{"id":32207293,"url":"https://github.com/cu-dbmi-peds/phoenix","last_synced_at":"2025-10-22T05:50:59.969Z","repository":{"id":221442894,"uuid":"754369850","full_name":"CU-DBMI-Peds/phoenix","owner":"CU-DBMI-Peds","description":"R, Python, and SQL implementations of the Phoenix Sepsis Criteria","archived":false,"fork":false,"pushed_at":"2025-10-18T00:53:13.000Z","size":11353,"stargazers_count":3,"open_issues_count":2,"forks_count":3,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-10-22T05:50:40.142Z","etag":null,"topics":["pediatric","phoenix","python","r","sepsis","septic-shock","sql"],"latest_commit_sha":null,"homepage":"http://cu-dbmi-peds.github.io/phoenix/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CU-DBMI-Peds.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-02-07T22:56:23.000Z","updated_at":"2025-10-18T00:13:38.000Z","dependencies_parsed_at":"2024-04-08T22:27:54.521Z","dependency_job_id":"b68cb009-832b-4f9a-b8ea-7f399499e0dd","html_url":"https://github.com/CU-DBMI-Peds/phoenix","commit_stats":null,"previous_names":["dewittpe/phoenix","cu-dbmi-peds/phoenix"],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/CU-DBMI-Peds/phoenix","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CU-DBMI-Peds%2Fphoenix","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CU-DBMI-Peds%2Fphoenix/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CU-DBMI-Peds%2Fphoenix/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CU-DBMI-Peds%2Fphoenix/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CU-DBMI-Peds","download_url":"https://codeload.github.com/CU-DBMI-Peds/phoenix/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CU-DBMI-Peds%2Fphoenix/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280389295,"owners_count":26322507,"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","status":"online","status_checked_at":"2025-10-22T02:00:06.515Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["pediatric","phoenix","python","r","sepsis","septic-shock","sql"],"created_at":"2025-10-22T05:50:56.332Z","updated_at":"2025-10-22T05:50:59.951Z","avatar_url":"https://github.com/CU-DBMI-Peds.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\"\n)\n```\n\n# phoenix: Phoenix Sepsis and Phoenix-8 Sepsis Criteria \u003cimg src=\"man/figures/hexsticker.png\" width=\"150px\" align=\"right\" alt = \"Phoenix Hex Sticker Logo\"/\u003e\n\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![R-CMD-check](https://github.com/CU-DBMI-Peds/phoenix/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/CU-DBMI-Peds/phoenix/actions/workflows/R-CMD-check.yaml)\n[![codecov](https://codecov.io/gh/CU-DBMI-Peds/phoenix/graph/badge.svg?token=PKLXJ9SQOD)](https://app.codecov.io/gh/CU-DBMI-Peds/phoenix)\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/phoenix)](https://cran.r-project.org/package=phoenix)\n[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/phoenix)](https://www.r-pkg.org/pkg/phoenix)\n\nImplementation of the Phoenix and Phoenix-8 Sepsis Criteria as\ndescribed in:\n\n* [\"Development and Validation of the Phoenix Criteria for Pediatric Sepsis and Septic Shock\"](doi:10.1001/jama.2024.0196) by Sanchez-Pinto\u0026ast;, Bennett\u0026ast;, DeWitt\u0026ast;\u0026ast;, Russell\u0026ast;\u0026ast; et al. (2024)\n\n  * \u003csmall\u003e \u0026ast; Drs Sanchez-Pinto and Bennett contributed equally; \u0026ast;\u0026ast; Dr DeWitt and Mr Russell contributed equally.\u003c/small\u003e\n\n* [\"International Consensus Criteria for Pediatric Sepsis and Septic Shock\"](doi:10.1001/jama.2024.0179) by Schlapbach, Watson, Sorce, et al. (2024).