{ "_id": "6a4794932f27a93436c0db28", "Package": "panelPomp", "Type": "Package", "Title": "Inference for Panel Partially Observed Markov Processes", "Version": "1.7.0.1", "Authors@R": "c(person(given=\"Carles\",family=\"Breto\",role=\"aut\",email=\"carles.breto@uv.es\",comment=c(ORCID=\"0000-0003-4695-4902\")),\nperson(given=c(\"Edward\",\"L.\"),family=\"Ionides\",role=\"aut\",comment=c(ORCID=\"0000-0002-4190-0174\")),\nperson(given=c(\"Aaron\",\"A.\"),family=\"King\",role=\"aut\",comment=c(ORCID=\"0000-0001-6159-3207\")),\nperson(given=\"Jesse\",family=\"Wheeler\",role=c(\"aut\",\"cre\"),email=\"jeswheel@umich.edu\",comment=c(ORCID=\"0000-0003-3941-3884\")),\nperson(given=\"Aaron\",family=\"Abkemeier\",role=c(\"ctb\"),email=\"aaronabk@umich.edu\"))", "Description": "Data analysis based on panel partially-observed Markov\nprocess (PanelPOMP) models. To implement such models, simulate\nthem and fit them to panel data, 'panelPomp' extends some of\nthe facilities provided for time series data by the 'pomp'\npackage. Implemented methods include filtering (panel particle\nfiltering) and maximum likelihood estimation (Panel Iterated\nFiltering) as proposed in Breto, Ionides and King (2020) \"Panel\nData Analysis via Mechanistic Models\"\n.", "License": "GPL-3", "Encoding": "UTF-8", "Collate": "'panelPomp-package.R' 'aaa.R' 'contacts.R' 'generics.R'\n'get_col_row.R' 'panel_loglik.R' 'panel_logmeanexp.R'\n'panelPomp.R' 'panelPomp_methods.R' 'params.R' 'pfilter.R'\n'pfilter_methods.R' 'mif2.R' 'mif2_methods.R' 'panelGompertz.R'\n'panelGompertzLikelihood.R' 'panelMeasles.R'\n'panelRandomWalk.R' 'panel_designs.R' 'plot.R' 'simulate.R'\n'twentycities.R' 'uk_measles.R'", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "LazyData": "true", "Config/roxygen2/version": "8.0.0", "Repository": "https://jeswheel.r-universe.dev", "Date/Publication": "2026-07-02 21:52:42 UTC", "RemoteUrl": "https://github.com/jeswheel/panelpomp", "RemoteRef": "HEAD", "RemoteSha": "ff296716484e3197a7f135ad47c883923c8dd7fd", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-07-03 00:03:37 UTC", "User": "root" }, "Author": "Carles Breto [aut] (ORCID: ),\nEdward L. Ionides [aut] (ORCID:\n),\nAaron A. King [aut] (ORCID: ),\nJesse Wheeler [aut, cre] (ORCID:\n),\nAaron Abkemeier [ctb]", "Maintainer": "Jesse Wheeler ", "_user": "jeswheel", "_type": "src", "_file": "panelPomp_1.7.0.1.tar.gz", "_fileid": "https://r2.ropensci.org/ed073d4a451b4595a9646fe4c824eda4de4ff367fb114f5eb18d3d4e0ac763b5", "_filesize": 570813, "_sha256": "ed073d4a451b4595a9646fe4c824eda4de4ff367fb114f5eb18d3d4e0ac763b5", "_expires": "2026-10-11T10:53:06.000Z", "_created": "2026-07-03T00:03:37.000Z", "_published": "2026-07-03T10:53:07.341Z", "_jobs": [ { "job": 84984621281, "time": 186, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "8054633178" }, { "job": 84984620578, "time": 161, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8054627111" }, { "job": 84984620791, "time": 193, "config": "linux-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8054634516" }, { "job": 84984620864, "time": 178, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8054630403" }, { "job": 84984620960, "time": 115, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8054617361" }, { "job": 84984620965, "time": 279, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "8054654076" }, { "job": 84984620689, "time": 150, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8054624549" }, { "job": 84984621142, "time": 275, "config": "macos-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8054653103" }, { "job": 84984620551, "time": 161, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8054592219" }, { "job": 84984620904, "time": 102, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8054614667" }, { "job": 84984620617, "time": 180, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8054630803" }, { "job": 84984620850, "time": 192, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8054633721" }, { "job": 84984620896, "time": 213, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8054639012" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134", "_status": "success", "_upstream": "https://github.com/jeswheel/panelpomp", "_commit": { "id": "ff296716484e3197a7f135ad47c883923c8dd7fd", "author": "Jesse Wheeler ", "committer": "GitHub ", "message": "Fix indentation for push to panelPomp-org page step", "time": 1783029162 }, "_maintainer": { "name": "Jesse Wheeler", "email": "jeswheel@umich.edu", "login": "jeswheel", "description": "Assistant Professor, Department of Mathematics and Statistics, Utah State University, Logan, UT", "uuid": 70770493, "orcid": "0000-0003-3941-3884" }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "pomp", "version": ">= 4.5.2", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "bookdown", "role": "Suggests" } ], "_owner": "jeswheel", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-27", "n": 