Update "About" files (#312)

Author: edelarua

_quarto.yml

@@ -86,7 +86,8 @@ website:
         file: quarto/resources.qmd
       - text: Help
         menu:
-          - quarto/getting_started.qmd
+          - text: Getting Started
+            file: quarto/getting_started.qmd
           - text: Report a Bug
             url: https://github.com/pharmaverse/cardinal/issues/new/choose
           - text: FAQ

index.qmd

@@ -2,19 +2,13 @@
 title: cardinal
 ---
 
-::: {.callout-warning}
-Please note that the cardinal project is currently undergoing major structural changes and is subject to change without notice.
-
-Some informational pages may show outdated information while the restructuring is in progress.
-:::
-
 ```{css, echo=FALSE}
 h3 {
   text-align: center;
 }
 ```
 
-### Implementation of FDA Safety Tables and Figures
+### A Harmonized Catalog of Pharmaceutical Tables, Listings, and Graphs
 
 #### 
 
@@ -27,7 +21,7 @@ knitr::include_graphics("quarto/assets/images/logo/cardinal.png")
 
 #### What is cardinal?
 
-The cardinal initiative (formerly "falcon") is an industry collaborative effort under pharmaverse that brings together pharmaceutical companies with the aspiration of building and open-sourcing a catalog of harmonized tables, listings, and graphs (TLGs) in clinical study reporting. Leveraging existing open-source R packages, cardinal aims to simplify the process of output review, comparison, and meta-analyses, fostering efficient communication among stakeholders in the pharmaceutical sector while aligning with CDISC's ARD/ARM effort at the same time. Drawing inspiration from the FDA Standard Safety Tables and Figures Integrated Guide, we develop open-source templates. Future plans entail expanding the catalog of templates through continuous collaboration from participating companies and inviting wider industry to promote harmonization of TLGs for clinical reporting.
+The cardinal initiative (formerly "falcon") is an industry collaborative effort under pharmaverse that brings together pharmaceutical companies with the aspiration of building and open-sourcing a catalog of harmonized tables, listings, and graphs (TLGs) in clinical study reporting. Leveraging existing open-source R packages, cardinal aims to simplify the process of output review, comparison, and meta-analyses, fostering efficient communication among stakeholders in the pharmaceutical sector while aligning with CDISC's ARD/ARM effort at the same time. Drawing initial inspiration from the FDA Standard Safety Tables and Figures Integrated Guide, we develop open-source templates from this guide as well as additional sources. Future plans entail expanding the catalog of templates through continuous collaboration from participating companies and inviting wider industry to promote harmonization of TLGs for clinical reporting.
 
 ```{=html}
 <div class="divButton">
@@ -43,7 +37,7 @@ The cardinal initiative (formerly "falcon") is an industry collaborative effort
 
 #### Upcoming Talks & Presentations
 
-No upcoming talks or presentations currently scheduled. Stay tuned!
+- November 3-7, 2025 -- R/Pharma 2025 Online Workshop
 
 See resources from past talks & presentations [here](quarto/resources.html#past-talks-presentations).
 

inst/WORDLIST

@@ -1,37 +1,26 @@
-ADAE
-ADEX
-ADSL
-ADSUB
-ADVS
 ADaM
-AE
-AEs
 ARD
 Abinaya
 Assuied
 CDISC's
-FMQ
 Harsha
 Huan
 Kalikivayi
 Knizia
 Korbinian
 Koujin
+Pharma
 Pharmaverse
-Pre
 Rua
 TLG
 TLGs
 Yichen
 Yogasekaram
 Yoshito
 Yuye
-callout
 cardx
-datetime
 de
 gtsummary
 ncol
 pharmaverse
 pharmaverseadam
-pre

inst/empty-template.qmd

@@ -1,15 +1,13 @@
 ---
-title: Your TLG Title
-subtitle: (Optional Field) Short Description of TLG
-categories: [table, FDA, safety] ## ** REPLACE WITH RELEVANT TAGS **
+title: <Title/Short Description of TLG>
+subtitle: <TLG Source/Identifier>
+categories: [table, FDA, safety] ## TODO: Replace with relevant tags
 ---
 
 ::: panel-tabset
 ## Table Preview
 
