{ "_id": "6a1f3913b401979e73428e80", "Package": "bistablehistory", "Title": "Cumulative History Analysis for Bistable Perception Time Series", "Version": "1.1.4", "Date": "2026-03-02", "Authors@R": "person(given = \"Alexander\",\nfamily = \"Pastukhov\",\nrole = c(\"aut\", \"cre\"),\nemail = \"pastukhov.alexander@gmail.com\",\ncomment = c(ORCID = \"0000-0002-8738-8591\"))", "Description": "Estimates cumulative history for time-series for\ncontinuously viewed bistable perceptual rivalry displays.\nComputes cumulative history via a homogeneous first order\ndifferential process. I.e., it assumes exponential growth/decay\nof the history as a function time and perceptually dominant\nstate, Pastukhov & Braun (2011) .\nSupports Gamma, log normal, and normal distribution families.\nProvides a method to compute history directly and example of\nusing the computation on a custom Stan code.", "License": "GPL (>= 3)", "URL": "https://github.com/alexander-pastukhov/bistablehistory/,\nhttps://alexander-pastukhov.github.io/bistablehistory/", "BugReports": "https://github.com/alexander-pastukhov/bistablehistory/issues/", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Biarch": "true", "SystemRequirements": "GNU make", "Config/pak/sysreqs": "make libicu-dev", "Repository": "https://alexander-pastukhov.r-universe.dev", "Date/Publication": "2026-03-11 11:06:30 UTC", "RemoteUrl": "https://github.com/alexander-pastukhov/bistablehistory", "RemoteRef": "HEAD", "RemoteSha": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-10 08:53:11 UTC", "User": "root" }, "Author": "Alexander Pastukhov [aut, cre] (ORCID:\n)", "Maintainer": "Alexander Pastukhov ", "MD5sum": "62f8c80d3dd19847a607486eac5d128f", "_user": "alexander-pastukhov", "_type": "src", "_file": "bistablehistory_1.1.4.tar.gz", "_fileid": "920395f043e29d9376927cdfe897865bb0be955a54d905ec255652aa2424ff3c", "_filesize": 3593606, "_sha256": "920395f043e29d9376927cdfe897865bb0be955a54d905ec255652aa2424ff3c", "_created": "2026-05-10T08:53:11.000Z", "_published": "2026-06-02T20:12:03.065Z", "_distro": "noble", "_jobs": [ { "job": 79162451338, "time": 303, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "6902493505" }, { "job": 79162451178, "time": 293, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6902492514" }, { "job": 79162451759, "time": 286, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902491894" }, { "job": 79162451453, "time": 267, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902490133" }, { "job": 79162451804, "time": 249, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6902708867" }, { "job": 79162451245, "time": 686, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "6902637885" }, { "job": 79162451342, "time": 343, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6902597107" }, { "job": 79162451337, "time": 453, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6902626486" }, { "job": 79162450086, "time": 354, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902464875" }, { "job": 79162450610, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79162451366, "time": 352, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6902498213" }, { "job": 79162451974, "time": 301, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6902493271" }, { "job": 79162451548, "time": 358, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6902498591" } ], "_buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/alexander-pastukhov/bistablehistory", "_commit": { "id": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "author": "Alexander (Sasha) Pastukhov ", "committer": "Alexander (Sasha) Pastukhov ", "message": "Refactoring due to depricated functions.