{"id":22151667,"url":"https://github.com/epiverse-trace/quickfit","last_synced_at":"2026-01-24T04:36:30.681Z","repository":{"id":119521254,"uuid":"588239854","full_name":"epiverse-trace/quickfit","owner":"epiverse-trace","description":"[SUSPENDED] Toolbox of model fitting helper functions","archived":false,"fork":false,"pushed_at":"2024-08-07T14:47:08.000Z","size":4819,"stargazers_count":2,"open_issues_count":8,"forks_count":1,"subscribers_count":4,"default_branch":"main","last_synced_at":"2024-08-08T15:47:09.104Z","etag":null,"topics":["distributions","likelihood","mle","r","r-package"],"latest_commit_sha":null,"homepage":"https://epiverse-trace.github.io/quickfit/","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/epiverse-trace.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"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":"2023-01-12T16:52:52.000Z","updated_at":"2024-08-07T14:45:38.000Z","dependencies_parsed_at":"2024-02-26T14:05:17.728Z","dependency_job_id":null,"html_url":"https://github.com/epiverse-trace/quickfit","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":"epiverse-trace/packagetemplate","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fquickfit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fquickfit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fquickfit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiverse-trace%2Fquickfit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiverse-trace","download_url":"https://codeload.github.com/epiverse-trace/quickfit/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":227652601,"owners_count":17799229,"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":["distributions","likelihood","mle","r","r-package"],"created_at":"2024-12-02T00:35:06.293Z","updated_at":"2026-01-24T04:36:30.653Z","avatar_url":"https://github.com/epiverse-trace.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\u003c!-- The code to render this README is stored in .github/workflows/render-readme.yaml --\u003e\n\u003c!-- Variables marked with double curly braces will be transformed beforehand: --\u003e\n\u003c!-- `packagename` is extracted from the DESCRIPTION file --\u003e\n\u003c!-- `gh_repo` is extracted via a special environment variable in GitHub Actions --\u003e\n\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# _quickfit_: Toolbox of model fitting helper functions \u003cimg src=\"man/figures/logo.svg\" align=\"right\" width=\"120\" /\u003e\n\n\u003c!-- badges: start --\u003e\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![R-CMD-check](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/{{ gh_repo }}/actions/workflows/R-CMD-check.yaml)\n[![Codecov test coverage](https://codecov.io/gh/{{ gh_repo }}/branch/main/graph/badge.svg)](https://app.codecov.io/gh/{{ gh_repo }}?branch=main)\n[![Project Status: Suspended – Initial development has started, but there has not yet been a stable, usable release; work has been stopped for the time being but the author(s) intend on resuming work.](https://www.repostatus.org/badges/latest/suspended.svg)](https://www.repostatus.org/#suspended)\n\u003c!-- badges: end --\u003e\n\n\n`{quickfit}` was intended to be an `R` package to help with simple model fitting tasks in epidemiology and as a central place to store helper functions used in Epiverse-TRACE.\n\nThe development of `{quickfit}` has been **suspended** it is no longer considered necessary to have a dedicated package within Epiverse-TRACE to conduct model fitting, and helper functions will remain in the package they were developed in and shared/copied directly across packages rather than requiring taking on a dependency to import them. Development may resume if the need for a utility package becomes apparent.\n\n`{quickfit}` was developed at the [Centre for the Mathematical Modelling of Infectious Diseases](https://www.lshtm.ac.uk/research/centres/centre-mathematical-modelling-infectious-diseases) at the London School of Hygiene and Tropical Medicine as part of the [Epiverse Initiative](https://data.org/initiatives/epiverse/).\n\n\n## Installation\n\nYou can install the development version of {{ packagename }} from\n[GitHub](https://github.com/) with:\n\n``` r\n# check whether {pak} is installed\nif(!require(\"pak\")) install.packages(\"pak\")\npak::pak(\"epiverse-trace/quickfit\")\n```\n\n## Quick start\n\n**The examples below show the existing functionality; this is not currently planned to be developed further.**\n\nThese examples illustrate some of the current functionalities:\n\n```{r}\nlibrary(quickfit)\n```\n\nGenerate some simulated data, define a likelihood, then estimate MLE, \nor MLE and 95% confidence interval based on profile likelihood:\n\n```{r}\nsim_data \u003c- rnorm(50, 4, 2)\n\n# Define likelihood function\nlog_l \u003c- function(x,a,b) dnorm(x, a, b, log = TRUE)\n\n# Estimate MLE\nestimate_mle(log_l, sim_data, n_param = 2, a_initial = 3, b_initial = 1)\n\n# Estimate 95% CI based on profile likelihood\ncalculate_profile(\n  log_l, \n  data_in = sim_data, \n  n_param = 2, \n  a_initial = 3, \n  b_initial = 1, \n  precision = 0.01\n)\n```\n\nAdditionally, multiple distribution models can be compared (for censored and \nnon-censored data).\n\n```{r}\nmulti_fitdist(\n  data = rlnorm(n = 100, meanlog = 1, sdlog = 1), \n  models = c(\"lnorm\", \"gamma\", \"weibull\"), \n  func = fitdistrplus::fitdist\n)\n```\n\n## Help \n\nTo report a bug please open an [issue](https://github.com/epiverse-trace/quickfit/issues/new/choose); please note that development on `{quickfit}` has been suspended, therefore it is not guaranteed that all issues will be responded to. \n\n### Contributions\n\nContributions are welcome via [pull requests](https://github.com/{{ gh_repo }}/pulls).\n\nDevelopment on `{quickfit}` has been suspended.\n\nHowever, if you think this package could be developed for a specific use case then contributions are very welcome as issues, or on the main [Epiverse Discussion board](https://github.com/orgs/epiverse-trace/discussions).\n\n### Code of Conduct\n\nPlease note that the {{ packagename }} project is released with a \n[Contributor Code of Conduct](https://github.com/epiverse-trace/.github/blob/main/CODE_OF_CONDUCT.md).\nBy contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiverse-trace%2Fquickfit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiverse-trace%2Fquickfit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiverse-trace%2Fquickfit/lists"}