https://github.com/shixiangwang/ezcox

Easily Process a Batch of Cox Models
https://github.com/shixiangwang/ezcox

batch-processing cox-model r-package

Last synced: about 1 month ago
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Easily Process a Batch of Cox Models

• Host: GitHub
• URL: https://github.com/shixiangwang/ezcox
• Owner: ShixiangWang
• License: gpl-3.0
• Created: 2019-08-06T09:55:11.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2024-01-05T01:47:41.000Z (over 1 year ago)
• Last Synced: 2024-08-09T08:07:35.131Z (9 months ago)
• Topics: batch-processing, cox-model, r-package
• Language: R
• Homepage: https://shixiangwang.github.io/ezcox/
• Size: 7.1 MB
• Stars: 20
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.Rmd
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE.md

Awesome Lists containing this project

README

        
---

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)

[![Hits](https://hits.seeyoufarm.com/api/count/incr/badge.svg?url=https%3A%2F%2Fgithub.com%2FShixiangWang%2Fezcox&count_bg=%2379C83D&title_bg=%23555555&icon=fandom.svg&icon_color=%23E7E7E7&title=hits&edge_flat=false)](https://hits.seeyoufarm.com)

![R-CMD-check](https://github.com/ShixiangWang/ezcox/workflows/R-CMD-check/badge.svg)

[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html)

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.