Revert "Merge branch 'main' into render_rmd2"

This reverts commit aea3685, reversing changes made to fc7f895.
nhs-r-community · Aug 6, 2024 · 6efff45 · 6efff45
1 parent aea3685
commit 6efff45
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diff --git a/.github/workflows/render-rmarkdown.yml b/.github/workflows/render-rmarkdown.yml
@@ -5,6 +5,7 @@ on:
     paths: ['README.Rmd']
 
 name: render-rmarkdown.yml
+
 permissions: read-all
 
 jobs:

diff --git a/.lintr b/.lintr
@@ -2,13 +2,10 @@ linters: linters_with_defaults(
   line_length_linter(120),
   cyclocomp_linter(23),
   indentation_linter(hanging_indent_style = "tidy"),
-  object_name_linter("snake_case"),
-  trailing_blank_lines_linter = NULL
-  )
+  object_name_linter("snake_case"))
 exclusions: list(
-  "R/ptd_spc_colours.R" = 5
-  )
+  "R/ptd_spc_colours.R" = 5)
 exclude: "# Exclude Linting|#\\s?nolint"
 exclude_start: "# Begin Exclude Linting|#\\s?nolint-start"
 exclude_end: "# End Exclude Linting|#\\s?nolint-end"
-
+encoding: "ISO-8859-1"
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,32 +3,26 @@ Type: Package
 Title: Draw XmR Charts for NHSE/I 'Making Data Count' Programme
 Version: 0.1.0.9000
 Authors@R: c(
-        person("Christopher", "Reading", ,"christopher.reading1@nhs.net", c("cre", "aut")),
-        person("Simon", "Wellesley-Miller", ,"simon.wellesley-miller@nhs.net", "aut"),
-        person("Zoë", "Turner", , "Zoe.Turner2@nottshc.nhs.uk", "aut", comment = c(ORCID = "0000-0003-1033-9158")),
-        person("Tom", "Jemmett", ,"thomas.jemmett@nhs.net", "aut", comment = c(ORCID="0000-0002-6943-2990")),
-        person("Tom", "Smith", ,"thomas.smith5@nuh.nhs.uk", "aut"),
-        person("Chris", "Mainey", ,"c.mainey@nhs.net", "aut", comment = c(ORCID ="0000-0002-3018-6171")),
-        person("John", "MacKintosh", ,"john.mackintosh3@nhs.scot", "aut"),
-        person("Marcos", "Fabietti", ,"marcos.fabietti@nuh.nhs.uk", "aut"),
-        person("Fran", "Barton",
-            email = "francis.barton@nhs.net",
-            role = "aut",
-            comment = c(ORCID = "0000-0002-5650-1176")
-          ),
-          person("NHS-R community",
-            email = "nhs.rcommunity@nhs.net",
-            role = "cph"
+          person("Christopher", "Reading", ,"christopher.reading1@nhs.net", c("cre", "aut")),
+          person("Simon", "Wellesley-Miller", ,"simon.wellesley-miller@nhs.net", "aut"),
+          person("Zoë", "Turner", , "Zoe.Turner2@nottshc.nhs.uk", "aut", comment = c(ORCID = "0000-0003-1033-9158")),
+          person("Tom", "Jemmett", ,"thomas.jemmett@nhs.net", "aut", comment = c(ORCID="0000-0002-6943-2990")),
+          person("Tom", "Smith", ,"thomas.smith5@nuh.nhs.uk", "aut"),
+          person("Chris", "Mainey", ,"c.mainey@nhs.net", "aut", comment = c(ORCID ="0000-0002-3018-6171")),
+          person("John", "MacKintosh", ,"john.mackintosh3@nhs.scot", "aut"),
+          person("Marcos", "Fabietti", ,"marcos.fabietti@nuh.nhs.uk", "aut"),
+          person("NHS-R community", email = "nhs.rcommunity@nhs.net", role = "cph")
           )
-        )
 Maintainer: Christopher Reading <christopher.reading1@nhs.net>
-Description: Provides tools for drawing Statistical Process Control (SPC) charts. This package supports the NHSE/I programme 'Making Data Count', and allows users to draw XmR charts, use change points and apply rules with summary indicators for when rules are breached.
+Description: Provides tools for drawing Statistical Process Control (SPC) charts. This package supports the NHSE/I
+  programme 'Making Data Count', and allows users to draw XmR charts, use change points and apply rules with summary
+  indicators for when rules are breached.
 URL: https://nhs-r-community.github.io/NHSRplotthedots,
     https://github.com/nhs-r-community/NHSRplotthedots
 BugReports: https://nhs-r-community.github.io/NHSRplotthedots/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Imports: 
     assertthat,
@@ -61,4 +55,4 @@ Suggests:
 Depends: R (>= 4.1.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
-Language: en-GB
+Language: en-US
diff --git a/R/ptd_create_ggplot.R b/R/ptd_create_ggplot.R
@@ -238,7 +238,7 @@ ptd_create_ggplot <- function(
   sec_breaks <- .data |>
     # should already be sorted in date order but just in case
     dplyr::arrange(x) |>
-    dplyr::select(c("lpl", "mean_col", "upl")) |>
+    dplyr::select(all_of(c("lpl", "mean_col", "upl"))) |>
     dplyr::slice_tail(n = 1) |>
     unlist() |>
     unname()
@@ -248,53 +248,93 @@ ptd_create_ggplot <- function(
     start <- floor(min(yaxis, na.rm = TRUE) / y_axis_breaks) * y_axis_breaks
     end <- max(yaxis, na.rm = TRUE)
     y_axis_labels <- seq(from = start, to = end, by = y_axis_breaks)
-  } else {
-    # if no y-axis breaks supplied by user, we just use the built-in heuristic
-    y_axis_labels <- ggplot2::waiver()
   }
 