\n", "time": 1773227190 }, "_maintainer": { "name": "Alexander Pastukhov", "email": "pastukhov.alexander@gmail.com", "login": "alexander-pastukhov", "orcid": "0000-0002-8738-8591", "twitter": "@PastukhovSasha", "uuid": 12910993 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.3.0", "role": "Depends" }, { "package": "loo", "role": "Depends" }, { "package": "rlang", "role": "Depends" }, { "package": "rstantools", "version": ">= 2.1.1", "role": "Depends" }, { "package": "BH", "version": ">= 1.66.0", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.3.3.0", "role": "LinkingTo" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "LinkingTo" }, { "package": "rstan", "version": ">= 2.26.0", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.26.0", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "Imports" }, { "package": "rstan", "version": ">= 2.26.0", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "boot", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "alexander-pastukhov", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-41", "n": 3 }, { "week": "2026-11", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "alexander-pastukhov", "count": 274, "uuid": 12910993 }, { "user": "fernandomayer", "count": 5, "uuid": 650253 }, { "user": "andrjohns", "count": 1, "uuid": 27717896 } ], "_userbio": { "uuid": 12910993, "type": "user", "name": "Alexander (Sasha) Pastukhov" }, "_downloads": { "count": 301, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/bistablehistory" }, "_devurl": "https://github.com/alexander-pastukhov/bistablehistory", "_pkgdown": "https://alexander-pastukhov.github.io/bistablehistory/", "_searchresults": 7, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/bistablehistory.html", "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/alexander-pastukhov/bistablehistory", "_realowner": "alexander-pastukhov", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2021-09-28" }, { "version": "1.1.0", "date": "2022-01-14" }, { "version": "1.1.1", "date": "2022-03-22" }, { "version": "1.1.2", "date": "2023-09-13" }, { "version": "1.1.3", "date": "2025-10-11" }, { "version": "1.1.4", "date": "2026-03-03" } ], "_exports": [ "bayes_R2", "check_fixed_history_parameter", "check_normal_prior", "compute_history", "evaluate_history_init", "evaluate_history_option", "extract_history", "extract_history_parameter", "extract_replicate_term_to_matrix", "extract_term_to_matrix", "fast_history_compute", "fit_cumhist", "fixef", "history_mixed_state", "history_parameter", "history_tau", "historyef", "loo", "predict_history", "predict_samples", "preprocess_data" ], "_datasets": [ { "name": "br", "title": "Binocular rivalry data", "object": "br", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Observer", "Display", "Block", "Time", "State", "Duration" ], "rows": 3769, "table": true, "tojson": true }, { "name": "br_contrast", "title": "Binocular rivalry, variable contrast", "object": "br_contrast", "class": [ "grouped_df", "tbl_df", "tbl", "data.frame" ], "fields": [ "Observer", "Block", "Contrast", "State", "Time", "Duration" ], "rows": 4616, "table": true, "tojson": true }, { "name": "br_single_subject", "title": "Single experimental session for binocular rivalry stimulus", "object": "br_single_subject", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Observer", "Display", "Block", "Time", "State", "Duration" ], "rows": 642, "table": true, "tojson": true }, { "name": "br_singleblock", "title": "Single run for binocular rivalry stimulus", "object": "br_singleblock", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Observer", "Group", "Block", "Time", "State", "Duration" ], "rows": 76, "table": true, "tojson": true }, { "name": "kde", "title": "Kinetic-depth effect data", "object": "kde", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Observer", "Display", "Block", "Time", "State", "Duration" ], "rows": 38698, "table": true, "tojson": true }, { "name": "kde_two_observers", "title": "Multirun data for two participants, kinetic-depth effect display", "object": "kde_two_observers", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Observer", "Block", "State", "Time", "Duration" ], "rows": 1186, "table": true, "tojson": true }, { "name": "nc", "title": "Necker cube data", "object": "nc", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "Observer", "Display", "Block", "Time", "State", "Duration" ], "rows": 3464, "table": true, "tojson": true } ], "_help": [ { "page": "bistablehistory-package", "title": "Cumulative History Analysis for Bistable Perception Time Series", "topics": [ "bistablehistory-package", "bistablehistory" ] }, { "page": "bayes_R2", "title": "Computes R-squared using Bayesian R-squared approach.", "topics": [ "bayes_R2", "bayes_R2.cumhist" ] }, { "page": "br", "title": "Binocular rivalry data", "topics": [ "br" ] }, { "page": "br_contrast", "title": "Binocular rivalry, variable contrast", "topics": [ "br_contrast" ] }, { "page": "br_single_subject", "title": "Single experimental session for binocular rivalry stimulus", "topics": [ "br_single_subject" ] }, { "page": "br_singleblock", "title": "Single run for binocular rivalry stimulus", "topics": [ "br_singleblock" ] }, { "page": "coef.cumhist", "title": "Extract Model Coefficients", "topics": [ "coef.cumhist" ] }, { "page": "compute_history", "title": "Computes cumulative history for the time-series", "topics": [ "compute_history" ] }, { "page": "cumhist-class", "title": "Class 'cumhist'.", "topics": [ "cumhist", "cumhist-class" ] }, { "page": "extract_history", "title": "Computes history for a fitted model", "topics": [ "extract_history" ] }, { "page": "extract_history_parameter", "title": "Extracts a history parameter as a matrix", "topics": [ "extract_history_parameter" ] }, { "page": "extract_replicate_term_to_matrix", "title": "Extract a term and replicates it randomN times for each linear model", "topics": [ "extract_replicate_term_to_matrix" ] }, { "page": "extract_term_to_matrix", "title": "Extracts a term with one column per fixed or random-level into a matrix", "topics": [ "extract_term_to_matrix" ] }, { "page": "fast_history_compute", "title": "Computes cumulative history", "topics": [ "fast_history_compute" ] }, { "page": "fit_cumhist", "title": "Fits cumulative history for bistable perceptual rivalry displays.", "topics": [ "fit_cumhist" ] }, { "page": "fixef", "title": "Extract the fixed-effects estimates", "topics": [ "fixef" ] }, { "page": "history_mixed_state", "title": "Extract values of used or fitted history parameter mixed_state", "topics": [ "history_mixed_state" ] }, { "page": "history_parameter", "title": "Extract values of used or fitted history parameter", "topics": [ "history_parameter" ] }, { "page": "history_tau", "title": "Extract values of used or fitted history parameter tau", "topics": [ "history_tau" ] }, { "page": "historyef", "title": "Extract the history-effects estimates", "topics": [ "historyef" ] }, { "page": "kde", "title": "Kinetic-depth effect data", "topics": [ "kde" ] }, { "page": "kde_two_observers", "title": "Multirun data for two participants, kinetic-depth effect display", "topics": [ "kde_two_observers" ] }, { "page": "loo.cumhist", "title": "Computes an efficient approximate leave-one-out cross-validation via loo library. It can be used for a model comparison via loo::loo_compare() function.", "topics": [ "loo.cumhist" ] }, { "page": "nc", "title": "Necker cube data", "topics": [ "nc" ] }, { "page": "predict_history", "title": "Computes predicted cumulative history using posterior predictive distribution.", "topics": [ "predict_history" ] }, { "page": "predict_samples", "title": "Computes prediction for a each sample.", "topics": [ "predict_samples" ] }, { "page": "predict.cumhist", "title": "Computes predicted dominance phase durations using posterior predictive distribution.", "topics": [ "predict.cumhist" ] }, { "page": "preprocess_data", "title": "Preprocesses time-series data for fitting", "topics": [ "preprocess_data" ] }, { "page": "print.cumhist", "title": "Prints out cumhist object", "topics": [ "print.cumhist" ] }, { "page": "summary.cumhist", "title": "Summary for a cumhist object", "topics": [ "summary.cumhist" ] }, { "page": "waic.cumhist", "title": "Computes widely applicable information criterion (WAIC).", "topics": [ "waic.cumhist" ] } ], "_readme": "https://github.com/alexander-pastukhov/bistablehistory/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "boot", "callr", "checkmate", "cli", "cpp11", "desc", "distributional", "dplyr", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lifecycle", "loo", "magrittr", "matrixStats", "numDeriv", "pillar", "pkgbuild", "pkgconfig", "posterior", "processx", "ps", "purrr", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "rstantools", "S7", "scales", "StanHeaders", "stringi", "stringr", "tensorA", "tibble", "tidyr", "tidyselect", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "cumulative-history.Rmd", "filename": "cumulative-history.html", "title": "Cumulative