 ```{r img, echo=FALSE, fig.align='center', out.width='60%'}
-## ** (OPTIONAL) INCLUDE AN IMAGE OF YOUR TLG HERE **
-## If no image to show, the `Table Preview` section can be removed
 knitr::include_graphics("result.png")
 ```
 
@@ -20,47 +18,46 @@ knitr::include_graphics("result.png")
 library(dplyr)
 library(cards)
 library(gtsummary)
+## TODO: Load any additional packages needed
 
-## ** LOAD ADDITIONAL PACKAGES USED HERE **
-
-## ** LOAD ALL DATASETS USED IN EXAMPLES HERE **
+## TODO: Load all datasets used in example TLG
 
 # Pre-processing --------------------------------------------
 
-## ** ADD CODE FOR ANY NECESSARY DATA PRE-PROCESSING HERE **
-```
-
-## Build ARD
-
-```{r ard, message=FALSE, warning=FALSE, results='hide'}
-## ** INSERT YOUR ARD CODE HERE **
-## `ard` should return an ARD of class `card`
-ard <- NULL
-
-ard
-```
-
-```{r, echo=FALSE}
-# Print ARD
-withr::local_options(width = 9999)
-print(ard, columns = "all", n = 40)
+## TODO: Insert code for all necessary data pre-processing steps
 ```
 
 ## Build Table
 
 ```{r tbl, results = 'hide'}
-## ** INSERT YOUR TABLE CODE HERE **
-## `tbl` should return a `gtsummary` table
+## TODO: Insert your TLG code - `tbl` should return a `gtsummary` object
 tbl <- NULL
 
 tbl
 ```
 
 ```{r eval=FALSE, include=FALSE}
-## ** (OPTIONAL) RUN THIS CHUNK LOCALLY TO GENERATE AN IMAGE FILE **
+## Run this chunk locally to generate an image file
 gt::gtsave(as_gt(tbl), filename = "result.png")
 ```
 
 ```{r img, echo=FALSE, fig.align='center', out.width='60%'}
 ```
+
+## Build ARD
+
+```{r ard, message=FALSE, warning=FALSE, results='hide'}
+## TODO: Replace with your ARD code and reorder tabs if using an
+##   ARD-first approach - `ard` should return an ARD of class `card`
+ard <- gather_ard(tbl)
+
+ard
+```
+
+```{r, echo=FALSE}
+# Print ARD
+withr::local_options(width = 9999)
+print(ard, columns = "all", n = 40) ## TODO: Replace with `print(ard)` if `ard` is a list of ARDs
+```
+
 :::

quarto/about.qmd

@@ -4,7 +4,7 @@ title: About the Project
 
 The cardinal project (previously "falcon") is a product of industry collaboration to encourage the development of shared code, expertise, knowledge, and products.
 
-In the near future, the goal is to develop functionality to create regulatory reporting tables suitable for FDA filing. The long-term objective of this collaboration is to develop an R package that can be used industry wide - developing a cross-industry standard and reducing manual work from a reporting perspective.
+The goal of this collaboration is to develop an extensive catalog of harmonized ARD-based table, listing, and graph (TLG) templates that can be used industry wide - developing a cross-industry standard and reducing manual work from a reporting perspective.
 
 ## Our Collaboration Journey
 
@@ -18,12 +18,14 @@ As always we invite further collaboration and welcome additional companies to jo
 
 As a pharmaverse collaboration, we invite any interested developers to join the cardinal team and contribute to template development. To onboard as a developer, please reach out to one of the cardinal Product Owners ([Vincent Shen](https://github.com/telepath37), [Freeman Wang](https://github.com/freestatman), Kavitha Allala, Lian Lin) to receive access to the cardinal GitHub repository.
 
-Tasks are assigned and prioritized via issues on our GitHub project board and worked on in development branches. Members of the team will review each other's code and make suggestions before new functions and features are incorporated into the package.
+Tasks are assigned and prioritized via issues on our GitHub project board and worked on in development branches. Members of the team will review each other's code and make suggestions before new templates are incorporated into the project catalog.
 
-We encourage onboarding developers to familiarize themselves with the following packages as they contain functions leveraged by cardinal for table creation:
-
--   [`gtsummary`](https://www.danieldsjoberg.com/gtsummary/): Table creation
--   [`cards`](https://insightsengineering.github.io/cards/main/): Analysis Results Dataset creation
--   [`cardx`](https://insightsengineering.github.io/cardx/main/): Extended ARD creation functions
+For information on the process by which developers can add new templates to the catalog, see the [Getting Started page](getting_started.qmd).
 
+We encourage onboarding developers to familiarize themselves with the following packages as they contain functions leveraged by the cardinal team for TLG creation:
 
+-   [{gtsummary}](https://www.danieldsjoberg.com/gtsummary/): Table creation
+-   [{cards}](https://insightsengineering.github.io/cards/): ARD creation
+-   [{cardx}](https://insightsengineering.github.io/cardx/): Extended ARD creation functions
+-   [{crane}](https://insightsengineering.github.io/crane/): Pharmaceutical-specific table creation functions
+-   [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/): Example synthetic ADaM datasets

quarto/faq.qmd

@@ -10,33 +10,27 @@ format:
 
 ------------------------------------------------------------------------
 
-#### 1. \ How do I install the cardinal package?
-
-For instructions on installing the cardinal package please see the [Environment Setup and Package Installation](https://pharmaverse.github.io/cardinal/quarto/getting_started.html#environment-setup-and-package-installation) section of the Getting Started page.
-<br/><br/>
-
-
-#### 2. \ How can I join this initiative?
+#### 1. \ How can I join this initiative?
 
