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Merge branch 'main' into 218_table2_ard@main # Conflicts: # DESCRIPTION
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‎.github/ISSUE_TEMPLATE/bug.yml

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description: File a bug report
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title: "[Bug]: <title>"
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labels: ["bug"]
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projects: ["falcon"]
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projects: ["cardinal"]
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body:
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- type: markdown
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attributes:

‎.github/ISSUE_TEMPLATE/feature.yml

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description: Request or propose a new feature
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title: "[Feature Request]: <title>"
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labels: ["enhancement"]
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projects: ["falcon"]
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projects: ["cardinal"]
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body:
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- type: textarea
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attributes:

‎.github/ISSUE_TEMPLATE/new_template.yml

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description: Add a new table template
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title: "[New Table]: Table XX"
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labels: ["new template"]
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projects: ["falcon"]
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projects: ["cardinal"]
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body:
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- type: textarea
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id: table-layout
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value: |
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[Replace this line with your table screenshot by dragging the file here.]
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Please refer to page XX of the [FDA guideline document](https://github.com/pharmaverse/falcon/files/10744259/FDA-2022-N-1961-0002_attachment_1.pdf) for more details.
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Please refer to page XX of the [FDA guideline document](https://github.com/pharmaverse/cardinal/files/10744259/FDA-2022-N-1961-0002_attachment_1.pdf) for more details.
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- type: textarea
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id: table-description
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attributes:

‎.github/ISSUE_TEMPLATE/question.yml

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description: Question about usage or documentation
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title: "[Question]: <title>"
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labels: ["question"]
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projects: ["falcon"]
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projects: ["cardinal"]
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body:
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- type: textarea
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attributes:

‎.github/workflows/docs.yaml

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name: Quarto Docs 📕
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runs-on: ubuntu-latest
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container:
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image: rocker/verse:4.3.0
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image: rocker/verse:4.4.0
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permissions:
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contents: write
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steps:
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- name: Check out repository 🛎️
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uses: actions/checkout@v3
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uses: actions/checkout@v4.1.1
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- name: Run Staged dependencies 🎦
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uses: insightsengineering/staged-dependencies-action@fix-remotes-self-install
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uses: insightsengineering/staged-dependencies-action@v1
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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with:
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enable-check: false
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run-system-dependencies: true
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direction: upstream
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- name: Install package 📦

‎.gitignore

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quarto/.quarto/
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quarto/site_libs/
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/.quarto/
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site_libs
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_site
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_freeze
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_cache

‎.pre-commit-config.yaml

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# R specific hooks: https://github.com/lorenzwalthert/precommit
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repos:
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- repo: https://github.com/lorenzwalthert/precommit
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rev: v0.4.2
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rev: v0.4.3.9001
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hooks:
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- id: style-files
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args: [--style_pkg=styler, --style_fun=tidyverse_style]
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files: '\.Rhistory|\.RData|\.Rds|\.rds$'
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# `exclude: <regex>` to allow committing specific files.
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- repo: https://github.com/igorshubovych/markdownlint-cli
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rev: v0.39.0
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rev: v0.41.0
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hooks:
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- id: markdownlint

‎DESCRIPTION

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Type: Package
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Package: falcon
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Package: cardinal
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Title: FDA Safety Tables and Figures
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Version: 0.1.0.9055
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Date: 2024-04-24
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Version: 0.1.0.9062
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Date: 2024-09-19
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Authors@R:
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person("Pawel", "Rucki", , "[email protected]", role = c("aut", "cre"))
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Description: R package with implementation of Safety Tables and Figures
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issued by FDA.
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License: Apache License (>= 2)
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URL: https://github.com/pharmaverse/falcon/
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BugReports: https://github.com/pharmaverse/falcon/issues
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URL: https://github.com/pharmaverse/cardinal/
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BugReports: https://github.com/pharmaverse/cardinal/issues
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Depends:
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R (>= 3.6),
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tern (>= 0.9.4)
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tern (>= 0.9.5)
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Imports:
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cards,
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cardx,
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checkmate,
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cowplot (>= 0.7.0),
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dplyr,
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formatters (>= 0.5.6),
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ggplot2 (>= 3.4.0),
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gt,
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gtsummary,
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lubridate,
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magrittr,
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cards (>= 0.2.0),
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cardx (>= 0.2.0),
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checkmate (>= 2.1.0),
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cowplot (>= 1.0.0),
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dplyr (>= 1.0.0),
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formatters (>= 0.5.8),
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ggplot2 (>= 3.5.0),
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ggsurvfit (>= 1.1.0),
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gt (>= 0.10.1),
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gtsummary (>= 2.0.0),
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lubridate (>= 1.7.10),
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magrittr (>= 1.5),
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purrr (>= 1.0.1),
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rlang (>= 0.4.11),
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rlistings (>= 0.2.8),
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rtables (>= 0.6.7),
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tfrmt,
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tidyr,
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Tplyr
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rlistings (>= 0.2.9),
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rtables (>= 0.6.9),
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tfrmt (>= 0.1.1),
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tidyr (>= 0.8.3),
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Tplyr (>= 1.2.1)
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Suggests:
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knitr,
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random.cdisc.data (>= 0.3.14),
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knitr (>= 1.42),
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random.cdisc.data (>= 0.3.15),
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svglite (>= 2.1.2),
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testthat (>= 3.0.0),
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testthat (>= 3.1.9),
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withr (>= 2.0.0)
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Remotes:
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insightsengineering/random.cdisc.data@*release
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biocViews:
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Config/testthat/edition: 3
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Encoding: UTF-8
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Language: en-US
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.1
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RoxygenNote: 7.3.2

