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ezcox

Easily Process a Batch of Cox Models

https://github.com/shixiangwang/ezcox

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: arxiv.org
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.0%) to scientific vocabulary

Keywords

batch-processing cox-model r-package
Last synced: 6 months ago · JSON representation

Repository

Easily Process a Batch of Cox Models

Basic Info
Statistics
  • Stars: 21
  • Watchers: 1
  • Forks: 2
  • Open Issues: 0
  • Releases: 6
Topics
batch-processing cox-model r-package
Created over 6 years ago · Last pushed about 2 years ago
Metadata Files
Readme Changelog Contributing License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```
# ezcox: Easily Process a Batch of Cox Models


[![CRAN status](https://www.r-pkg.org/badges/version/ezcox)](https://CRAN.R-project.org/package=ezcox)
[![](https://cranlogs.r-pkg.org/badges/grand-total/ezcox?color=blue)](https://cran.r-project.org/package=ezcox)
[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)


**A new R package [bregr](https://github.com/WangLabCSU/bregr/) has been developed for more general analysis and future development**

The goal of ezcox is to operate a batch of univariate or multivariate Cox models and return tidy result.

## :arrow_double_down: Installation

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

```r
install.packages("ezcox")
```

And the development version from [GitHub](https://github.com/) with:

```r
# install.packages("remotes")
remotes::install_github("ShixiangWang/ezcox")
```

It is possible to install **ezcox** from Conda `conda-forge` channel:

```r
conda install r-ezcox --channel conda-forge
```

Visualization feature of **ezcox** needs the recent version of **forestmodel**, please run the following commands:

```r
remotes::install_github("ShixiangWang/forestmodel")
```

## :beginner: Example

This is a basic example which shows you how to get result from a batch of cox models.

```{r example}
library(ezcox)
library(survival)

# Build unvariable models
ezcox(lung, covariates = c("age", "sex", "ph.ecog"))

# Build multi-variable models
# Control variable 'age'
ezcox(lung, covariates = c("sex", "ph.ecog"), controls = "age")
```

```{r}
lung$ph.ecog = factor(lung$ph.ecog)
zz = ezcox(lung, covariates = c("sex", "ph.ecog"), controls = "age", return_models=TRUE)
mds = get_models(zz)
str(mds, max.level = 1)

show_models(mds)
```


## :star2: Vignettes

- [ezcox: Easily Process a Batch of Cox Models](https://CRAN.R-project.org/package=ezcox/vignettes/ezcox.html)
- [ezcox: Easily Show Cox Forestplot in One Command](https://CRAN.R-project.org/package=ezcox/vignettes/ezforest.html)
- [ezcox: Easy Group Cox Analysis and Visualization](https://CRAN.R-project.org/package=ezcox/vignettes/ezgroup.html)
- [ezcox: an R Package for Cox Model Batch Processing and Visualization - An Use Case](https://shixiangwang.github.io/ezcox-adv-usage/)

## :page_with_curl: Citation

If you are using it in academic research,
please cite the preprint [arXiv:2110.14232](https://arxiv.org/abs/2110.14232) along with URL of this repo.

Owner

  • Name: Shixiang Wang (王诗翔)
  • Login: ShixiangWang
  • Kind: user
  • Location: Guangzhou, China
  • Company: SYSUCC

纯素之道，惟神是守。守而勿失，与神为一

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 80
  • Total Committers: 2
  • Avg Commits per committer: 40.0
  • Development Distribution Score (DDS): 0.012
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
ShixiangWang w****x@s****n 79
olivroy 5****y 1
Committer Domains (Top 20 + Academic)
shanghaitech.edu.cn: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 25
  • Total pull requests: 1
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 4 hours
  • Total issue authors: 5
  • Total pull request authors: 1
  • Average comments per issue: 1.8
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 5
  • 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
View more stats
Top Authors
Issue Authors
  • ShixiangWang (17)
  • weekly-digest[bot] (5)
  • qingjian1991 (1)
  • demi0304 (1)
  • lijing-lin (1)
Pull Request Authors
  • olivroy (2)
Top Labels
Issue Labels
enhancement (7) weekly-digest (4)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 656 last-month
  • Total docker downloads: 524
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 3
    (may contain duplicates)
  • Total versions: 17
  • Total maintainers: 1
cran.r-project.org: ezcox

Easily Process a Batch of Cox Models

  • Versions: 13
  • Dependent Packages: 2
  • Dependent Repositories: 3
  • Downloads: 656 Last month
  • Docker Downloads: 524
Rankings
Stargazers count: 12.2%
Dependent packages count: 13.7%
Average: 15.9%
Dependent repos count: 16.5%
Docker downloads count: 16.5%
Forks count: 17.0%
Downloads: 19.5%
Maintainers (1)
w_shixiang@163.com
Last synced: 6 months ago
conda-forge.org: r-ezcox
  • Versions: 4
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 41.1%
Stargazers count: 47.3%
Forks count: 54.2%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • dplyr >= 0.8.3 imports
  • forestmodel * imports
  • ggplot2 * imports
  • magrittr >= 1.5 imports
  • purrr >= 0.3.2 imports
  • rlang >= 0.1.2 imports
  • scales * imports
  • survival * imports
  • tibble * imports
  • utf8 * imports
  • utils * imports
  • covr >= 3.2.1 suggests
  • furrr * suggests
  • future * suggests
  • knitr * suggests
  • prettydoc * suggests
  • rmarkdown * suggests
  • roxygen2 >= 6.1.1 suggests
  • testthat >= 2.1.0 suggests