Add full check workflow

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,51 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

R/data.R

@@ -11,10 +11,59 @@
 #'  \item{Within_4h}{Total attendances that were < 4 hours}
 #'  \item{Over_4h}{Total attendances that were > 4 hours}
 #'  \item{Percent_in_4h}{Percentage of attendances within 4 hours}
-#'  \item{E_Adm_ViaAE}{Total emergency admissions via emergency department}
+#'  \item{E_Adm_Via_ED}{Total emergency admissions via emergency department}
 #'  \item{E_Adm_Over_4h}{Total > 4 hours from decision to admit to admission}
 #' }
 #' 
 #' @source <https://www.england.nhs.uk/statistics/statistical-work-areas/ae-waiting-times-and-activity/ae-attendances-and-emergency-admissions-2023-24/>
 #' 
 "ed_attendances_monthly"
+
+#' Example Time Series 1
+#' 
+#' A simulated example time series used in illustrating features of the Stable
+#' Shift Algorithm.
+#' 
+#' @format
+#' A data frame with 125 rows and 2 columns
+#' \describe{
+#'  \item{x}{Consecutive integer time}
+#'  \item{y}{Numeric time series}
+#' } 
+#' 
+#' @source Simulated data
+#' 
+"example_series_1"
+
+#' Example Time Series 2a
+#' 
+#' A second simulated example time series used in illustrating features of the
+#' Stable Shift Algorithm.
+#' 
+#' @format
+#' A data frame with 43 rows and 2 columns
+#' \describe{
+#'  \item{x}{Consecutive integer time}
+#'  \item{y}{Integer time series}
+#' } 
+#' 
+#' @source Simulated data
+#' 
+"example_series_2a"
+
+#' Example Time Series 2b
+#' 
+#' A third simulated example time series used in illustrating features of the
+#' Stable Shift Algorithm. Identical to example_series_2a except at seven time
+#' points, all occurring at or after x = 27.
+#' 
+#' @format
+#' A data frame with 43 rows and 2 columns
+#' \describe{
+#'  \item{x}{Consecutive integer time}
+#'  \item{y}{Integer time series}
+#' } 
+#' 
+#' @source Simulated data
+#' 
+"example_series_2b"

R/plot_code.R

@@ -32,6 +32,8 @@
 #' "XMR", "MR", "C", "C'", "P", "P'".
 #' 
 #' ## Algorithm Parameters
+#' Parameters that control behaviour of the algorithm used to re-establish
+#' control limits.
 #' @param periodMin The minimum number of points (subgroups) per period,
 #' i.e. the minimum number of points required to form control limits. 
 #' @param baseline Integer, overrides periodMin for the first calculation period
@@ -51,6 +53,8 @@
 #' calculation period. Set to FALSE only with noRegrets = FALSE.
 #' 
 #' ## SPC Parameters
+#' Parameters that control how cetnre line and control limits are established
+#' for each period, and details of how SPC rules are applied
 #' @param maxNoOfExclusions The maximum number of extreme points to exclude from 
 #' limit calculations.
 #' @param highlightExclusions Boolean signifying whether excluded points are
@@ -73,6 +77,7 @@
 #' floating median, if present.
 
 #' ## Output Type
+#' Arguments that control how the result is outputted
 #' @param plotChart Boolean specifying whether to plot the chart. If not, the
 #' data is returned with centre line, control limits and other analytic output
 #' appended as columns.
@@ -90,6 +95,7 @@
 #' log data is saved to. Full log data is saved, regardless of verbosity.
 #' 
 #' ## Chart Appearance
+#' Arguments that control aspects of chart visualisation 
 #' @param title Optional string specifying chart title. Overrides df$title.
 #' @param subtitle Optional string specifying subtitle. Overrides df$subtitle.
 #' @param use_caption Boolean controlling whether the caption is displayed.

README.md

@@ -2,6 +2,7 @@
 
 <!-- badges: start -->
 [![Codecov test coverage](https://codecov.io/gh/HorridTom/autospc/graph/badge.svg)](https://app.codecov.io/gh/HorridTom/autospc)
+[![R-CMD-check](https://github.com/HorridTom/autospc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/HorridTom/autospc/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## Overview