{"id":26902579,"url":"https://github.com/santikka/dosearch","last_synced_at":"2025-04-01T09:44:20.228Z","repository":{"id":118628921,"uuid":"316444904","full_name":"santikka/dosearch","owner":"santikka","description":"dosearch: R Package for Identifying General Causal Queries","archived":false,"fork":false,"pushed_at":"2024-07-16T06:50:23.000Z","size":2740,"stargazers_count":7,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-02-28T20:32:41.717Z","etag":null,"topics":["c-plus-plus","causal-inference","causal-models","causality","causality-algorithms","directed-acyclic-graph","graphs","labeled-graphs","r"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/santikka.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":".github/CONTRIBUTING.md","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":"codemeta.json"}},"created_at":"2020-11-27T08:37:30.000Z","updated_at":"2024-07-16T06:50:28.000Z","dependencies_parsed_at":null,"dependency_job_id":"709561cd-18f9-421b-a68d-ed68c1633a80","html_url":"https://github.com/santikka/dosearch","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/santikka%2Fdosearch","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/santikka%2Fdosearch/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/santikka%2Fdosearch/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/santikka%2Fdosearch/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/santikka","download_url":"https://codeload.github.com/santikka/dosearch/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246385385,"owners_count":20768668,"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":["c-plus-plus","causal-inference","causal-models","causality","causality-algorithms","directed-acyclic-graph","graphs","labeled-graphs","r"],"created_at":"2025-04-01T09:44:19.601Z","updated_at":"2025-04-01T09:44:20.219Z","avatar_url":"https://github.com/santikka.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 setup, include=FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\"\n)\n```\n\n```{r srr-tags, eval = FALSE, echo = FALSE}\n#' @srrstats {G1.0} Primary reference is:\n#'   S. Tikka, A. Hyttinen and J. Karvanen.\n#'   \"Causal effect identification from multiple incomplete data sources:\n#'   a general search-based approach.\" \\emph{Journal of Statistical Software},\n#'   99(5):1--40, 2021.\n#' @srrstats {G1.1} First implementation of an original algorithm.\n#' @srrstats {G1.2} Life Cycle Statement is included in the README.\n```\n\n# dosearch\n\n\u003c!-- badges: start --\u003e\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![R-CMD-check](https://github.com/santikka/dosearch/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/santikka/dosearch/actions/workflows/R-CMD-check.yaml)\n[![Codecov test coverage](https://codecov.io/gh/santikka/dosearch/branch/master/graph/badge.svg)](https://app.codecov.io/gh/santikka/dosearch?branch=master)\n[![CRAN version](https://www.r-pkg.org/badges/version/dosearch)](https://CRAN.R-project.org/package=dosearch)\n\n\u003c!-- badges: end --\u003e\n\nThe `dosearch` [R](https://www.r-project.org/) package facilitates \nidentification of causal effects from arbitrary observational and experimental \nprobability distributions via do-calculus and standard probability \nmanipulations using a search-based algorithm (Tikka et al., 2019, 2021).\nFormulas of identifiable target distributions are returned in character format\nusing LaTeX syntax. The causal graph may additionally include mechanisms \nrelated to: \n\n* Selection bias (Bareinboim and Tian, 2015)\n* Transportability (Bareinboim and Pearl, 2014) \n* Missing data (Mohan et al., 2013)\n* Context-specific independence (Corander et al., 2019)\n  \nSee the package vignette or the references for further information.\n  \n### Citing the package\n\nIf you use the `dosearch` package in a publication, please cite the \ncorresponding paper in the Journal of Statistical Software:\n\nTikka S, Hyttinen A, Karvanen J (2021). “Causal Effect Identification from \nMultiple Incomplete Data Sources: A General Search-Based Approach.” \n*Journal of Statistical Software*, 99(5), 1--40. \n[doi:10.18637/jss.v099.i05](https://doi.org/10.18637/jss.v099.i05).\n\n## Installation\n\nYou can install the latest release version from CRAN:\n```{r, eval = FALSE}\ninstall.packages(\"dosearch\")\n```\n\nAlternatively, you can install the latest development version of `dosearch`:\n```{r, eval = FALSE}\n# install.packages(\"devtools\")\ndevtools::install_github(\"santikka/dosearch\")\n```\n\n## Examples\n\n```{r, echo = FALSE}\nlibrary(dosearch)\n```\n\n```{r, eval = TRUE}\n# back-door formula\ndata \u003c- \"p(x,y,z)\"\nquery \u003c- \"p(y|do(x))\"\ngraph \u003c- \"\n  x -\u003e y\n  z -\u003e x\n  z -\u003e y\n\"\ndosearch(data, query, graph)\n\n# front-door formula\ngraph \u003c- \"\n  x -\u003e z\n  z -\u003e y\n  x \u003c-\u003e y\n\"\ndosearch(data, query, graph)\n\n# the 'napkin' graph\ndata \u003c- \"p(x,y,z,w)\"\ngraph \u003c- \"\n  x -\u003e y\n  z -\u003e x\n  w -\u003e z\n  x \u003c-\u003e w\n  w \u003c-\u003e y\n\"\ndosearch(data, query, graph)\n\n# case-control design\ndata \u003c- \"\n  p(x*,y*,r_x,r_y)\n  p(y)\n\"\ngraph \u003c- \"\n  x -\u003e y\n  y -\u003e r_y\n  r_y -\u003e r_x\n\"\nmd \u003c- \"r_x : x, r_y : y\"\ndosearch(data, query, graph, missing_data = md)\n```\n\n## References\n\n* Tikka S, Hyttinen A, Karvanen J (2021).\n  \"Causal effect identification from multiple incomplete data sources: a general search-based approach.\" \n  *Journal of Statistical Software*, \n  99(5), 1--40.\n  [doi:10.18637/jss.v099.i05](https://doi.org/10.18637/jss.v099.i05)\n* Tikka S, Hyttinen A, Karvanen J (2019). \n  \"Identifying causal effects via context-specific independence relations.\" \n  In *Proceedings of the 33rd Annual Conference on Neural Information Processing Systems*.\n  (https://papers.nips.cc/paper/2019/hash/d88518acbcc3d08d1f18da62f9bb26ec-Abstract.html)\n* Bareinboim E, Tian J (2015).\n  \"Recovering causal effects from selection bias.\" \n  In *Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence*,\n  (http://ftp.cs.ucla.edu/pub/stat_ser/r445.pdf)\n* Bareinboim E, Pearl J (2014).\n  \"Transportability from multiple environments with limited Experiments: completeness Results.\" \n  In *Advances of Neural Information Processing Systems 27*,\n  (http://ftp.cs.ucla.edu/pub/stat_ser/r443.pdf)\n* Mohan K, Pearl J, Tian J (2013).\n  \"Graphical models for inference with missing data.\" \n  In *Advances of Neural Information Processing Systems 26*,\n  (http://ftp.cs.ucla.edu/pub/stat_ser/r410.pdf)\n* Corander J, Hyttinen A, Kontinen J, Pensar J, Väänänen J (2019).\n  \"A logical approach to context-specific independence.\" \n  *Annals of Pure and Applied Logic*,\n  170(9), 975--992. \n  [doi:10.1016/j.apal.2019.04.004](https://doi.org/10.1016/j.apal.2019.04.004)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsantikka%2Fdosearch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsantikka%2Fdosearch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsantikka%2Fdosearch/lists"}