https://github.com/astrazeneca/survextrap-excesshazards
Demonstration of excess hazard and excess hazard cure models for survival extrapolation
https://github.com/astrazeneca/survextrap-excesshazards
Last synced: 12 months ago
JSON representation
Demonstration of excess hazard and excess hazard cure models for survival extrapolation
- Host: GitHub
- URL: https://github.com/astrazeneca/survextrap-excesshazards
- Owner: AstraZeneca
- License: apache-2.0
- Created: 2023-02-23T10:05:14.000Z (over 3 years ago)
- Default Branch: master
- Last Pushed: 2023-02-23T10:52:46.000Z (over 3 years ago)
- Last Synced: 2025-03-12T09:43:59.728Z (over 1 year ago)
- Language: R
- Homepage:
- Size: 17.6 KB
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
README
# survextrap_excesshazards
This repository contains example R and Stata scripts to estimate parametric excess hazard and excess hazard cure survival models, and to derive predictions of all-cause survival, hazard and restricted mean survival.
The repository contains two main scripts:
- ``R/gbsg_extrapolations_examplecode.R`` - Example R script to fit parametric survival models and obtain predictions.
- ``stata/gbsg_extrapolations_examplecode.do`` - Example Stata do file to fit parametric survival models and obtain predictions;
Requirements
------------
Analyses were performed using R 4.1.0 and Stata/MP 17.0.
The project requires the following R packages. The version numbers indicate the version of the packages
that were used in the analysis.
```
ggpubr==0.4.0
gridExtra==2.3
condSURV==2.0.2
ggplot2==3.3.6
tidyr==1.2.0
dplyr==1.0.9
flexsurvcure==1.2.0
flexsurv==2.2
survival==3.2-13
```
Folder Contents
----------------
This folder contains the data files that was used in the analysis. The file descriptions are listed below:
```
|---- README.md : readme file for the data folder
|
|---- R : This folder contains the R scripts
|------- R/gbsg_extrapolations_examplecode.R : The demonstration R script for fitting parametric survival models and obtaining predictions
|------- R/gbsg_stata_data.R : An R script for generating Stata data files for the GBCS data and US population lifetable data
|
|---- stata: This folder contains the Stata script.
|------- stata/gbsg_extrapolations_examplecode.do : The demonstration Stata do file for fitting parametric survival models and obtaining predictions
|---- ado: This folder contains additional ado files for use with the Stata script
|------- stexpect.ado : Calculates expected survival for a cohort of individuals using age at diagnosis, calendar year,
sex and other matching variables in the popmort file
```
Contact
--------
michael.sweeting@astrazeneca.com