{ "_id": "6a54859dff0138dec5d64a85", "Package": "rbi", "Version": "1.0.1", "Title": "Interface to 'LibBi'", "Authors@R": "c(\nperson(\"Pierre E.\", \"Jacob\",\nemail = \"pierre.jacob.work@gmail.com\", role = \"aut\"),\nperson(\"Anthony\", \"Lee\",\nemail = \"awllee@gmail.com\", role = \"ctb\"),\nperson(\"Lawrence M.\", \"Murray\",\nemail = \"lawrence.murray@csiro.au\", role = \"ctb\"),\nperson(\"Sebastian\", \"Funk\",\nemail = \"sebastian.funk@lshtm.ac.uk\", role = c(\"aut\", \"cre\")),\nperson(\"Sam\", \"Abbott\",\nemail = \"contact@samabbott.co.uk\", role = c(\"ctb\"))\n)", "Description": "Provides a complete interface to 'LibBi', a library for\nBayesian inference (see and Murray, 2015\n for more information). This\nincludes functions for manipulating 'LibBi' models, for reading\nand writing 'LibBi' input/output files, for converting 'LibBi'\noutput to provide traces for use with the coda package, and for\nrunning 'LibBi' to conduct inference.", "License": "GPL-3", "URL": "https://github.com/sbfnk/rbi", "BugReports": "https://github.com/sbfnk/rbi/issues", "SystemRequirements": "LibBi (>= 1.4.2)", "LazyLoad": "no", "RoxygenNote": "7.3.3", "Language": "en-GB", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libnetcdf-dev", "Repository": "https://epiforecasts.r-universe.dev", "Date/Publication": "2026-02-11 16:29:43 UTC", "RemoteUrl": "https://github.com/sbfnk/RBi", "RemoteRef": "v1.0.1", "RemoteSha": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-13 06:24:56 UTC", "User": "root" }, "Author": "Pierre E. Jacob [aut],\nAnthony Lee [ctb],\nLawrence M. Murray [ctb],\nSebastian Funk [aut, cre],\nSam Abbott [ctb]", "Maintainer": "Sebastian Funk ", "_user": "epiforecasts", "_type": "src", "_file": "rbi_1.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/27670d77c9b3371c020d55834e508b86133c6c60f2c0492b29c6270952a89adf", "_filesize": 341145, "_sha256": "27670d77c9b3371c020d55834e508b86133c6c60f2c0492b29c6270952a89adf", "_expires": "2026-10-21T06:28:43.000Z", "_created": "2026-07-13T06:24:56.000Z", "_published": "2026-07-13T06:28:45.493Z", "_jobs": [ { "job": 86748820420, "time": 187, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8270829541" }, { "job": 86748820434, "time": 141, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8270817027" }, { "job": 86748820441, "time": 108, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8270806952" }, { "job": 86748820490, "time": 88, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8270801559" }, { "job": 86748295196, "time": 211, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8270775483" }, { "job": 86748820427, "time": 137, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8270815386" }, { "job": 86748820470, "time": 89, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8270801744" }, { "job": 86748820493, "time": 97, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8270804316" }, { "job": 86748820449, "time": 90, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8270802087" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546", "_status": "success", "_upstream": "https://github.com/sbfnk/RBi", "_commit": { "id": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "author": "Sebastian Funk ", "committer": "GitHub ", "message": "Release rbi 1.0.1 (#58)\n\nCo-authored-by: sbfnk-bot <242615673+sbfnk-bot@users.noreply.github.com>\n", "time": 1770827383 }, "_maintainer": { "name": "Sebastian Funk", "email": "sebastian.funk@lshtm.ac.uk", "login": "sbfnk", "mastodon": "@sbfnk@fosstodon.org", "bluesky": "@sbfnk.bsky.social", "description": "Professor of Infectious Disease Dynamics at LSHTM. epiforecasts.io", "uuid": 1156307 