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riskclustr

riskclustr: Functions to Study Etiologic Heterogeneity - Published in JOSS (2019)

https://github.com/zabore/riskclustr

Science Score: 93.0%

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    Found 6 DOI reference(s) in README and JOSS metadata
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Last synced: 6 months ago · JSON representation

Repository

R package of functions for the study of etiologic heterogeneity

Basic Info
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  • Stars: 1
  • Watchers: 0
  • Forks: 1
  • Open Issues: 0
  • Releases: 4
Created about 9 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog

README.Rmd 

---
output: github_document
---



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# riskclustr

Etiologic heterogeneity refers to the concept of subtypes of disease that are influenced by different risk factors. Likely the best known example of this is in breast cancer research, where subtypes are often formed based on immunohistochemical staining of estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2). Risk factors including patient characteristics such as age and BMI as well as hormonal risk factors such as age at menarche, parity, and menopausal status have been shown to have different relative risks for these disease subtypes.

`riskclustr` is a collection of functions related to the study of etiologic heterogeneity both across disease subtypes and across individual disease markers. The included functions allow one to quantify the extent of etiologic heterogeneity in the context of a case-control study or case-only study, and provide p-values to test for etiologic heterogeneity with respect to either disease subtypes or individual disease markers in the context of a case-control study.


## Installation

You can install the development version of `riskclustr` by running:

```{r, eval = FALSE}
devtools::install_github("zabore/riskclustr")
library(riskclustr)
```

Or the prodcution version from CRAN by running:

```{r, eval = FALSE}
install.packages("riskclustr")
library(riskclustr)
```


## Documentation

This package is documented using [pkgdown](https://pkgdown.r-lib.org/articles/pkgdown.html), and the resulting website is available at [https://www.emilyzabor.com/riskclustr/](https://www.emilyzabor.com/riskclustr/), where detailed Tutorials can be found covering all of the package functionality.

See [https://www.emilyzabor.com/riskclustr/reference/](https://www.emilyzabor.com/riskclustr/reference/) for detailed function documentation.


## References

> Begg CB, Zabor EC, Bernstein JL, Bernstein L, Press MF, Seshan VE. A conceptual and methodological framework for investigating etiologic heterogeneity. *Stat Med.* 2013;32(29):5039-52. doi: 10.1002/sim.5902

> Begg CB, Seshan VE, Zabor EC, et al. Genomic investigation of etiologic heterogeneity: methodologic challenges. *BMC Med Res Methodol.* 2014;14:138. doi: 10.1186/1471-2288-14-138

> Zabor, EC. riskclustr: Functions to Study Etiologic Heterogeneity. *Journal of Open Source Software.* 2019;4(35):1269. doi:10.21105/joss.01269

Owner

  • Name: Emily C. Zabor
  • Login: zabore
  • Kind: user
  • Location: Cleveland, OH
  • Company: Cleveland Clinic

JOSS Publication

riskclustr: Functions to Study Etiologic Heterogeneity
Published
March 28, 2019
DOI
Volume 4, Issue 35, Page 1269
Authors
Emily C. Zabor ORCID
Memorial Sloan Kettering Cancer Center
Editor
Pjotr Prins ORCID
Tags
biostatistics epidemiology etiologic heterogeneity clustering disease subtypes multinomial logistic regression polytomous logistic regression
View PDF Review Thread Software Archive

GitHub Events

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Last Year

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 124
  • Total Committers: 3
  • Avg Commits per committer: 41.333
  • Development Distribution Score (DDS): 0.056
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Emily C. Zabor e****r@g****m 117
Zabor Z****E@m****g 5
zabore z****e@m****g 2
Committer Domains (Top 20 + Academic)
mskcc.org: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 5
  • Average time to close issues: 4 months
  • Average time to close pull requests: less than a minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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  • mpadge (1)
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  • zabore (5)
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Packages

  • Total packages: 1
  • Total downloads:
    • cran 284 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: riskclustr

Functions to Study Etiologic Heterogeneity

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 284 Last month
Rankings
Forks count: 21.9%
Dependent packages count: 29.8%
Stargazers count: 31.7%
Dependent repos count: 35.5%
Average: 35.8%
Downloads: 60.4%
Maintainers (1)
zabore2@ccf.org
Last synced: 6 months ago