 For information on how to join the cardinal initiative please see the [Joining as a Collaborator](https://pharmaverse.github.io/cardinal/quarto/about.html#joining-as-a-collaborator) section of the About page.
 <br/><br/>
 
 
-#### 3. \ I copied the example "Table Setup" code for one of the cardinal tables. How can I customize the table?
+#### 2. \ I copied the example code for one of the cardinal TLGs. How can I customize the TLG?
 
-For each table template page, next to the "Table Setup" tab is the "Function Details" tab. This tab contains information about each of the customizable parameters available for the table, and what the default settings for each are. If you require a customization option that is not available for a given table, please file a Feature Request issue on GitHub [here](https://github.com/pharmaverse/cardinal/issues/new/choose).
+Every template in the catalog generates a `gtsummary` object (or `ggplot2` object for graphs) which can be customized using the standard modification functions available in the {gtsummary} (or {ggplot2} for graphs) package. Please see this package for more information on customization and formatting options.
 <br/><br/>
 
 
-#### 4. \ I need a table that isn't available on the cardinal website. Can I request a table be added?
+#### 3. \ I need a TLG that isn't available on the cardinal website. Can I request a table be added?
 
-The cardinal team is actively maintaining and adding new table functions to the package. If you would like an FDA safety table that is not listed on the cardinal website, please file a New Table Template issue on GitHub [here](https://github.com/pharmaverse/cardinal/issues/new/choose) with the table number and the team will work on adding it to the package.
+The cardinal team is actively maintaining and adding new TLG templates to the project catalog. If you would like to see a TLG that is not listed on the cardinal website, please file a New TLG Template issue on GitHub [here](https://github.com/pharmaverse/cardinal/issues/new/choose) and the team will work on adding it to the catalog. Please also consider adding the template to the catalog yourself! We are always happy to have new contributors join the initiative (even if you can only add a single TLG!) - for information on how to add a new template yourself see the [Getting Started](getting_started.qmd) page.
 <br/><br/>
 
 
-#### 5. \ I don't know the number of the FDA safety table I am interested in. Is there a list of tables by title?
+#### 4. \ I don't know the ID of the table I am interested in. Is there a list of TLGs by description?
 
-A list of all available tables by title is available on the [Template Catalog](index-catalog.qmd) page.
+A list of all available TLGs by both description and ID/source is available on the [Template Catalog](index-catalog.qmd) page, and can be sorted/filtered accordingly. The category tags on the right-hand side of the page can be used to filter for specific TLGs.
 <br/><br/>
 
 

quarto/getting_started.qmd

@@ -1,5 +1,5 @@
 ---
-title: "Getting Started"
+title: "Adding a New Template"
 toc: true
 toc-depth: 4
 ---
@@ -8,62 +8,60 @@ toc-depth: 4
 
 #### Environment Setup
 
-Please ensure that R version 3.6 or higher is installed on your computer. This is required to install the `cardinal` package and its dependencies. You can check your current version of R by running `sessionInfo()` within the R console.
+Please ensure that R version 4.2 or higher is installed on your computer. This is required to install the packages you will need to create your TLG template. You can check your current version of R by running `sessionInfo()` within the R console.
 
-#### Installing Package Dependencies
+#### Installing Packages for Template Creation
 
-The `cardinal` package requires several packages available on CRAN.
+To create your TLG template the {gtsummary}, {cards}, and {cardx} packages available on CRAN are required.
 
-To use the `cardinal` package, ensure you have these necessary package dependencies installed by running the following code:
+Please ensure you have these necessary packages installed by running the following code:
 
 ```{r, echo=TRUE, eval=FALSE}
-if (!require("gtsummary")) install.packages("gtsummary")
 if (!require("cards")) install.packages("cards")
 if (!require("cardx")) install.packages("cardx")
-if (!require("formatters")) install.packages("formatters")
-if (!require("rtables")) install.packages("rtables")
-if (!require("rlistings")) install.packages("rlistings")
-if (!require("tern")) install.packages("tern")
+if (!require("gtsummary")) install.packages("gtsummary")
 ```
 
-Optionally, to run the examples provided within the `cardinal` package and on this site you can also install the random CDISC data package, which contains example datasets, by running the following:
+To create your example TLG/ARD, we recommend using datasets from the {pharmaverseadam} package (or the {random.cdisc.data} package) which contains example synthetic ADaM datasets and is available on CRAN. Optionally, you may want to also install the {crane} package which contains several helpful pharmaceutical-specific table creation functions:
 
 ```{r, echo=TRUE, eval=FALSE}
-if (!require("random.cdisc.data")) install.packages("random.cdisc.data")
+if (!require("pharmaverseadam")) install.packages("pharmaverseadam")
+if (!require("crane")) install.packages("crane")
 ```
 
 For more information on these packages, see the [Additional Resources](#additional-resources) section below.
 
