# ezcox

**Repository Path**: ShixiangWang/ezcox

## Basic Information

- **Project Name**: ezcox
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: GPL-3.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2020-07-01
- **Last Updated**: 2024-05-03

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README


<!-- README.md is generated from README.Rmd. Please edit that file -->

# ezcox: Easily Process a Batch of Cox Models

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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
library(ezcox)
#> Welcome to 'ezcox' package!
#> =======================================================================
#> You are using ezcox version 0.8.1
#> 
#> Github page  : https://github.com/ShixiangWang/ezcox
#> Documentation: https://shixiangwang.github.io/ezcox/articles/ezcox.html
#> 
#> Run citation("ezcox") to see how to cite 'ezcox'.
#> =======================================================================
#> 
library(survival)

# Build unvariable models
ezcox(lung, covariates = c("age", "sex", "ph.ecog"))
#> => Processing variable age
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable sex
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable ph.ecog
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> # A tibble: 3 × 12
#>   Variable is_control contrast_level ref_level n_contrast n_ref    beta    HR
#>   <chr>    <lgl>      <chr>          <chr>          <int> <int>   <dbl> <dbl>
#> 1 age      FALSE      age            age              228   228  0.0187 1.02 
#> 2 sex      FALSE      sex            sex              228   228 -0.531  0.588
#> 3 ph.ecog  FALSE      ph.ecog        ph.ecog          227   227  0.476  1.61 
#> # … with 4 more variables: lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>,
#> #   global.pval <dbl>

# Build multi-variable models
# Control variable 'age'
ezcox(lung, covariates = c("sex", "ph.ecog"), controls = "age")
#> => Processing variable sex
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable ph.ecog
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> # A tibble: 4 × 12
#>   Variable is_control contrast_level ref_level n_contrast n_ref    beta    HR
#>   <chr>    <lgl>      <chr>          <chr>          <int> <int>   <dbl> <dbl>
#> 1 sex      FALSE      sex            sex              228   228 -0.513  0.599
#> 2 sex      TRUE       age            age              228   228  0.017  1.02 
#> 3 ph.ecog  FALSE      ph.ecog        ph.ecog          227   227  0.443  1.56 
#> 4 ph.ecog  TRUE       age            age              228   228  0.0113 1.01 
#> # … with 4 more variables: lower_95 <dbl>, upper_95 <dbl>, p.value <dbl>,
#> #   global.pval <dbl>
```

``` r
lung$ph.ecog = factor(lung$ph.ecog)
zz = ezcox(lung, covariates = c("sex", "ph.ecog"), controls = "age", return_models=TRUE)
#> => Processing variable sex
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
#> => Processing variable ph.ecog
#> ==> Building Surv object...
#> ==> Building Cox model...
#> ==> Done.
mds = get_models(zz)
str(mds, max.level = 1)
#> List of 2
#>  $ Surv ~ sex + age    :List of 19
#>   ..- attr(*, "class")= chr "coxph"
#>   ..- attr(*, "Variable")= chr "sex"
#>  $ Surv ~ ph.ecog + age:List of 22
#>   ..- attr(*, "class")= chr "coxph"
#>   ..- attr(*, "Variable")= chr "ph.ecog"
#>  - attr(*, "class")= chr [1:2] "ezcox_models" "list"
#>  - attr(*, "has_control")= logi TRUE

show_models(mds)
```

<img src="man/figures/README-unnamed-chunk-2-1.png" width="100%" />

## :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.