\n\nThe best overview for this package is the R vignette which you can view locally\nafter installing the R package via\n```r\nvignette(\"phoenix\")\n```\nor you can read it online\n[here](https://cu-dbmi-peds.github.io/phoenix/articles/phoenix.html)\n\nThe Phoenix Criteria have been implemented in\n\n* an R package\n  * [article](https://cu-dbmi-peds.github.io/phoenix/articles/phoenix.html)\n  * [CRAN](https://cran.r-project.org/package=phoenix)\n\n* a Python module\n  * [article](https://cu-dbmi-peds.github.io/phoenix/articles/python.html)\n  * [PyPi](https://pypi.org/project/phoenix-sepsis/)\n\n* example SQL queries\n  * [article](https://cu-dbmi-peds.github.io/phoenix/articles/sql.html)\n\n* Notes for implementing in Electronic Health Records (EHRs)\n  * [article](https://cu-dbmi-peds.github.io/phoenix/articles/ehr_implementation_notes.html)\n\n## Citation\nIf you use this package in your work, please cite the Phoenix criteria by citing\nthe two JAMA papers.  Please cite this code base by citing the application note,\nand if using the R package, cite it explicitly as well.\n\n    Peter E DeWitt, Seth Russell, Margaret N Rebull, L Nelson Sanchez-Pinto, Tellen\n    D Bennett, phoenix: an R package and Python module for calculating the Phoenix\n    pediatric sepsis score and criteria, JAMIA Open, Volume 7, Issue 3, October\n    2024, ooae066, [doi:10.1093/jamiaopen/ooae066](doi:10.1093/jamiaopen/ooae066)\n\nBibtex formatted citations can be retrieved within R via\n```{r, eval = FALSE}\n# Manuscripts\nprint(citation(\"phoenix\"), bibtex = TRUE)\n\n# R package\nprint(citation(\"phoenix\", auto = TRUE), bibtex = TRUE)\n```\nOr in this repo from the file\n[`inst/CITATION`](https://github.com/CU-DBMI-Peds/phoenix/blob/main/inst/CITATION)\n\n\n## R\n\n### Install\n\n#### From CRAN\nInstall the current release from the Comprehensive R Archive Network (CRAN).\nWithin R call:\n```{r, eval = FALSE}\ninstall.packages(\"phoenix\", repos = \"https://cran.rstudio.com\")\n```\n\n#### Developmental\nInstall the development version of `phoenix` directly from github via the\n[`remotes`](https://github.com/r-lib/remotes/) package:\n\n    if (!(\"remotes\" %in% rownames(installed.packages()))) {\n      warning(\"installing remotes from https://cran.rstudio.com\")\n      install.packages(\"remotes\", repo = \"https://cran.rstudio.com\")\n    }\n\n    remotes::install_github(\"cu-dbmi-peds/phoenix\")\n\n*NOTE:* If you are working on a Windows machine you will need to download and\ninstall [`Rtools`](https://cran.r-project.org/bin/windows/Rtools/).\n\n### Examples\n\nDetails on the Phoenix criteria and the use of the R package can be found in the\nmanual for the package, the\n[Get started](https://cu-dbmi-peds.github.io/phoenix/articles/phoenix.html) on\nthe website, or the vignette within R\n```{r eval = FALSE}\nvignette(\"phoenix\")\n```\n\n## Python\n\nA python module is available on PyPi.  You can install it via `pip`\n\n```{python, eval = FALSE}\npip install phoenix-sepsis\n```\n\n\n### Examples\n\nRead the article [The Phoenix Septic Criteria in Python](https://cu-dbmi-peds.github.io/phoenix/articles/python.html)\nfor details and examples of using the python code as is.\n\n## SQL\n\nRead [The Phoenix Sepsis Criteria in SQL](https://cu-dbmi-peds.github.io/phoenix/articles/sql.html)\narticle for details and examples of implementing the scoring rubrics in SQL.\nThese examples are done in SQLite but will be easily translated into other SQL\ndialects.\n\n## Electronic Health Record (EHR)\n\nRead [Phoenix Sepsis EHR Implementation Notes](https://cu-dbmi-peds.github.io/phoenix/articles/ehr_implementation_notes.html)\nfor details about the expected inputs for the scoring in order to assist EHR\nimplementation. The phoenix R package and Python module, along with the example\nSQL code assumes that the data have been prepared as expected and returns scores\naccordingly.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcu-dbmi-peds%2Fphoenix","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcu-dbmi-peds%2Fphoenix","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcu-dbmi-peds%2Fphoenix/lists"}