{ "_id": "6a103293acfb0bcc41c97a11", "Package": "rbi", "Version": "1.0.1.9000", "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://sbfnk.r-universe.dev", "Date/Publication": "2026-02-11 16:32:05 UTC", "RemoteUrl": "https://github.com/sbfnk/rbi", "RemoteRef": "HEAD", "RemoteSha": "c00b101069fb10b52b972eaef29b97001d33db87", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-12 08:39:21 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 ", "MD5sum": "6c0eec10dbb902791e6fafb6fc3b1754", "_user": "sbfnk", "_type": "src", "_file": "rbi_1.0.1.9000.tar.gz", "_fileid": "46193d0eb525f1dd1d083055f709a4c0c46b31744d1c985bdbed68d4c60010da", "_filesize": 341044, "_sha256": "46193d0eb525f1dd1d083055f709a4c0c46b31744d1c985bdbed68d4c60010da", "_created": "2026-05-12T08:39:21.000Z", "_published": "2026-05-22T10:40:19.748Z", "_distro": "noble", "_jobs": [ { "job": 77363450587, "time": 144, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6939524292" }, { "job": 77363450759, "time": 134, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6939521518" }, { "job": 77363450782, "time": 146, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6939516358" }, { "job": 77363450635, "time": 187, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6939526800" }, 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Funk", "email": "sebastian.funk@lshtm.ac.uk", "login": "sbfnk", "mastodon": "@sbfnk@fosstodon.org", "bluesky": "@sbfnk.bsky.social", "uuid": 1156307 }, "_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": true, "_usedby": 1, "_updates": [ { "week": "2026-04", "n": 3 }, { "week": "2026-07", "n": 2 } ], "_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": 1156307, "type": "user", "name": "Sebastian Funk", "description": "Professor of Infectious Disease Dynamics at LSHTM. epiforecasts.io" }, "_downloads": { "count": 259, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rbi" }, "_mentions": 2, "_devurl": "https://github.com/sbfnk/rbi", "_searchresults": 380, "_rbuild": "4.6.0", "_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 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