3 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "cbreto", "count": 261, "uuid": 14112732 }, { "user": "jeswheel", "count": 102, "uuid": 70770493 }, { "user": "kingaa", "count": 58, "uuid": 1863307 }, { "user": "ionides", "count": 20, "uuid": 5505743 }, { "user": "ajabkemeier", "count": 1, "uuid": 52518359 } ], "_userbio": { "uuid": 70770493, "type": "user", "name": "Jesse Wheeler", "followers": 8, "description": "Assistant Professor, Department of Mathematics and Statistics, Utah State University, Logan, UT" }, "_downloads": { "count": 307, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/panelPomp" }, "_devurl": "https://github.com/jeswheel/panelpomp", "_searchresults": 255, "_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/panelPomp.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jeswheel/panelpomp", "_realowner": "jeswheel", "_cranurl": true, "_releases": [ { "version": "1.1", "date": "2023-03-29" }, { "version": "1.4", "date": "2024-09-12" }, { "version": "1.5.0.0", "date": "2024-12-08" }, { "version": "1.6.0.0", "date": "2025-04-03" }, { "version": "1.7.0.0", "date": "2025-05-09" } ], "_exports": [ "coef", "coef<-", "contacts", "get_col", "get_row", "logLik", "mif2", "panel_logmeanexp", "panelGompertz", "panelGompertzLikelihood", "panelMeasles", "panelPomp", "panelRandomWalk", "pfilter", "plot", "print", "runif_panel_design", "shared", "shared<-", "show", "simulate", "specific", "specific<-", "toMatrixPparams", "toParamList", "toParamVec", "traces", "unit_objects", "unitLogLik", "window", "wQuotes" ], "_datasets": [ { "name": "twentycities", "title": "He et al. 2010 twenty UK cities weekly reported measles data", "object": "twentycities", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "uk_measles", "title": "Weekly reported measles data for 362 locations in the UK", "object": "uk_measles", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "panelPomp-package", "title": "Inference for PanelPOMPs (Panel Partially Observed Markov Processes)", "topics": [ "panelPomp-package" ] }, { "page": "dot-modifyOther", "title": "Internal function for modifying pparamArray in Mif2", "topics": [ ".modifyOther" ] }, { "page": "dot-modifySelf", "title": "Internal function for modifying pparamArray in Mif2", "topics": [ ".modifySelf" ] }, { "page": "as", "title": "Coercing 'panelPomp' objects as 'list', 'pompList' or 'data.frame'", "concept": [ "panelPomp methods" ], "topics": [ "as" ] }, { "page": "pfilterd-setter", "title": "Modifying parameters of filtered objects", "topics": [ "coef<-,pfilterd.ppomp-method", "shared<-,pfilterd.ppomp-method", "specific<-,pfilterd.ppomp-method" ] }, { "page": "contacts", "title": "Contacts model", "concept": [ "panelPomp examples" ], "topics": [ "contacts" ] }, { "page": "get_dim", "title": "Get single column or row without dropping names", "topics": [ "get_col", "get_dim", "get_row" ] }, { "page": "mif2", "title": "PIF: Panel iterated filtering", "concept": [ "panelPomp workhorse functions" ], "topics": [ "mif2", "mif2,mif2d.ppomp-method", "mif2,panelPomp-method", "mif2d.ppomp-class", "traces,mif2d.ppomp-method" ] }, { "page": "panel_loglik", "title": "Handling of loglikelihood replicates", "concept": [ "panelPomp workhorse functions" ], "topics": [ "logLik,matrix-method", "panel_loglik" ] }, { "page": "panel_logmeanexp", "title": "Log-mean-exp for panels", "topics": [ "panel_logmeanexp" ] }, { "page": "panel-designs", "title": "#' Create design matrix for panelPomp calculations", "concept": [ "panel-designs" ], "topics": [ "panel-designs", "runif_panel_design" ] }, { "page": "panelGompertz", "title": "Panel Gompertz model", "concept": [ "panelPomp examples" ], "topics": [ "panelGompertz" ] }, { "page": "panelGompertzLikelihood", "title": "Likelihood for a panel Gompertz model via a Kalman filter", "topics": [ "panelGompertzLikelihood" ] }, { "page": "panelMeasles", "title": "Make a panelPomp model using UK measles data.", "concept": [ "panelPomp examples" ], "topics": [ "panelMeasles" ] }, { "page": "panelPomp", "title": "Constructing 'panelPomp' objects", "concept": [ "panelPomp workhorse functions" ], "topics": [ "panelPomp", "panelPomp-class" ] }, { "page": "panelPomp_methods", "title": "Manipulating 'panelPomp' objects", "concept": [ "panelPomp methods" ], "topics": [ "coef,panelPomp-method", "coef<-,panelPomp-method", "length,panelPomp-method", "names,panelPomp-method", "panelPomp_methods", "print,panelPomp-method", "shared,panelPomp-method", "shared<-,panelPomp-method", "show,panelPomp-method", "specific,panelPomp-method", "specific<-,panelPomp-method", "toParamList", "unit_objects,panelPomp-method", "window,panelPomp-method", "[,panelPomp-method", "[[,panelPomp-method" ] }, { "page": "panelRandomWalk", "title": "Panel random walk model", "concept": [ "panelPomp examples" ], "topics": [ "panelRandomWalk" ] }, { "page": "params", "title": "Manipulating 'panelPomp' object parameter formats", "topics": [ "params", "toMatrixPparams", "toParamVec" ] }, { "page": "pfilter", "title": "Particle filtering for panel data", "concept": [ "panelPomp workhorse functions" ], "topics": [ "logLik,pfilterd.ppomp-method", "pfilter", "pfilter,panelPomp-method", "pfilterd.ppomp-class", "unitLogLik,pfilterd.ppomp-method" ] }, { "page": "plot", "title": "panelPomp plotting facilities", "topics": [ "plot", "plot,panelPomp_plottable-method" ] }, { "page": "simulate", "title": "Simulations of a panel of partially observed Markov process", "topics": [ "simulate", "simulate,panelPomp-method" ] }, { "page": "twentycities", "title": "He et al. 2010 twenty UK cities weekly reported measles data", "topics": [ "twentycities" ] }, { "page": "uk_measles", "title": "Weekly reported measles data for 362 locations in the UK", "topics": [ "uk_measles" ] } ], "_readme": "https://github.com/jeswheel/panelpomp/raw/HEAD/README.md", "_rundeps": [ "coda", "data.table", "deSolve", "digest", "lattice", "mvtnorm", "pomp" ], "_vignettes": [ { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Getting Started", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Mathematical Notation", "Likelihood Function", "panelPomp objects", "Constructing panelPomp objects" ], "created": "2024-06-24 14:36:02", "modified": "2024-09-12 13:21:12", "commits": 2 } ], "_score": 5.707570176097937, "_indexed": true, "_nocasepkg": "panelpomp", "_universes": [ "jeswheel" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.0.1", "date": "2026-07-03T00:06:26.000Z", "distro": "resolute", "arch": "aarch64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/cfd98af8f5f6ccd3ec1c6c7b48797c69cf4006930ad1244960ffd4806011f1af", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.7.0", "os": "linux", "version": "1.7.0.1", "date": "2026-07-03T00:05:54.000Z", "distro": "resolute", "arch": "x86_64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/d98748d4d33bc6a2ab22af0b8a48bab155bc9707c8a7be0e6a10d650f4ef261c", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.6.1", "os": "linux", "version": "1.7.0.1", "date": "2026-07-03T00:06:30.000Z", "distro": "resolute", "arch": "aarch64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/9b6e3cfd7f011896e5a7135b28ba5dbbf782fb5bf4055f396e03eb10af1f69fd", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.6.1", "os": "linux", "version": "1.7.0.1", "date": "2026-07-03T00:06:12.000Z", "distro": "resolute", "arch": "x86_64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/6cb9a1071180f980629d4bafb76d9ed58979114257b7927fec239ba6a70d6fa6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.5.3", "os": "mac", "version": "1.7.0.1", "date": "2026-07-03T00:05:09.000Z", "arch": "aarch64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/1e432bd2850c08e113fd2b8aa597c1eb7a6df4eabe2b263c91afd4b704257109", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.5.3", "os": "mac", "version": "1.7.0.1", "date": "2026-07-03T00:06:53.000Z", "arch": "x86_64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/0ab4188c36aa74dfc9d050d243dfbad5649186a26df4427a67b35db5b941f6e3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.6.1", "os": "mac", "version": "1.7.0.1", "date": "2026-07-03T00:05:30.000Z", "arch": "aarch64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/8778cdf791f1014b63fd19f5008cb031e140c0b1c4621cad66b7a5002a16ca97", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.6.1", "os": "mac", "version": "1.7.0.1", "date": "2026-07-03T00:06:42.000Z", "arch": "x86_64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/b84723141e076e3b2b0d4fc04c56b4e5d8a90aeddc849e4cc7133a9783f71151", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.0.1", "date": "2026-07-03T00:05:38.000Z", "arch": "emscripten", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/53597de8b0ea27d8c34c0eec65bc8ac22ef4b1d33faaf1d6e61a9bc7eac13362", "status": "success", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.7.0", "os": "win", "version": "1.7.0.1", "date": "2026-07-03T00:04:48.000Z", "arch": "x86_64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/73f98a975d774125749014518eadcc092eef2ee461e271cf642eae99471843b7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.5.3", "os": "win", "version": "1.7.0.1", "date": "2026-07-03T00:04:56.000Z", "arch": "x86_64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/87cfdb58218f99f3a675ff6b179e643470f7d16bd2e7dcb746aa5802a102de8b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" }, { "r": "4.6.1", "os": "win", "version": "1.7.0.1", "date": "2026-07-03T00:05:09.000Z", "arch": "x86_64", "commit": "ff296716484e3197a7f135ad47c883923c8dd7fd", "fileid": "https://r2.ropensci.org/dadf4674403bab2a256cad5acca6acc3d4b190cc2e2f62287fc793b82768f678", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jeswheel/actions/runs/28629275134" } ] }