History", "author": "Alexander (Sasha) Pastukhov", "engine": "knitr::rmarkdown", "headings": [ "References" ], "created": "2021-07-25 09:40:02", "modified": "2026-03-11 11:06:30", "commits": 8 }, { "source": "usage-examples.Rmd", "filename": "usage-examples.html", "title": "Usage examples", "engine": "knitr::rmarkdown", "headings": [ "Minimal example", "Passing Stan control parameters", "Run", "Experimental session", "Random effect", "Fixed effects", "Cumulative history parameters", "Distribution family", "Gamma", "Log-normal", "Normal", "Model comparison", "Predicted values", "Computing and using cumulative history", "References" ], "created": "2021-09-23 14:22:06", "modified": "2026-03-11 11:06:30", "commits": 6 }, { "source": "writing-stan-code.Rmd", "filename": "writing-stan-code.html", "title": "Writing Stan code", "engine": "knitr::rmarkdown", "headings": [ "Stan model", "Data preparation", "Using the model" ], "created": "2021-09-23 14:22:19", "modified": "2022-01-07 18:54:35", "commits": 3 } ], "_score": 4.778151250383644, "_indexed": true, "_nocasepkg": "bistablehistory", "_universes": [ "alexander-pastukhov" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.1.4", "date": "2026-05-10T08:56:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "85b6e0e0d3246942df0604be879adddbf4e3132880d6629e8c7403a91e4f6f96", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.7.0", "os": "linux", "version": "1.1.4", "date": "2026-05-10T08:56:57.000Z", "distro": "noble", "arch": "x86_64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "103e9fc35c69992963d84523f4ac1de1a1dabfec089a7204a0410c190dac7d68", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.6.0", "os": "linux", "version": "1.1.4", "date": "2026-05-10T08:56:51.000Z", "distro": "noble", "arch": "aarch64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "afd61d2a957309692237423425883696ecbf9ab620cf8f7ee5c3c23f7c833ac6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.6.0", "os": "linux", "version": "1.1.4", "date": "2026-05-10T08:56:41.000Z", "distro": "noble", "arch": "x86_64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "3fdf73e821760d90fd1bea09cb30425c482f8241c1adbc14c81d54e16270fe01", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.5.3", "os": "mac", "version": "1.1.4", "date": "2026-05-10T09:35:00.000Z", "arch": "aarch64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "0a11dc6592a6881f74b1b18200abeb36a5e995cfbc34c6cd26dbbbc96fd20e4a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.5.3", "os": "mac", "version": "1.1.4", "date": "2026-05-10T09:19:39.000Z", "arch": "x86_64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "5c532c68ef502c4470c7c77113cd124482529566d550e5c4d497a4143de0bca7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.6.0", "os": "mac", "version": "1.1.4", "date": "2026-05-10T09:15:11.000Z", "arch": "aarch64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "34e8a6a573247e2c342bf37ae7ee0789abad950f24b0ddb8aab3ecbb71362e2d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.6.0", "os": "mac", "version": "1.1.4", "date": "2026-05-10T09:19:03.000Z", "arch": "x86_64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "e37b30ce2a9ace8f46a1f54fc972993b20a148be859e2621d36dc9b1594635e9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.7.0", "os": "win", "version": "1.1.4", "date": "2026-05-10T08:56:23.000Z", "arch": "x86_64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "b9750e62beb385ddb9253995befc5a778c203e59c6408611431bff6b9584c39d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.5.3", "os": "win", "version": "1.1.4", "date": "2026-05-10T08:55:54.000Z", "arch": "x86_64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "ceb63d89dc75f2dbca53bbd74110d3d19ce2d1b97c1e5084edb73ebdf8df731d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" }, { "r": "4.6.0", "os": "win", "version": "1.1.4", "date": "2026-05-10T08:56:43.000Z", "arch": "x86_64", "commit": "39e6223fed10b3fb32f06e7288aaec28163a8c48", "fileid": "632f41d695ea5d3046d120e5305bb35d769f7f093d93a39fe5dca34c72d7a56a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/alexander-pastukhov/actions/runs/25624430169" } ] }