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "data.table", "role": "Imports" }, { "package": "ncdf4", "role": "Imports" }, { "package": "processx", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "coda", "role": "Suggests" }, { "package": "covr", "version": ">= 3.2.0", "role": "Suggests" }, { "package": "stringi", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "sbfnk", "_selfowned": false, "_usedby": 1, "_updates": [ { "week": "2026-04", "n": 3 }, { "week": "2026-07", "n": 1 } ], "_tags": [ { "name": "v1.0.1", "date": "2026-02-11" } ], "_stars": 25, "_contributors": [ { "user": "sbfnk", "count": 1155, "uuid": 1156307 }, { "user": "pierrejacob", "count": 24, "uuid": 4506645 }, { "user": "bisaloo", "count": 4, "uuid": 10783929 }, { "user": "blackedder", "count": 2, "uuid": 845741 } ], "_userbio": { "uuid": 54675094, "type": "organization", "name": "Epiforecasts", "followers": 76, "description": "Researchers at the London School of Hygiene & Tropical Medicine doing research to forecast infectious diseases and perform real-time analyses." }, "_downloads": { "count": 304, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rbi" }, "_mentions": 2, "_devurl": "https://github.com/sbfnk/rbi", "_searchresults": 432, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/rbi.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/sbfnk/rbi", "_realowner": "sbfnk", "_cranurl": true, "_releases": [ { "version": "0.4.1", "date": "2016-10-18" }, { "version": "0.5.0", "date": "2016-11-18" }, { "version": "0.6.0", "date": "2016-12-23" }, { "version": "0.7.0", "date": "2017-02-06" }, { "version": "0.8.0", "date": "2017-08-14" }, { "version": "0.9.0", "date": "2018-03-06" }, { "version": "0.9.1", "date": "2018-05-14" }, { "version": "0.10.0", "date": "2018-12-11" }, { "version": "0.10.1", "date": "2019-01-08" }, { "version": "0.10.2", "date": "2019-07-10" }, { "version": "0.10.3", "date": "2020-04-17" }, { "version": "0.10.4", "date": "2021-11-08" }, { "version": "1.0.0", "date": "2023-08-15" }, { "version": "1.0.1", "date": "2026-02-16" } ], "_exports": [ "add_block", "attach_data", "bi_contents", "bi_file_summary", "bi_generate_dataset", "bi_model", "bi_read", "bi_write", "enable_outputs", "extract_sample", "filter", "fix", "flatten", "generate_dataset", "get_block", "get_const", "get_dims", "get_name", "get_traces", "insert_lines", "installed_libbi_version", "join", "libbi", "locate_libbi", "optimise", "predict", "print_log", "read_libbi", "remove_lines", "replace_all", "rewrite", "run", "sample", "sample_obs", "save_libbi", "set_name", "simulate", "update", "var_names", "write_model" ], "_help": [ { "page": "add_block", "title": "Add a block to a LibBi model", "topics": [ "add_block", "add_block.bi_model" ] }, { "page": "attach_data", "title": "Attach a new file or data set to a 'libbi' object", "topics": [ "attach_data", "attach_data.libbi" ] }, { "page": "bi_contents", "title": "Bi contents", "topics": [ "bi_contents" ] }, { "page": "bi_file_summary", "title": "NetCDF File Summary", "topics": [ "bi_file_summary" ] }, { "page": "bi_generate_dataset", "title": "Bi Generate Dataset", "topics": [ "bi_generate_dataset" ] }, { "page": "bi_model", "title": "Bi Model", "topics": [ "bi_model" ] }, { "page": "bi_read", "title": "Bi Read", "topics": [ "bi_read" ] }, { "page": "bi_write", "title": "Create (e.g., init or observation) files for LibBi", "topics": [ "bi_write" ] }, { "page": "enable_outputs", "title": "Enable outputting variables in a 'bi_model'", "topics": [ "enable_outputs" ] }, { "page": "Equals.bi_model", "title": "Check if two models are equal", "topics": [ "==.bi_model", "Equals.bi_model", "`==.bi_model`" ] }, { "page": "Extract_assign.bi_model", "title": "Subset and replace model lines", "topics": [ "Extract_assign.bi_model", "[<-.bi_model", "`[<-.bi_model`" ] }, { "page": "extract_sample", "title": "Extract