https://github.com/bblodfon/survmob

An R package for benchmarking survival ML models on multi-omics data
https://github.com/bblodfon/survmob

Last synced: 9 months ago
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An R package for benchmarking survival ML models on multi-omics data

• Host: GitHub
• URL: https://github.com/bblodfon/survmob
• Owner: bblodfon
• License: other
• Created: 2023-01-07T02:25:51.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-07-06T08:10:41.000Z (about 3 years ago)
• Last Synced: 2024-12-20T01:44:16.671Z (over 1 year ago)
• Language: R
• Homepage:
• Size: 163 KB
• Stars: 4
• Watchers: 2
• Forks: 0
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS.md
  • License: LICENSE

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README

          
# survmob

`survmob` is an R library that makes it easier to benchmark survival models across multiomics datasets.

It builds upon [mlr3proba](https://github.com/mlr-org/mlr3proba/) and other packages from the [mlr3](https://github.com/mlr-org/) ML ecosystem using [R6](https://github.com/r-lib/R6/) classes.

Key classes and functions implemented:

- Preprocessing - [link](https://github.com/bblodfon/survmob/blob/main/R/preprocess.R)

- Survival learners and hyperparameter spaces class - [link](https://github.com/bblodfon/survmob/blob/main/R/SurvLPS.R)

- Survival measures - [link](https://github.com/bblodfon/survmob/blob/main/R/measures.R)

- Ensemble Feature Selection (eFS) class (uses Random Survival Forest learners and RFE algorithm for finding best feature subsets) - [link](https://github.com/bblodfon/survmob/blob/main/R/eFS.R)

- Multi-omics benchmarking - [link](https://github.com/bblodfon/survmob/blob/main/R/MOBenchmark.R)

## Installation

Install the latest development version of `survmob` using:

```r

remotes::install_github('bblodfon/survmob')

```