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‎.github/workflows/R-CMD-check.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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#
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# NOTE: This workflow is overkill for most R packages and
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# check-standard.yaml is likely a better choice.
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# usethis::use_github_action("check-standard") will install it.
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on:
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push:
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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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# use 4.0 or 4.1 to check with rtools40's older compiler
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- {os: windows-latest, r: 'oldrel-4'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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- {os: ubuntu-latest, r: 'oldrel-2'}
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- {os: ubuntu-latest, r: 'oldrel-3'}
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- {os: ubuntu-latest, r: 'oldrel-4'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/test-coverage.yaml

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v4
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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file: ./cobertura.xml
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plugin: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎R/flowchart.b.R

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#' @title Study Flowchart
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#' @importFrom R6 R6Class
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#' @import jmvcore
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#'
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flowchartClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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"flowchartClass",
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inherit = flowchartBase,
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private = list(
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.run = function() {
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# Show initial help message if no variables selected
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if (is.null(self$options$nodes)) {
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todo <- "
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<br>Welcome to ClinicoPath Flowchart Creator
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<br><br>
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This tool helps create CONSORT-style flow diagrams showing participant flow through studies.
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<br><br>
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To create a flowchart:
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1. Add variables containing node descriptions to 'Node Data'
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2. Add corresponding count variables to 'Node Counts'
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3. Adjust direction and style options as needed
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<hr>
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"
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html <- self$results$todo
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html$setContent(todo)
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return()
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}
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if (nrow(self$data) == 0)
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stop('Data contains no (complete) rows')
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# Prepare data for plotting
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plotData <- list(
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"data" = self$data,
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"nodes" = self$options$nodes,
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"counts" = self$options$counts,
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"direction" = self$options$direction,
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"style" = self$options$style,
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"showCounts" = self$options$showCounts,
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"title" = self$options$title
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)
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# Save state for plot function
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image <- self$results$diagram
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image$setState(plotData)
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},
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.plot = function(image, ggtheme, theme, ...) {
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# Get plot data
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plotData <- image$state
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# Create nodes and edges dataframe
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nodes_df <- data.frame(
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id = seq_along(plotData$nodes),
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label = paste0(
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plotData$data[[plotData$nodes[1]]],
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ifelse(
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plotData$showCounts,
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paste0("\n(n=", plotData$data[[plotData$counts[1]]], ")"),
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""
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)
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),
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stringsAsFactors = FALSE
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)
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edges_df <- data.frame(
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from = head(nodes_df$id, -1),
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to = tail(nodes_df$id, -1),
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stringsAsFactors = FALSE
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)
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# Create graph
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graph <- DiagrammeR::create_graph()
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graph <- DiagrammeR::add_nodes_from_table(
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graph,
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nodes_df,
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label_col = "label"
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)
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graph <- DiagrammeR::add_edges_from_table(
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graph,
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edges_df,
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from_col = "from",
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to_col = "to"
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)
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# Set graph attributes based on style
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if (plotData$style == "detailed") {
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graph <- DiagrammeR::set_global_graph_attrs(
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graph,
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"layout", plotData$direction,
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"rankdir", plotData$direction,
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"splines", "ortho"
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)
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} else {
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graph <- DiagrammeR::set_global_graph_attrs(
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graph,
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"layout", plotData$direction,
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"rankdir", plotData$direction
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)
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}
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# Add title
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graph <- DiagrammeR::add_global_graph_attrs(
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graph,
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"label", plotData$title,
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"labelloc", "t"
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)
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# Render graph
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print(graph)
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TRUE
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}
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)
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)

‎README.md

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See https://sbalci.github.io/ClinicoPathJamoviModule/
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[![R-CMD-check](https://github.com/sbalci/ClinicoPathDescriptives/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/sbalci/ClinicoPathDescriptives/actions/workflows/R-CMD-check.yaml)
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[![Codecov test coverage](https://codecov.io/gh/sbalci/ClinicoPathDescriptives/graph/badge.svg)](https://app.codecov.io/gh/sbalci/ClinicoPathDescriptives)
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‎jamovi/flowchart.a.yaml

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---
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name: flowchart
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title: Study Flowchart
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menuGroup: Exploration
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menuSubgroup: ClinicoPath Descriptive Plots
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version: '1.0.0'
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jas: '1.2'
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options:
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- name: data
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type: Data
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description:
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R: >
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The data as a data frame.
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- name: title
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title: Flowchart Title
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type: String
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default: "Study Flow Diagram"
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- name: nodes
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title: Node Data
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type: Variables
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suggested: [nominal]
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permitted: [factor]
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description:
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R: >
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Variables containing node labels/descriptions
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- name: counts
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title: Node Counts
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type: Variables
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suggested: [continuous]
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permitted: [numeric]
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description:
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R: >
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Variables containing counts for each node
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- name: direction
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title: Direction
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type: List
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options:
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- title: Top to Bottom
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name: tb
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- title: Left to Right
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name: lr
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default: tb
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- name: style
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title: Style
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type: List
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options:
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- title: Simple
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name: simple
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- title: Detailed
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name: detailed
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default: simple
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- name: showCounts
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title: Show Counts
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type: Bool
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default: true
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...

‎jamovi/flowchart.r.yaml

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---
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name: flowchart
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title: Study Flowchart
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jrs: '1.1'
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items:
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- name: todo
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title: To Do
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type: Html
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- name: diagram
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title: 'Flowchart Diagram'
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type: Image
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width: 800
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height: 600
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renderFun: .plot
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requiresData: true
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clearWith:
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- nodes
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- counts
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- direction
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- style
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- showCounts
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- name: diagramCode
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title: 'Diagram Code'
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type: Preformatted
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visible: false
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refs:
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- ClinicoPathJamoviModule
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...

‎jamovi/flowchart.u.yaml

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title: Study Flowchart
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name: flowchart
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jus: '3.0'
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stage: 0
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compilerMode: tame
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children:
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- type: VariableSupplier
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persistentItems: false
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stretchFactor: 1
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children:
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- type: TargetLayoutBox
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label: Node Data
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children:
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- type: VariablesListBox
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name: nodes
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isTarget: true
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- type: TargetLayoutBox
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label: Node Counts
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children:
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- type: VariablesListBox
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name: counts
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isTarget: true
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- type: CollapseBox
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label: Options
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collapsed: true
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children:
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- type: LayoutBox
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margin: large
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children:
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- type: TextBox
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name: title
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format: string
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- type: ComboBox
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name: direction
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- type: ComboBox
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name: style
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- type: CheckBox
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name: showCounts

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