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Improve readme style and add links #34

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<!-- badges: start -->
# R Submission Pilot 1

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[![R-CMD-check](https://github.com/RConsortium/submissions-pilot1/workflows/R-CMD-check/badge.svg)](https://rconsortium.github.io/submissions-pilot1/)
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## Overview

The objective of the R Consortium R submission Pilot 1 Project is to
test the concept that a R-language based submission package can meet
the needs and the expectations of the FDA reviewers,
including assessing code review and analyses reproducibility.
All submission materials and communications from this pilot are publicly available,
The objective of the R Consortium R submission pilot 1 project is to
test the concept that an R language based submission package can meet
the needs and the expectations of the FDA reviewers,
including assessing code review and analyses reproducibility.
All submission materials and communications from this pilot are publicly available,
with the aim of providing a working example for future R language based FDA submissions.
This is a FDA-industry collaboration through the non-profit organization R consortium.
This is a FDA-industry collaboration through the non-profit organization R Consortium.

The [working group website](https://rconsortium.github.io/submissions-wg/).

The [RConsortium/submissions-pilot1](https://github.com/RConsortium/submissions-pilot1) repo demonstrates an approach to organize internal developed R function and
table, listing, figure generation program using an R package.
The [RConsortium/submissions-pilot1](https://github.com/RConsortium/submissions-pilot1)
repo demonstrates an approach to organize internal developed R functions and
tables, listings, and figures (TLFs) generation programs using an R package.

The [RConsortium/submissions-pilot1-to-fda](https://github.com/RConsortium/submissions-pilot1-to-fda)
repo demonstrates the eCTD submission package based on the [RConsortium/submissions-pilot1](https://github.com/RConsortium/submissions-pilot1) repo.
repo demonstrates the eCTD submission package based on the
[RConsortium/submissions-pilot1](https://github.com/RConsortium/submissions-pilot1) repo.

## FDA response

## FDA Response
- Initial submission (2021-11-22)
- Version: [v0.1.0](https://github.com/RConsortium/submissions-pilot1/releases/tag/v0.1.0)
- [FDA statistical review and evaluation](https://github.com/RConsortium/submissions-pilot1/blob/main/vignettes/fda/fda-response-2021-11-22.pdf) (2021-12-03)
- Updated submission (2022-02-11)
- Version: [v0.1.1](https://github.com/RConsortium/submissions-pilot1/releases/tag/v0.1.1)
- [FDA statistical review and evaluation](https://github.com/RConsortium/submissions-wg/blob/main/_Documents/Summary_R_Pilot_Submission2.pdf) (2022-03-14)

- Initial submission
+ version: [v0.1.0](https://github.com/RConsortium/submissions-pilot1/releases/tag/v0.1.0)
+ [FDA statistical review and evaluation](https://github.com/RConsortium/submissions-pilot1/blob/main/vignettes/fda/fda-response-2021-11-22.pdf)

## Running Environment
## Running environment

The project is developed and tested in the environment below:

- OS: Ubuntu 20.04
- R version: R4.1.3
- Snapshot date: 2021-08-31
- Snapshot repository: https://mran.microsoft.com/snapshot/2021-08-31
- R version: R 4.1.3
- CRAN snapshot date: 2021-08-31
- CRAN snapshot repository: <https://mran.microsoft.com/snapshot/2021-08-31>

## Folder Structure
## Folder structure

The work in this repo is organized as an R package following the concepts discussed in:

- [Marwick, B., Boettiger, C., & Mullen, L. (2018). Packaging data analytical work reproducibly using R (and friends). The American Statistician, 72(1), 80-88.](https://peerj.com/preprints/3192/)
- [Wu, P., Palukuru, U. P., Luo, Y., Nepal, S., & Zhang, Y. (2021) Analysis and reporting in regulated clinical trial environment using R. PharmaSUG 2021](https://www.pharmasug.org/proceedings/2021/AD/PharmaSUG-2021-AD-079.pdf)

More details related to organize a clinical project and submission package can be found in Chapter 10-15
of the [R for Clinical Study Reports and Submission](https://r4csr.org/index.html) book.
More details related to organize a clinical project and submission package can
be found in Chapter 10--15 of the
[R for Clinical Study Reports and Submission](https://r4csr.org/) book.

### R function and Analysis Scripts
### R functions and analysis scripts

In short, the project is organized as an R package.
In short, the project is organized as an R package.

- `pilot1wrappers.Rproj`: RStudio project file used to open RStudio project.
- `DESCRIPTION`: Metadata for a package including authors, license, dependency etc.
- `vignettes/`: Analysis scripts using Rmarkdown.
- `R/`: Project specific R functions.
- `man/`: Manual of project specific R functions.
- `pilot1wrappers.Rproj`: RStudio project file used to open the project.
- `DESCRIPTION`: Metadata for a package including authors, license, dependency, etc.
- `vignettes/`: Analysis scripts using R Markdown.
- `R/`: Project-specific R functions.
- `man/`: Manual of project-specific R functions.

### Datasets

The source dataset is in `adam\` folder. The original data is from [the PHUSE Github Repository](https://github.com/phuse-org/phuse-scripts/blob/master/data/adam/TDF_ADaM_v1.0.zip)
The source dataset is in the `adam/` folder. The original data is from the
[PHUSE Github repository](https://github.com/phuse-org/phuse-scripts/blob/master/data/adam/TDF_ADaM_v1.0.zip).

### Startup file
- `.Rprofile`: Project startup file to setup running environment including R version, repository, folder path etc.
- We further use `inst/startup.R` and `R/zzz.R` to allow the startup file is executed while running. `devtools::load_all()` and RStudio build panel.

### Results
### Startup files

- `output\`: TLFs output generated by Rmarkdown files in `vignettes\` folder.
- `inst/startup.R`: The primary startup file.
It configures the running environment, including R version,
package repository, folder paths, and other parameters.
- `.Rprofile`: An entry point file ensuring `inst/startup.R` execution
during development, such as opening the project in RStudio,
using `devtools::load_all()`, or using RStudio build panel features.
- `R/zzz.R`: Another entry point file, triggering `inst/startup.R`
during package loading via `library()`.

### Results

- `output/`: TLF outputs generated by R Markdown files in the `vignettes/` folder.

### Reproducibility

The original code is prepared and executed on Ubuntu 20.04.3 LTS.
We use `renv` to ensure reproducibility for R version and R package version.
We use renv to ensure reproducibility for R version and R package versions.

- `renv.lock` and `renv\` folder: R package management using `renv` package. ([Introduction](https://rstudio.github.io/renv/articles/renv.html))
- `renv.lock` and `renv/` folder: R package management using the renv package.
([Introduction](https://rstudio.github.io/renv/articles/renv.html))

### Utilities

- `_pkgdown.yml`: [pkgdown](https://pkgdown.r-lib.org/articles/pkgdown.html) configuration file.