‎NAMESPACE

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export(basic_table_annot)
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export(make_fig_01)
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export(make_fig_02)
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export(make_fig_03)
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export(make_fig_14)
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export(make_table_02)
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export(make_table_03)

‎NEWS.md

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# falcon 0.1.0.9055
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# cardinal 0.1.0.9062
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* Initial release.

‎R/argument_convention.R

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#' Standard Arguments
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#'
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#' This documentation lists all the arguments in `falcon` that are used repeatedly by functions to output tables.
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#' This documentation lists all the arguments in `cardinal` that are used repeatedly by functions to output tables.
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#'
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#' @param show_colcounts (`flag`)\cr Whether column counts should be printed. Boolean.
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#' @param arm_var (`character`)\cr Name of the treatment arm variable used to split table into columns.

‎R/falcon.R ‎R/cardinal.R

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#' falcon Package
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#' cardinal Package
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#'
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#' Implementation of FDA Safety Tables and Figures
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#'
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utils::globalVariables(c(
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".", "AEACN", "AESCONG", "AESDISAB", "AESDTH", "AESER", "AESHOSP", "AESIFL", "AESLIFE", "AESMIE", "AGE",
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"AGESEX", "AVAL", "AVALU", "AVISITN", "DOSAGE", "DOSDUR", "DTHADY", "DTHCAT", "DTHCAUS", "DTHFL", "DCSREAS",
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"MAX_DIABP", "MAX_SYSBP", "PARAMCD", "SEX", "TRTDUR", "TRTDUR_MONTHS", "TRTEDT", "ASER", "DCTREAS",
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"EOSSTT", "EOTSTT", "ITTFL", "PPROTFL", "RANDFL", "TRTEMFL", "TRTSDT", "USUBJID", "column", "median", "ord_layer_1",
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"ord_layer_2", "ord_layer_index", "param", "pct", "row_label1", "row_label2", "sd", "tbl_lbl", "value",
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"ENRLDT", "RANDDT", "G110", "G60", "G90", "GE120", "L60", "N", "val", "id_var", "PT_PCT", "arm", "x", "TLSTFU",
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"se", "lower_ci", "upper_ci", "SBP90", "DBP60"
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"MAX_DIABP", "MAX_SYSBP", "PARAMCD", "SEX", "TRTDUR", "TRTDUR_MONTHS", "TRTEDT", "ASER", "EOSSTT", "EOTSTT",
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"ITTFL", "PPROTFL", "RANDFL", "TRTEMFL", "TRTSDT", "USUBJID", "column", "median", "ord_layer_1", "ord_layer_2",
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"ord_layer_index", "param", "pct", "row_label1", "row_label2", "sd", "tbl_lbl", "value", "ENRLDT", "RANDDT",
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"G110", "G60", "G90", "GE120", "L60", "N", "val", "id_var", "PT_PCT", "arm", "x", "TLSTFU", "se", "lower_ci",
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"upper_ci", "SBP90", "DBP60", "STATUS"
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))

‎R/fda-fig_01.R

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geom_line() +
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labs(
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title = annotations[["title"]],
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subtitle = annotations[["subtitle"]],
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subtitle = annotations[["subtitles"]],
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caption = annotations[["caption"]],
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x = x_lab,
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y = y_lab

‎R/fda-fig_02.R

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labs(
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title = annotations[["title"]],
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subtitle = annotations[["subtitle"]],
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subtitle = annotations[["subtitles"]],
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caption = annotations[["caption"]],
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x = x_lab,
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y = y_lab

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