{"id":23466204,"url":"https://github.com/kklot/endtb","last_synced_at":"2025-04-12T17:29:19.165Z","repository":{"id":153377086,"uuid":"626605938","full_name":"kklot/EndTB","owner":"kklot","description":"TB models in TMB","archived":false,"fork":false,"pushed_at":"2023-06-28T21:26:53.000Z","size":409,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-16T03:29:23.550Z","etag":null,"topics":["epidemic","modelling","simulation","tb","tmb","tuberculosis"],"latest_commit_sha":null,"homepage":"","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/kklot.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}},"created_at":"2023-04-11T20:03:25.000Z","updated_at":"2023-04-11T21:10:44.000Z","dependencies_parsed_at":"2023-07-10T06:47:17.039Z","dependency_job_id":null,"html_url":"https://github.com/kklot/EndTB","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kklot%2FEndTB","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kklot%2FEndTB/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kklot%2FEndTB/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kklot%2FEndTB/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kklot","download_url":"https://codeload.github.com/kklot/EndTB/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248604573,"owners_count":21131996,"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":["epidemic","modelling","simulation","tb","tmb","tuberculosis"],"created_at":"2024-12-24T11:55:22.207Z","updated_at":"2025-04-12T17:29:19.144Z","avatar_url":"https://github.com/kklot.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n\u003cimg src=\"man/figures/logo.png\" align=\"right\" /\u003e\n\n# EndTB \n\n\u003c!-- badges: start --\u003e\n[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)\n\u003c!-- badges: end --\u003e\n\nThe goal of EndTB is to provide a convinient set of established TB models for\nthe simulation, estimation, and projection of Tuberculosis Epidemic.\n\nMoreover\n\n- the models are implemented in C++ which provides fast simulations.\n- the models are called within the [TMB\n  framework](https://kaskr.github.io/adcomp/Introduction.html), allowing advanced\n  and fast parameter estimation with emprical Bayes approach.\n\n## Installation\n\nYou can install the development version of EndTB like so:\n\n```{r eval=FALSE}\nremotes::install_github('kklot/EndTB')\n```\n\nDocuments of the package and functions can be view as normal R's documentation\nor online at [EndTB.](https://kklot.github.io/EndTB)\n\n## Example\n\nThis is a basic example which shows you how to start a model:\n\n```{r}\nlibrary(EndTB)\nTB \u003c- TBM$new(c(sigma = 2))\n```\n\nwhere the default parameters $\\sigma$ was replaced with 2.\n\nSteady-state of the model without treatments and no population growth\nfor that set of parameters can be ploted with.\n\n```{r plot}\nTB$plot()\n```\n\nList of states to be plotted can be supplied into the arguments of the `plot`\nfunction above. \n\nFurther details can be read in **References** in the top navigation. For\nexample, [the\ndocumentation of `plot`](https://kklot.github.io/EndTB/reference/TBM.html#method-plot-). \n\nCheck out model's parameters and states for Moldova model.\n\n```{r para}\nEndTB:::states_moldova\nEndTB:::pars_moldova\n```\n\n## TODO\n\n- [x] 1st revision of the WHO's model (and currently the only)\n- [ ] Revise model to Argentina data\n- [ ] Add fitting example\n- [ ] Add other model variations","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkklot%2Fendtb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkklot%2Fendtb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkklot%2Fendtb/lists"}