+  # Nested combinations of 3 binary options = 2^3 (8) possible plot designs
   if (percentage_y_axis) {
+    if (!is.null(y_axis_breaks)) {
+      if (label_limits) {
+        # %age axes + specified breaks + sec labelling axis
+        plot <- plot +
+          ggplot2::scale_y_continuous(
+            breaks = y_axis_labels,
+            labels = scales::label_percent(accuracy = y_axis_breaks),
+            sec.axis = ggplot2::sec_axis(
+              trans = identity,
+              name = NULL,
+              breaks = sec_breaks,
+              labels = scales::label_percent(accuracy = y_axis_breaks)
+            )
+          )
+      } else {
+        # %age axes + specified breaks - no sec labelling axis
+        plot <- plot +
+          ggplot2::scale_y_continuous(
+            breaks = y_axis_labels,
+            labels = scales::label_percent(accuracy = y_axis_breaks)
+          )
+      }
+    } else if (label_limits) {
+      # %age axes + sec labelling axis - no specified breaks
+      plot <- plot +
+        ggplot2::scale_y_continuous(
+          labels = scales::label_percent(accuracy = y_axis_breaks),
+          sec.axis = ggplot2::sec_axis(
+            trans = identity,
+            name = NULL,
+            breaks = sec_breaks,
+            labels = scales::label_percent(accuracy = y_axis_breaks)
+          )
+        )
+    } else {
+      # %age axes - no specified breaks - no sec labelling axis
+      plot <- plot +
+        ggplot2::scale_y_continuous(
+          labels = scales::label_percent(accuracy = y_axis_breaks)
+        )
+    }
+  } else if (!is.null(y_axis_breaks)) {
     if (label_limits) {
-      # percentage y-axis, secondary labelling axis
+      # integer axes + specified breaks + sec labelling axis
       plot <- plot +
         ggplot2::scale_y_continuous(
-          breaks = y_axis_labels, # see above - can mean "just use waiver()"
-          labels = scales::label_percent(),
+          breaks = y_axis_labels,
+          labels = scales::label_number(accuracy = y_axis_breaks),
           sec.axis = ggplot2::sec_axis(
-            transform = identity,
+            trans = identity,
             name = NULL,
             breaks = sec_breaks,
-            labels = scales::label_percent(accuracy = 0.1)
+            labels = scales::label_number(accuracy = 0.01)
           )
         )
     } else {
-      # percentage y-axis, no secondary labelling axis
+      # integer axes + specified breaks - no sec labelling axis
       plot <- plot +
         ggplot2::scale_y_continuous(
           breaks = y_axis_labels,
-          labels = scales::label_percent()
+          labels = scales::label_number(accuracy = y_axis_breaks)
         )
     }
-  } else if (label_limits) {
-    # integer y-axis, secondary labelling axis
-    plot <- plot +
-      ggplot2::scale_y_continuous(
-        breaks = y_axis_labels,
-        labels = scales::label_number(),
-        sec.axis = ggplot2::sec_axis(
-          transform = identity,
-          name = NULL,
-          breaks = sec_breaks,
-          labels = scales::label_number()
-        )
-      )
   } else {
-    # integer y-axis, no secondary axis
-    plot <- plot +
-      ggplot2::scale_y_continuous(
-        breaks = y_axis_labels,
-        labels = scales::label_number()
-      )
+    if (label_limits) {
+      # integer axes + sec labelling axis - no specified breaks
+      plot <- plot +
+        ggplot2::scale_y_continuous(
+          labels = scales::label_number(accuracy = y_axis_breaks),
+          sec.axis = ggplot2::sec_axis(
+            trans = identity,
+            name = NULL,
+            breaks = sec_breaks,
+            labels = scales::label_number(accuracy = 0.01)
+          )
+        )
+    } else {
+      # integer axes - no specified breaks - no sec labelling axis
+      plot <- plot +
+        ggplot2::scale_y_continuous(
+          labels = scales::label_number(accuracy = y_axis_breaks)
+        )
+    }
   }