{"id":20837781,"url":"https://github.com/astrazeneca/survextrap-excesshazards","last_synced_at":"2025-06-28T05:33:06.828Z","repository":{"id":103037968,"uuid":"605510173","full_name":"AstraZeneca/survextrap-excesshazards","owner":"AstraZeneca","description":"Demonstration of excess hazard and excess hazard cure models for survival extrapolation","archived":false,"fork":false,"pushed_at":"2023-02-23T10:52:46.000Z","size":18,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-12T09:43:59.728Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/AstraZeneca.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-02-23T10:05:14.000Z","updated_at":"2024-12-12T10:00:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"d0a55354-aa5d-4080-be0e-cd48a4d78c18","html_url":"https://github.com/AstraZeneca/survextrap-excesshazards","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/AstraZeneca/survextrap-excesshazards","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2Fsurvextrap-excesshazards","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2Fsurvextrap-excesshazards/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2Fsurvextrap-excesshazards/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2Fsurvextrap-excesshazards/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AstraZeneca","download_url":"https://codeload.github.com/AstraZeneca/survextrap-excesshazards/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2Fsurvextrap-excesshazards/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262381980,"owners_count":23302256,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-18T01:08:33.535Z","updated_at":"2025-06-28T05:33:06.807Z","avatar_url":"https://github.com/AstraZeneca.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# survextrap_excesshazards\n![Maturity level-Prototype](https://img.shields.io/badge/Maturity%20Level-Prototype-red) \n\nThis 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. \nThe repository contains two main scripts: \n - ``R/gbsg_extrapolations_examplecode.R`` - Example R script to fit parametric survival models and obtain predictions.\n - ``stata/gbsg_extrapolations_examplecode.do`` - Example Stata do file to fit parametric survival models and obtain predictions;\n\nRequirements\n------------\nAnalyses were performed using R 4.1.0 and Stata/MP 17.0. \n\nThe project requires the following R packages. The version numbers indicate the version of the packages \nthat were used in the analysis. \n```\n  ggpubr==0.4.0\n  gridExtra==2.3\n  condSURV==2.0.2\n  ggplot2==3.3.6\n  tidyr==1.2.0\n  dplyr==1.0.9\n  flexsurvcure==1.2.0 \n  flexsurv==2.2\n  survival==3.2-13 \n```\n\nFolder Contents\n----------------\nThis folder contains the data files that was used in the analysis. The file descriptions are listed below:\n\n```\n|---- README.md :  readme file for the data folder\n|\n|---- R : This folder contains the R scripts \n|------- R/gbsg_extrapolations_examplecode.R : The demonstration R script for fitting parametric survival models and obtaining predictions\n|------- R/gbsg_stata_data.R : An R script for generating Stata data files for the GBCS data and US population lifetable data\n|\n|---- stata:  This folder contains the Stata script.\n|------- stata/gbsg_extrapolations_examplecode.do : The demonstration Stata do file for fitting parametric survival models and obtaining predictions\n|---- ado: This folder contains additional ado files for use with the Stata script\n|------- stexpect.ado : Calculates expected survival for a cohort of individuals using age at diagnosis, calendar year, \nsex and other matching variables in the popmort file\n```\n\nContact\n--------\nmichael.sweeting@astrazeneca.com\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fastrazeneca%2Fsurvextrap-excesshazards","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fastrazeneca%2Fsurvextrap-excesshazards","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fastrazeneca%2Fsurvextrap-excesshazards/lists"}