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Demographics table (#5)
* Create presentation for "BDS finish example" * Added slides for ADVS * Restore BDS.qmd. Call BDS_ADVS.qmd in .yaml file so slides are added to the overall deck. * Presentation on demographics table * Update file types for listings
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‎slides/demographic_table.qmd‎

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---
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engine: knitr
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title: "Demographic Table"
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execute:
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echo: false
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---
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# Learning objectives
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::: nonincremental
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- THESE ARE NICE TO HAVE BUT NOT ABSOLUTELY NECESSARY
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:::
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# Introduction
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## SDTM
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- SDTM: a standard for organizing and formatting "raw" data (e.g from paper diaries, or e-diaries)
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- Defines **standard domains**
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- Relies on **standardized** variable names, metadata, and controlled terminology
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- Supports the submission of data to regulatory authorities
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Created with help of CDISC genius.
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## ADAM
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- ADaM: provides a standard framework for derivations for statistical analyses.
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- Promoting: transparency, reproducibility, and regulatory compliance.
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- **Traceability**: Clear linkage from analysis results back to source data (often SDTM).
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- **Standard structures**: Like ADSL (Subject-Level Analysis Dataset), BDS (Basic Data Structure), and OCCDS (Occurrence Data Structure).
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- **Derived variables**: Emphasis on clarity and documentation of derived data used in analysis.
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Created with help of CDISC genius.
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## ADAM
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- **Integration with Define-XML**:
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- Enables metadata-driven submissions to regulatory agencies
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- Explains derivation of variables
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- Enables re-creation of derivations & statistical analyses by regulatory authorities
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Created with help of CDISC genius.
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# Tables, Listings and Graphs/Figures (TLGs/TLFs)
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TLFs: Static output generation for Clinical Study Report
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- Listings: One proc away (filtering , subsetting etc. ), lay-out
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- Tables/ Figures: pre-processing, calculate summary statistics, lay-out (e.g.bars/lines/scatter/ presentation summary statistics) + formatting (e.g titles and footnotes) + export output (e.g. pdf, rtf & html)
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Created with help of CDISC genius.
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## TLGs
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Static outputs are part of the clinical reporting process. They are a vital part to summarise the results of the clinical trial. They can summarise safety, efficacy and exploratory outcomes, e.g. biomarkers, QOL, questionnares etc.
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Safety outputs (medical history, adverse events, and concomitant medications) are pretty much similar and standard outputs that you will see across all clinical trials ( regardless of sponsor/therapeutic area).
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Note. These domain names come from SDTM.
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## TLGs workflow
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```{r}
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#install.packages("DiagrammeR")
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library(DiagrammeR)
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mermaid("
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graph TD
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A[SAP/Protocol] --> B[MOCK TFLs]
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B --> C[ADAM]
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C --> D[TFLs]
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")
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```
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::: notes
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- You can add notes on each slide with blocks like this!
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- Load a deck in the browser and type "s" to see these notes.
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ProtocoL: Defines parameters to be analysed SAP: Defines how analyses to be conducted ADAM: Contains all variables and metadata that is required for the production of all outputs TLG: Present analysis results
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:::
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# SLIDE SECTION
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## TLGs Catalogs
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Catalogs with many examples are available here:
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- [TLG Catalog](https://insightsengineering.github.io/tlg-catalog/stable/)
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- [Biomarker Catalog](https://insightsengineering.github.io/biomarker-catalog/stable/tables/)
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- [Teal Gallery](https://insightsengineering.github.io/teal.gallery/)
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# Demographic Table
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[DMT01](https://insightsengineering.github.io/tlg-catalog/stable/tables/demography/dmt01.html)
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## Method 1
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- The {cards} package creates Analysis Results Datasets (ARDs, which are a part of the CDISC Analysis Results Standard).
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- The {gtsummary} utilizes ARDs to create tables.
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## Method 2
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- NEST Package: A collection of open-sourced R packages:
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- {rtables}: Foundational layer of the table creation - can create simple to complex table lay outs via nested splitting - in row- and column - space and the specification of analysis functions which will calculate cell values.
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- Customize tables by defining how to split data into rows and columns, and what calculations to perform in each cell.
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- Provide a framework to create, tabulate and render.
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- Provides a variety of options for table customization.
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- {rlistings}: create listings
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- {tern}: Layers analytics from descriptive summaries to more complex statistics on top of the foundational table layouts, analytic and content controls.
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- Act as wrapper around {rtables} / Reporting layer that sits on top of rtables.
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- Contains analytical functions for creating tables and graphs.
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- Functionalities included: data visualization functions, statistical modelling, analyze functions amongst others.
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- {formatters}
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- {teal}
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- Other Package:
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- GGPLOT2
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## SLIDE
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## {rtables}
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- DENOTE MAJOR SECTIONS WITH `# TITLE` (eg `# Installation`)
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- ADD INDIVIDUAL SLIDES WITH `##` (eg `## rustup on Linux/macOS`)
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- KEEP THEM RELATIVELY SLIDE-LIKE; THESE ARE NOTES, NOT THE BOOK ITSELF.
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+-------------------+--------------------+
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| | {rtables} function |
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+===================+====================+
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| Demographic table | basic_table() |
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+-------------------+--------------------+
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| | split_cols_by() |
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+-------------------+--------------------+
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| | add_overall_col() |
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+-------------------+--------------------+
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| | show_col_counts() |
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+-------------------+--------------------+
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| | build_table() |
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+-------------------+--------------------+
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| | export_as_rtf()/ |
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| | |
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| | export_as_pdf() |
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+-------------------+--------------------+
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## SLIDE
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## {Tern}
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# SLIDE SECTION
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+-------------------+------------------------------+
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| | {tern} analyze function |
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+===================+==============================+
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| Demographic table | analyze_vars() |
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| | |
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| | ( before: summarize_vars() ) |
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+-------------------+------------------------------+
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## SLIDE
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## Analyze functions
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## SLIDE
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- .stats: which statistics to be displayed in the ta
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- .formats: which value formats should be u
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- .labels: which row labels should be used
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- .indent_mods: indent modifiers for the labels
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- .show_labels: whether variable label(s) should be visible or hidden

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