-#### Installing the cardinal Package
+#### Creating Your TLG Template
 
-To install the `cardinal` package, run the following line of code:
+When adding a new template, start by initializing a new folder in the `quarto/catalog` folder with a name that uniquely identifies your TLG (e.g. `fda-table_01`, `lab-tests-summary`). Within this folder, add a file named `index.qmd` which will contain your new TLG template. To simplify the template-creation process we have provided an empty template file (`inst/empty-template.qmd`) which can be copied into your new `index.qmd` file and then modified.
 
-```{r, echo=TRUE, eval=FALSE}
-if (!require("cardinal")) remotes::install_github("pharmaverse/cardinal")
-```
+We recommend using datasets from the `pharmaverseadam` package to run your template code and generate a sample output TLG and ARD.
 
-### Loading Data
+Ensure that your template file contains four main sections in separate tabs. If, for example, you are creating a template for a table, these tabs should be named:
 
-The table functions provided by `cardinal` are designed to work with any datasets which adhere to CDISC standards. If you have access to CDISC data, load this into your R environment as usual to use when generating tables.
+1. Table Preview - provides a preview of the table that is created in the template.
+2. Setup - lists the data set-up and pre-processing steps needed prior to creating the table.
+3. Build Table - provides the code needed to build the table.
+4. Build ARD - provides the code needed to build the ARD associated with the table. If an ARD-first approach was used to create the table this section should appear prior to the "Build Table" tab.
 
-If you do not have access to CDISC data, or want to run the examples provided within the package, you can use the `random.cdisc.data` package to load a selection of datasets containing example synthetic randomized CDISC data. Datasets are stored in the package by name, prefixed by the letter `"c"` (for "cached"). For example, after loading the `random.cdisc.data` package you can access an ADSL dataset by running `cadsl`, or ADAE with `cadae`. This data is loaded in where necessary as part of the provided examples.
+### Finalizing Your TLG Template
 
-### Template Navigation
+Once you have created your template and ensured that all code runs without error, generate an image file named `result.png` containing a snapshot of your table. Confirm that the output image looks correct.
 
-A list of all templates currently available in `cardinal` is provided in the [Template Catalog](index-catalog.qmd), with tables designed based on the [FDA Standard Safety Tables and Figures: Integrated Guide](https://downloads.regulations.gov/FDA-2022-N-1961-0046/attachment_1.pdf).
+Once you have finalized your TLG template, open a pull request in the cardinal [GitHub repository](https://github.com/pharmaverse/cardinal/).
 
-### Feature Requests
+### Template Navigation
 
-If you would like to request the addition of a new feature to a pre-existing function within `cardinal`, or would like a specific table template to be added, please file an issue on GitHub [here](https://github.com/pharmaverse/cardinal/issues) or reach out to the cardinal team directly via our Slack channel [here](https://app.slack.com/client/T028PB489D3/C04MQS12MND).
+A list of all templates currently available in cardinal is provided in the [Template Catalog](index-catalog.qmd).
 
-You can access the source code for all currently available functions in the `cardinal` GitHub repository [here](https://github.com/pharmaverse/cardinal/tree/main/R).
+You can access the files for all currently available templates in the cardinal GitHub repository [here](https://github.com/pharmaverse/cardinal/tree/main/quarto/catalog).
 
 ### Additional Resources {#additional-resources}
 
-See the following packages used by `cardinal` for more information:
+See the following sites for more information on packages leveraged by the cardinal team for TLG template development:
 
--   [`tern`](https://insightsengineering.github.io/tern): Clinical trials analysis functions
--   [`rtables`](https://insightsengineering.github.io/rtables): Table creation
--   [`rlistings`](https://insightsengineering.github.io/rlistings): Listing creation
--   [`formatters`](https://insightsengineering.github.io/formatters): Additional rendering formatting
--   [`random.cdisc.data`](https://insightsengineering.github.io/random.cdisc.data): Example synthetic randomized CDISC datasets (required for examples only)
+-   [{gtsummary}](https://www.danieldsjoberg.com/gtsummary/): Table creation
+-   [{cards}](https://insightsengineering.github.io/cards/): ARD creation
+-   [{cardx}](https://insightsengineering.github.io/cardx/): Extended ARD creation functions
+-   [{crane}](https://insightsengineering.github.io/crane/): Pharmaceutical-specific table creation functions
+-   [{pharmaverseadam}](https://pharmaverse.github.io/pharmaverseadam/): Example synthetic ADaM datasets