") +
@@ -107,9 +99,7 @@ ggplot(bar_data, aes(x = pop, y = reorder(country, pop))) +
 
 To create a grouped bar chart, set `stat = "identity"` and `position = "dodge"` in the call to `geom_bar()`. Also assign a variable to `fill` within `aes()` to determine what variable is used to create bars within groups. The `legend` argument in `theme_sg()` can be used to set the position of the legend.
 
-```{r grouped-bar-chart, fig.height = 5.5}
-#| fig.alt = "A grouped bar chart using sgplot theme and colours from main palette"
-
+```{r grouped-bar-chart, fig.height = 5.5, fig.alt = "A grouped bar chart using sgplot theme and colours from main palette"}
 grouped_bar_data <-
   gapminder |>
   filter(year %in% c(1967, 2007) &
@@ -137,9 +127,7 @@ To create a stacked bar chart, set `stat = "identity` and `position = "fill"` in
 
 Caution should be taken when producing stacked bar charts. They can quickly become difficult to interpret if plotting non part-to-whole data, and/or if plotting more than two categories per stack. First and last categories in the stack will always be easier to compare across bars than those in the middle. Think carefully about the story you are trying to tell with your chart.
 
-```{r stacked-bar-chart, fig.height = 5.5}
-#| fig.alt = "A stacked bar chart using sgplot theme and colours from main palette"
-
+```{r stacked-bar-chart, fig.height = 5.5, fig.alt = "A stacked bar chart using sgplot theme and colours from main palette."}
 stacked_bar_data <-
   gapminder |>
   filter(year == 2007) |>
@@ -169,9 +157,7 @@ ggplot(stacked_bar_data,
 
 ## Histograms
 
-```{r histogram}
-#| fig.alt = "A histogram with sgplot theme and dark blue colour."
-
+```{r histogram, fig.alt = "A histogram with sgplot theme and dark blue colour."}
 gapminder |>
   filter(year == 2007) |>
   ggplot(aes(x = lifeExp)) +
@@ -192,9 +178,7 @@ gapminder |>
 
 ## Scatterplots
 
-```{r scatterplot, fig.height = 5}
-#| fig.alt = "A scatterplot using sgplot theme and dark blue colour."
-
+```{r scatterplot, fig.height = 5, fig.alt = "A scatterplot using sgplot theme and dark blue colour."}
 gapminder |>
   filter(year == 2007) |>
   ggplot(aes(x = gdpPercap, y = lifeExp)) +
@@ -218,9 +202,7 @@ gapminder |>
 
 ## Small multiples
 
-```{r small-multiples, fig.height = 5.5}
-#| fig.alt = "A small multiples area chart using sgplot theme and main colour palette."
-
+```{r small-multiples, fig.height = 5.5, fig.alt = "A small multiples area chart using sgplot theme and main colour palette."}
 gapminder |>
   filter(continent != "Oceania") |>
   group_by(continent, year) |>
@@ -246,9 +228,7 @@ gapminder |>
 
 ## Pie charts
 
-```{r pie-chart}
-#| fig.alt = "A pie chart using sgplot theme and main palette."
-
+```{r pie-chart, fig.alt = "A pie chart using sgplot theme and main palette."}
 stacked_bar_data |>
   filter(continent == "Europe") |>
   ggplot(aes(x = "", y = n_countries, fill = lifeExpGrouped)) +
@@ -271,9 +251,7 @@ stacked_bar_data |>
 
 ## Focus charts
 
-```{r focus-chart}
-#| fig.alt = "A bar chart with the bar for Brazil highlighted in dark blue and other bars in grey."
-
+```{r focus-chart, fig.alt = "A bar chart with the bar for Brazil highlighted in dark blue and other bars in grey."}
 bar_data |>
   ggplot(
     aes(x = reorder(country, -pop), y = pop,
@@ -305,9 +283,7 @@ To make a `ggplot2` chart interactive, use `ggplotly()` from the `plotly` packag
 
 * Subtitles and captions are not supported in `ggplotly()`. As stated elsewhere in this guidance, titles and subtitles should ideally be included in the body of text surrounding a chart rather than embedded in the chart itself, and so this is hopefully not a big issue. This example therefore has no title, subtitle or caption.
 
-```{r interactive-charts}
-#| fig.alt = "An interactive bar chart using sgplot theme and dark blue colour. A tooltip appears when hovering over each bar."
-
+```{r interactive-charts, fig.alt = "An interactive bar chart using sgplot theme and dark blue colour. A tooltip appears when hovering over each bar."}
 p <-
   bar_data |>
   # Format text for tooltips

vignettes/articles/cookbook/_colour-palettes.Rmd

@@ -17,9 +17,7 @@ The full list of available palettes can be found by running either `sgplot::sg_c
 
 To use the Scottish Government `main-extended` palette:
 
-```{r main-extended, fig.height = 5}
-#| fig.alt = "A multiple line chart using sgplot theme and SG main-extended colour palette."
-
+```{r main-extended, fig.height = 5, fig.alt = "A multiple line chart using sgplot theme and SG main-extended colour palette."}
 gapminder |>
   filter(country %in% c("United Kingdom", "China", "India",
                         "Sweden", "Namibia", "Brazil")) |>
@@ -46,9 +44,7 @@ Note: This chart is for demonstration purposes only. Accessibility guidance reco
 To use an Analysis Function palette, set `palette_type = "af"` when using any of the `scale_` [colour functions](../reference/index.html#colour-scales). 
 For example, to use the Analysis Function `main2` palette:
 
-```{r af-palette, fig.height = 5}
-#| fig.alt = "A multiple line chart using sgplot theme and AF main colour palette."
-
+```{r af-palette, fig.height = 5, fig.alt = "A multiple line chart using sgplot theme and AF main colour palette."}
 gapminder |>
   filter(country %in% c("United Kingdom", "China")) |>
   ggplot(aes(x = year, y = lifeExp, colour = country)) +
@@ -76,9 +72,7 @@ There may be instances where you'd like to use a colour palette that is not avai
 If so, this should be carefully considered to ensure it meets accessibility requirements. 
 The Analysis Function guidance outlines [appropriate steps for choosing your own accessible colour palette](https://analysisfunction.civilservice.gov.uk/policy-store/data-visualisation-colours-in-charts/#section-9) and should be used.
 
-```{r different-colour-palette-1}
-#| fig.alt = "A line chart using sgplot theme and first colour from custom palette."
-
+```{r different-colour-palette-1, fig.alt = "A line chart using sgplot theme and first colour from custom palette."}
 my_palette <- c("#0F820D", "#000000")
 
 gapminder |>
@@ -99,9 +93,7 @@ gapminder |>
   )
 ```
 
-```{r different-colour-palette-2, fig.height = 5.5}
-#| fig.alt = "A multiple line chart using sgplot theme and colours from custom palette."
-
+```{r different-colour-palette-2, fig.height = 5.5, fig.alt = "A multiple line chart using sgplot theme and colours from custom palette."}
 gapminder |>
   filter(country %in% c("United Kingdom", "China")) |>
   ggplot(aes(x = year, y = lifeExp, colour = country)) +