a sample from a 'LibBi' run.", "topics": [ "extract_sample" ] }, { "page": "Extract.bi_model", "title": "Subset model lines", "topics": [ "Extract.bi_model", "[.bi_model", "`[.bi_model`" ] }, { "page": "filter", "title": "Using the LibBi wrapper to filter", "topics": [ "filter", "filter.bi_model", "filter.libbi" ] }, { "page": "fix", "title": "Fix noise term, state or parameter of a libbi model", "topics": [ "fix", "fix.bi_model" ] }, { "page": "flatten", "title": "Flatten list of data frames This function takes a list of data frames (such as, for example, returned by 'bi_read') and converts it to a flat data frame", "topics": [ "flatten" ] }, { "page": "generate_dataset", "title": "Generate Dataset", "topics": [ "generate_dataset" ] }, { "page": "get_block", "title": "Get the contents of a block in a LibBi model", "topics": [ "get_block", "get_block.bi_model" ] }, { "page": "get_const", "title": "Get constants in a LibBi model", "topics": [ "get_const" ] }, { "page": "get_dims", "title": "Get dimensions in a LibBi model", "topics": [ "get_dims" ] }, { "page": "get_name", "title": "Get the name of a bi model", "topics": [ "get_name", "get_name.bi_model" ] }, { "page": "get_traces", "title": "Get the parameter traces", "topics": [ "get_traces" ] }, { "page": "insert_lines", "title": "Insert lines in a LibBi model", "topics": [ "insert_lines", "insert_lines.bi_model" ] }, { "page": "join", "title": "Join multiple 'libbi' objects", "topics": [ "join", "join.libbi" ] }, { "page": "libbi", "title": "LibBi Wrapper", "topics": [ "libbi" ] }, { "page": "logLik", "title": "Using the LibBi wrapper to logLik", "topics": [ "logLik", "logLik.libbi" ] }, { "page": "optimise", "title": "Using the LibBi wrapper to optimise", "topics": [ "optimise", "optimise.bi_model", "optimise.libbi" ] }, { "page": "predict", "title": "Using the LibBi wrapper to predict", "topics": [ "predict", "predict.libbi" ] }, { "page": "print_log", "title": "Print the log file a 'libbi' object", "topics": [ "print_log" ] }, { "page": "read_libbi", "title": "Read results of a 'LibBi' run from an RDS file or from a folder. This completely reconstructs the saved 'LibBi' object", "topics": [ "read_libbi" ] }, { "page": "remove_lines", "title": "Remove line(s) and/or block(s) in a libbi model", "topics": [ "remove_lines", "remove_lines.bi_model" ] }, { "page": "remove_vars", "title": "Remove variables", "topics": [ "remove_vars" ] }, { "page": "replace_all", "title": "Replace all instances of a string with another in a model", "topics": [ "replace_all", "replace_all.bi_model" ] }, { "page": "rewrite", "title": "Using the LibBi wrapper to rewrite", "topics": [ "rewrite", "rewrite.bi_model", "rewrite.libbi" ] }, { "page": "run", "title": "Using the LibBi wrapper to launch LibBi", "topics": [ "run", "run.libbi" ] }, { "page": "sample", "title": "Using the LibBi wrapper to sample", "topics": [ "sample", "sample.bi_model", "sample.libbi" ] }, { "page": "sample_obs", "title": "Sample observations from a LibBi model that has been run", "topics": [ "sample_obs" ] }, { "page": "save_libbi", "title": "Write results of a 'LibBi' run to an RDS file", "topics": [ "save_libbi", "save_libbi.libbi" ] }, { "page": "set_name", "title": "Set the name of a bi model", "topics": [ "set_name", "set_name.bi_model" ] }, { "page": "simulate", "title": "Using the LibBi wrapper to simulate", "topics": [ "simulate", "simulate.bi_model", "simulate.libbi" ] }, { "page": "summary", "title": "Print summary information about a 'libbi' object", "topics": [ "summary", "summary.libbi" ] }, { "page": "Unequals.bi_model", "title": "Check if two models are unequal", "topics": [ "!=.bi_model", "Unequals.bi_model", "`!