cancerR

:package: Classification of Cancer Using Administrative Health Data

https://github.com/giancarlodigi/cancerr

Repository

:package: Classification of Cancer Using Administrative Health Data

README.Rmd

---
output: github_document
---




```{r, include = FALSE}
knitr::opts_chunk$set(collapse  = TRUE,
                      comment   = "#>",
                      fig.path  = "man/figures/",
                      out.width = "100%")
```



cancerR 
=========================================================


[![CRAN status](https://www.r-pkg.org/badges/version/cancerR)](https://CRAN.R-project.org/package=cancerR)
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[![License: GPL (>= 2)](https://img.shields.io/badge/License-GPL%20%28%3E%3D%202%29-blue.svg)](https://choosealicense.com/licenses/gpl-2.0/)
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[![Dependencies](https://img.shields.io/badge/dependencies-0/0-brightgreen?style=flat)](#)





  • Overview

  • Features

  • Installation

  • Get started

  • Upcoming features

  • Citation

  • Contributing

  • References




## Overview


`cancerR` is designed to use administrative data to classify different cancer subtypes using 
data commonly collected by cancer registries. This package is meant for researchers
and data scientists who work with cancer data and need to classify the type of cancer
using the information available in pathology reports which have been coded using the
[International Classification of Diseases for Oncology (ICD-O)](https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology).



## Features

The main purpose of `cancerR` is to use information gathered using the standardized
collection system of the [ICD-O](https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology)
classification system of tumors to classify the type of cancer. Depending on the 
age of the patient, users of the package can classify the type of cancer according to 


The package provides functionality to:

- convert and validate tumor site (a.k.a. topography) codes
- classify childhood cancer according to the [International Classification of Childhood Cancer](https://doi.org/10.1002/cncr.20910)
- assign adolescent and young adult cancers using the [AYA Site](https://seer.cancer.gov/ayarecode/) from the Surveillance, Epidemiology, and End Results (SEER) program or the published [AYA classification by Barr et al](https://doi.org/10.1002/cncr.33041)



## Installation

You can install the released version of `cancerR` from [CRAN](https://CRAN.R-project.org) with:

```{r eval=FALSE}
## Install < cancerR > from CRAN ----
install.packages("cancerR")
```

or you can install the development version from [GitHub](https://github.com/) with:

```{r eval=FALSE}
## Install < remotes > package (if not already installed) ----
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

## Install < cancerR > from GitHub ----
remotes::install_github("giancarlodigi/cancerR")
```

Then you can attach the package `cancerR`:

```{r eval=FALSE}
library("cancerR")
```



## Getting started

For an overview of the main features of `cancerR`, please read the 
[Get started](https://giancarlodigi.github.io/cancerR/articles/cancerR.html)
vignette. This vignette provides a brief introduction to the package and its 
implementation for classifying cancer using administrative data.



## Upcoming features

The package is under active development and planning to add the following features:

- adult cancer classification according to the [ICD-O](https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology)
- implementing conversion and classification of cancers using ICD-O-2 codes 



## Citation

Please cite `cancerR` as: 

> Di Giuseppe Giancarlo (`r format(Sys.Date(), "%Y")`) cancerR: An R 
package to classify cancer using administrative data. R package version 0.1.0. 




## Contributing

All types of contributions are encouraged and valued. For more information, 
please reach out to the maintainer of the package.

Please note that the `cancerR` project is released with a 
[Contributor Code of Conduct](https://contributor-covenant.org/version/2/1/CODE_OF_CONDUCT.html). 
By contributing to this project, you agree to abide by its terms.



## References

Barr RD, Ries LAG, Trama A, et al. A system for classifying cancers diagnosed in adolescents and young adults. Cancer. 2020;126(21):4634-4659. doi: [10.1002/cncr.33041](https://doi.org/10.1002/cncr.33041).

Steliarova-Foucher E, Stiller C, Lacour B, Kaatsch P. International Classification of Childhood Cancer, third edition. Cancer. 2005;103(7):1457-1467. doi: [10.1002/cncr.20910](https://doi.org/10.1002/cncr.20910).

National Cancer Institute. Surveillance, Epidemiology, and End Results Program. Adolescent and Young Adult Site Recode ICD-O-3/WHO 2008. 2021. Available [here](https://seer.cancer.gov/ayarecode/).

World Health Organization. International Classification of Diseases for Oncology (ICD-O) - 3rd Edition, 1st Revision; 2013. Document manual found [here](https://apps.who.int/iris/bitstream/handle/10665/96612/9789241548496_eng.pdf)

Owner

Citation (CITATION.cff)

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "cancerR" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'cancerR: Classification of Cancer Using Administrative Data'
version: 0.1.0
abstract: Classifies the type of cancer using routinely collected data commonly found
  in cancer registries from pathology reports. The package implements the International
  Classification of Diseases for Oncology, 3rd Edition site (topography), histology
  (morphology), and behaviour codes of neoplasms to classify cancer type <https://www.who.int/standards/classifications/other-classifications/international-classification-of-diseases-for-oncology>.
  Classification in children utilize the International Classification of Childhood
  Cancer by Steliarova-Foucher et al. (2005) <https://doi.org/10.1002/cncr.20910>.
  Adolescent and young adult cancer classification is based on Barr et al. (2020)
  <https://doi.org/10.1002/cncr.33041>.
authors:
- family-names: Di Giuseppe
  given-names: Giancarlo
  email: digi.giancarlo@proton.me
  orcid: https://orcid.org/0000-0001-5112-7560
preferred-citation:
  type: manual
  title: 'cancerR: An R package to classify cancer using health data'
  authors:
  - name: Di Giuseppe Giancarlo
  year: '2024'
  notes: R package version 0.0.0.9000
  url: https://github.com/giancarlodigi/cancerR
repository-code: https://github.com/giancarlodigi/cancerR
url: https://github.com/giancarlodigi/cancerR
contact:
- family-names: Di Giuseppe
  given-names: Giancarlo
  email: digi.giancarlo@proton.me
  orcid: https://orcid.org/0000-0001-5112-7560
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
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  institution:
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    address: Vienna, Austria
  year: '2024'
  version: '>= 2.10'
- type: software
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  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2024'
  doi: 10.32614/CRAN.package.knitr
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@posit.co
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: Dervieux
    given-names: Christophe
    email: cderv@posit.co
    orcid: https://orcid.org/0000-0003-4474-2498
  - family-names: McPherson
    given-names: Jonathan
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  - family-names: Luraschi
    given-names: Javier
  - family-names: Ushey
    given-names: Kevin
    email: kevin@posit.co
  - family-names: Atkins
    given-names: Aron
    email: aron@posit.co
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  - family-names: Cheng
    given-names: Joe
    email: joe@posit.co
  - family-names: Chang
    given-names: Winston
    email: winston@posit.co
  - family-names: Iannone
    given-names: Richard
    email: rich@posit.co
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2024'
  doi: 10.32614/CRAN.package.rmarkdown
- type: software
  title: testthat
  abstract: 'testthat: Unit Testing for R'
  notes: Suggests
  url: https://testthat.r-lib.org
  repository: https://CRAN.R-project.org/package=testthat
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@posit.co
  year: '2024'
  doi: 10.32614/CRAN.package.testthat
  version: '>= 3.0.0'

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