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README.Rmd
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---
output: github_document
editor_options:
markdown:
wrap: 72
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# `ClinTrialX`
<!-- badges: start -->
[![R-CMD-check](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ineelhere/clintrialx/actions/workflows/R-CMD-check.yaml)
[![License:
Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-blue.svg)](https://opensource.org/license/apache-2-0)
[![pkgdown](https://img.shields.io/badge/pkgdown-docs-blue.svg)](https://www.indraneelchakraborty.com/clintrialx/)
[![Visitors](https://api.visitorbadge.io/api/visitors?path=https%3A%2F%2Fgithub.com%2Fineelhere%2Fclintrialx&label=Visitors&labelColor=%23f47373&countColor=%2337d67a&style=flat&labelStyle=upper)](https://github.com/ineelhere/clintrialx)
[![CRAN
status](https://www.r-pkg.org/badges/version/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
[![CRAN
downloads](https://cranlogs.r-pkg.org/badges/clintrialx)](https://CRAN.R-project.org/package=clintrialx)
[![Data Sources:
ClinicalTrials.gov](https://img.shields.io/badge/Data_Sources-ClinicalTrials.gov-blue)](https://clinicaltrials.gov/data-api/api)
[![Data Sources: CTTI
AACT](https://img.shields.io/badge/Data_Sources-CTTI%20AACT%20-purple)](https://aact.ctti-clinicaltrials.org/)
<!-- badges: end -->
The goal of `{clintrialx}` is to fetch clinical trials data from freely
available registries. Currently, it supports querying the
- [ClinicalTrials.gov](https://clinicaltrials.gov/) registry using its
[V2 API](https://clinicaltrials.gov/data-api/api) and
- [CTTI AACT](https://aact.ctti-clinicaltrials.org/) (Public Access to
Aggregate Content of ClinicalTrials.gov).
## Installation
Install the package from [CRAN](https://CRAN.R-project.org/package=clintrialx) with:
```r
install.packages("clintrialx")
```
You can install this package from
[GitHub](https://github.com/ineelhere/clintrialx) with:
*you'll need the `devtools` package for this*
``` r
# install.packages("devtools")
devtools::install_github("ineelhere/clintrialx")
```
### Check installation
``` r
library(clintrialx)
```
## Setup AACT account
#### `Only if you wish to use AACT as a source for the data`
- Visit <https://aact.ctti-clinicaltrials.org/users/sign_up>
- Sign up and create an account. It's free.
- The `username` and `password` will be needed to fetch data using
this package.
- Save it in a `.Renviron` file, for example-
``` r
user = "random_name"
password = "random_password"
```
- Now that the file is created, load the variable with the command
`readRenviron("path/to/.Renviron)`
- You're all set!
## Query the [ClinicalTrials.gov](https://clinicaltrials.gov/) Registry
#### Based on NCT IDs
Fetch one or multiple trial records based on NCT IDs. You can opt to
fetch some specific fields or all fields available at source (default).
```{r example1, eval = FALSE}
library(clintrialx)
ctg_get_nct(c("NCT02967965", "NCT04000165", "NCT01007279", "NCT02376244", "NCT01179776"),
fields = c("NCT Number", "Study Title", "Study Status", "Sponsor"))
```
#### Based on fileds
Supports filtering by condition, location, title keywords, intervention,
and overall status.
```{r example2, eval = FALSE}
ctg_get_fields(
condition = "Cancer",
location = "Kolkata",
title = NULL,
intervention = "Drug",
status = c("ACTIVE_NOT_RECRUITING", "RECRUITING"),
page_size = 10
)
```
#### Based on fields - Bulk download
Download all available data for your query. No limits!
*Supports filtering by condition, location, title keywords,
intervention, and overall status.*
```{r example5, eval = FALSE}
df <- ctg_bulk_fetch(location="india")
```
## Query the [CTTI AACT](https://aact.ctti-clinicaltrials.org/)
#### Run Custom Queries
```{r example4, eval = FALSE}
# Set environment variables for database credentials in .Renviron and load it
# readRenviron(".Renviron")
# Connect to the database
con <- aact_connection(Sys.getenv('user'), Sys.getenv('password'))
# Run a custom query
query <- "SELECT nct_id, source, enrollment, overall_status FROM studies LIMIT 5;"
results <- aact_custom_query(con, query)
# Print the results
print(results)
```
## Trial Data HTML Reports
*Currently works for data from ClinicalTrials.Gov*
Visit here for an exqample report -
<https://www.indraneelchakraborty.com/clintrialx/report.html>
```{r example6, eval = FALSE}
#first get the data in a R dataframe
my_clinical_trial_data <- ctg_bulk_fetch(condition="cancer")
#now pass it to the reports function
ctg_data_report(
ctg_data = my_clinical_trial_data,
title = "Clinical Trials Analysis",
author = "Indra",
output_file = "reports/clinical_trials.html",
theme = "flatly",
color_palette = c("#4E79A7", "#F28E2B", "#E15759", "#76B7B2", "#59A14F", "#EDC948"),
include_data_quality = TRUE,
include_interactive_plots = TRUE,
custom_footer = "Proprietary report generated by SomeGreatOrg Inc."
)
# Generate a report with static plots and no data quality assessment
ctg_data_report(
ctg_data = my_clinical_trial_data,
title = "Quick Clinical Trial Overview",
include_data_quality = FALSE,
include_interactive_plots = FALSE
)
```
Check the path `reports/clinical_trials.html` on your local. It will
have the html report file.
Cool stuff - It also has the codes to the plots!
## Data Sources
You can fetch version information directly from the package:
```{r example3, eval = FALSE}
version_info(source = "clinicaltrials.gov")
```
## Get Involved
🚀 Ready to contribute? Let's make clintrialx even better!
- Fork the [GitHub](https://github.com/ineelhere/clintrialx) repo.
- Check out your development branch from the dev branch.
- Do your work on a feature (ftr) branch.
- Raise a PR against the dev branch of the [clintrialx](https://github.com/ineelhere/clintrialx) repo.
- Sit back and [relax](https://www.youtube.com/watch?v=Uffjii1hXzU) while I review it!
💬 **Questions or Feedback?** Feel free to open an issue on [GitHub
Issues page](https://github.com/ineelhere/clintrialx/issues).
🌟 **Enjoying `clintrialx`?** Please consider giving it a star on
[GitHub](https://github.com/ineelhere/clintrialx)! Your support helps
this project grow and improve.
More updates to come. Happy coding! 🎉