=.bi_model`" ] }, { "page": "update", "title": "Update a libbi object", "topics": [ "update", "update.libbi" ] }, { "page": "var_names", "title": "Get variable names in a LibBi model", "topics": [ "var_names" ] }, { "page": "write_model", "title": "Writes a bi model to a file.", "topics": [ "write_model", "write_model.bi_model", "write_model.libbi" ] } ], "_readme": "https://github.com/sbfnk/RBi/raw/v1.0.1/README.md", "_rundeps": [ "cli", "data.table", "glue", "lifecycle", "magrittr", "ncdf4", "plyr", "processx", "ps", "R6", "Rcpp", "reshape2", "rlang", "stringi", "stringr", "vctrs" ], "_vignettes": [ { "source": "idd_models.Rmd", "filename": "idd_models.html", "title": "Collection of SIR models for LibBi", "author": "Sebastian Funk", "engine": "knitr::rmarkdown", "headings": [ "Deterministic SIR model, observations of prevalence", "Deterministic SIR model, observations of incidence", "Stochastic SIR model (SDE), observations of incidence", "Stochastic SIR model (jump), observations of incidence", "Example observation data frame" ], "created": "2023-07-11 09:39:48", "modified": "2023-07-12 21:11:57", "commits": 2 }, { "source": "rbi.Rmd", "filename": "rbi.html", "title": "Introduction to rbi", "author": "Sebastian Funk", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Loading the package", "Getting started", "The bi_model class", "Generating a dataset", "The libbi class", "Fitting a model to data using PMCMC", "Analysing an MCMC run", "Predictions", "Sample observations", "Filtering", "Plotting", "Saving and loading libbi objects", "Creating libbi objects from previous runs", "Debugging", "Related packages", "References" ], "created": "2023-07-26 13:09:42", "modified": "2026-02-11 16:29:43", "commits": 2 } ], "_score": 8.589726256254238, "_indexed": false, "_nocasepkg": "rbi", "_universes": [ "epiforecasts" ], "_indexurl": "https://sbfnk.r-universe.dev/rbi", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-07-13T06:28:04.000Z", "distro": "resolute", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/a374a595110510e6aad1dbd46d17eef8f08c1ac9974fec81e30147f2a33c4404", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" }, { "r": "4.6.1", "os": "linux", "version": "1.0.1", "date": "2026-07-13T06:27:20.000Z", "distro": "resolute", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/892d727759ebac736d281daceb90dc9ce979974678f8092396b76488a5c072b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-07-13T06:26:45.000Z", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/5929eb9eb4d72a6563403985f8a12c51267574db6d6a8adb4fea0902e80b43a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" }, { "r": "4.6.1", "os": "mac", "version": "1.0.1", "date": "2026-07-13T06:26:33.000Z", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/35d53880411cd6f64ea444dd39d573ecd2f11f76d167f8695dc218cd745603f6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-07-13T06:27:37.000Z", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/e6acd745c0d4d0b9e4895318eb45b65ac20b38e9aaad6ddb32d4e604655ebe0d", "status": "success", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-07-13T06:26:16.000Z", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/c7faea2ba2c33ca157a16792e71040ebf385199b3a9883325bf7feeb661ca089", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-07-13T06:26:27.000Z", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/885cc7ff4692214b1d8d18b4f7100feaf6a4bef4b6e9d9efe73594cc8aaa360d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" }, { "r": "4.6.1", "os": "win", "version": "1.0.1", "date": "2026-07-13T06:26:25.000Z", "commit": "01695ad82bbf80e9f1d93aa543eb6f683ee499ee", "fileid": "https://r2.ropensci.org/824d349e75d2f54e897dca068f684e983eb376ce51896936fd5d4f0c9fa95b85", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/29228758546" } ] }