{ "_id": "6a243f17a1338011a79f1e99", "Package": "rxode2", "Version": "5.1.2", "Title": "Facilities for Simulating from ODE-Based Models", "Authors@R": "c(\nperson(\"Matthew L.\",\"Fidler\", role = c(\"aut\", \"cre\"), email = \"matthew.fidler@gmail.com\", comment=c(ORCID=\"0000-0001-8538-6691\")),\nperson(\"Wenping\", \"Wang\", role = c(\"aut\"), email = \"wwang8198@gmail.com\"),\nperson(\"Alan\", \"Hindmarsh\",role=\"ctb\"),\nperson(\"Arun\", \"Srinivasan\", role=\"ctb\", email=\"arunkumar.sriniv@gmail.com\"),\nperson(\"Awad H.\", \"Al-Mohy\",role=\"ctb\"),\nperson(\"Bill\", \"Denney\", email=\"wdenney@humanpredictions.com\", role=\"ctb\", comment=c(ORCID=\"0000-0002-5759-428X\")),\nperson(\"Cleve\", \"Moler\", role=\"ctb\"),\nperson(\"David\", \"Cooley\", role=\"ctb\"),\nperson(\"Drew\", \"Schmidt\", role=\"ctb\"),\nperson(\"Ernst\", \"Hairer\", role=\"ctb\"),\nperson(\"Gabriel\", \"Staples\", role=\"ctb\"),\nperson(\"Gerhard\", \"Wanner\", role=\"ctb\"),\nperson(\"Gilbert\", \"Stewart\", role=\"ctb\"),\nperson(\"Goro\", \"Fuji\", role=\"ctb\", email=\"gfuji@cpan.org\"),\nperson(\"Hadley\", \"Wickham\", role=\"ctb\"),\nperson(\"Igor\", \"Kushnir\", email=\"igorkuo@gmail.com\", role=\"ctb\"),\nperson(\"Jack\", \"Dongarra\", role=\"ctb\"),\nperson(\"Jim\", \"Bunch\", role=\"ctb\"),\nperson(\"Kevin\", \"Ushey\", role=\"ctb\"),\nperson(\"Linda\", \"Petzold\", role=\"ctb\"),\nperson(\"Martin\", \"Maechler\", role=\"ctb\"),\nperson(\"Matt\", \"Dowle\", role=\"ctb\", email=\"mattjdowle@gmail.com\"),\nperson(\"Matteo\", \"Fasiolo\", email = \"matteo.fasiolo@gmail.com\", role = \"ctb\"),\nperson(\"Melissa\", \"Hallow\", role = \"aut\", email = \"hallowkm@uga.edu\"),\nperson(\"Michel\", \"Lang\", , \"michellang@gmail.com\", role = \"ctb\"),\nperson(\"Morwenn\",\"\", role=\"ctb\"),\nperson(\"Nicholas J.\", \"Higham\",role=\"ctb\"),\nperson(\"Omar\", \"Elashkar\", email=\"omar.i.elashkar@gmail.com\", role=\"ctb\"),\nperson(\"Richard\", \"Upton\", role = \"ctb\"),\nperson(\"Roger B.\", \"Sidje\", role=\"ctb\"),\nperson(\"Simon\", \"Frost\", role=\"ctb\"),\nperson(\"Yu\", \"Feng\", role=\"ctb\"),\nperson(\"Zufar\", \"Mulyukov\", role=\"ctb\", email=\"zufar.mulyukov@novartis.com\"))", "Maintainer": "Matthew L. Fidler ", "Description": "Facilities for running simulations from ordinary\ndifferential equation ('ODE') models, such as pharmacometrics\nand other compartmental models. A compilation manager\ntranslates the ODE model into C, compiles it, and dynamically\nloads the object code into R for improved computational\nefficiency. An event table object facilitates the\nspecification of complex dosing regimens (optional) and\nsampling schedules. NB: The use of this package requires both\nC and Fortran compilers, for details on their use with R please\nsee Section 6.3, Appendix A, and Appendix D in the \"R\nAdministration and Installation\" manual. Also the code is\nmostly released under GPL. The 'VODE' and 'LSODA' are in the\npublic domain. The information is available in the\ninst/COPYRIGHTS.", "BugReports": "https://github.com/nlmixr2/rxode2/issues/", "NeedsCompilation": "yes", "VignetteBuilder": "knitr", "License": "GPL (>= 3)", "URL": "https://nlmixr2.github.io/rxode2/,\nhttps://github.com/nlmixr2/rxode2/", "Biarch": "true", "Encoding": "UTF-8", "LazyData": "true", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "make", "Repository": "https://nlmixr2.r-universe.dev", "Date/Publication": "2026-06-06 13:56:35 UTC", "RemoteUrl": "https://github.com/nlmixr2/rxode2", "RemoteRef": "HEAD", "RemoteSha": "50e853ec1c1742e4f03b14b432f2a250de423128", "Packaged": { "Date": "2026-06-06 15:20:13 UTC", "User": "root" }, "Author": "Matthew L. Fidler [aut, cre] (ORCID:\n),\nWenping Wang [aut],\nAlan Hindmarsh [ctb],\nArun Srinivasan [ctb],\nAwad H. Al-Mohy [ctb],\nBill Denney [ctb] (ORCID: ),\nCleve Moler [ctb],\nDavid Cooley [ctb],\nDrew Schmidt [ctb],\nErnst Hairer [ctb],\nGabriel Staples [ctb],\nGerhard Wanner [ctb],\nGilbert Stewart [ctb],\nGoro Fuji [ctb],\nHadley Wickham [ctb],\nIgor Kushnir [ctb],\nJack Dongarra [ctb],\nJim Bunch [ctb],\nKevin Ushey [ctb],\nLinda Petzold [ctb],\nMartin Maechler [ctb],\nMatt Dowle [ctb],\nMatteo Fasiolo [ctb],\nMelissa Hallow [aut],\nMichel Lang [ctb],\nMorwenn [ctb],\nNicholas J. Higham [ctb],\nOmar Elashkar [ctb],\nRichard Upton [ctb],\nRoger B. Sidje [ctb],\nSimon Frost [ctb],\nYu Feng [ctb],\nZufar Mulyukov [ctb]", "MD5sum": "dad92398de8fbcc3c04a5bd687c41c0d", "_user": "nlmixr2", "_type": "src", "_file": "rxode2_5.1.2.tar.gz", "_fileid": "54e6449a1a237417672bf8fc167f6211527d98e563bffced0042db8b3f3294f2", "_filesize": 4751378, "_sha256": "54e6449a1a237417672bf8fc167f6211527d98e563bffced0042db8b3f3294f2", "_created": "2026-06-06T15:20:13.000Z", "_published": "2026-06-06T15:39:03.371Z", "_distro": "noble", "_jobs": [ { "job": 79887320174, "time": 556, "config": "linux-devel-arm64", "r": "4.7.0", "check": "ERROR", "artifact": "7455622819" }, { "job": 79887320164, "time": 461, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "ERROR", "artifact": "7455610899" }, { "job": 79887320150, "time": 554, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7455622645" }, { "job": 79887320155, "time": 381, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7455601169" }, { "job": 79887320162, "time": 311, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7455592804" }, { "job": 79887320151, "time": 865, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7455659722" }, { "job": 79887320159, "time": 413, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7455605128" }, { "job": 79887320154, "time": 823, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7455655035" }, { "job": 79886618057, "time": 721, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7455558276" }, { "job": 79887320169, "time": 205, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79887320158, "time": 590, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7455626750" }, { "job": 79887320153, "time": 638, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7455632778" }, { "job": 79887320146, "time": 666, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7455636501" } ], "_buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/nlmixr2/rxode2", "_commit": { "id": "50e853ec1c1742e4f03b14b432f2a250de423128", "author": "Matthew Fidler ", "committer": "GitHub ", "message": "Merge pull request #1063 from nlmixr2/mixest-fix\n\nMixest fix", "time": 1780754195 }, "_maintainer": { "name": "Matthew L. Fidler", "email": "matthew.fidler@gmail.com", "login": "mattfidler", "description": "Also a Novartis employee; Can reach me at my Novartis email: matt.fidler@novartis.com", "uuid": 514778, "orcid": "0000-0001-8538-6691" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "sitmo", "role": "LinkingTo" }, { "package": "lotri", "version": ">= 1.0.0", "role": "LinkingTo" }, { "package": "PreciseSums", "version": ">= 0.7", "role": "LinkingTo" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppArmadillo", "version": ">= 0.9.300.2.0", "role": "LinkingTo" }, { "package": "BH", "role": "LinkingTo" }, { "package": "RcppParallel", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.3.9.2", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.21.0.7", "role": "LinkingTo" }, { "package": "dparser", "version": ">= 1.3.1-12", "role": "LinkingTo" }, { "package": "PreciseSums", "version": ">= 0.7", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.3", "role": "Imports" }, { "package": "backports", "role": "Imports" }, { "package": "cli", "version": ">= 2.0.0", "role": "Imports" }, { "package": "checkmate", "role": "Imports" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Imports" }, { "package": "inline", "role": "Imports" }, { "package": "lotri", "version": ">= 1.0.4", "role": "Imports" }, { "package": "memoise", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "rex", "role": "Imports" }, { "package": "sys", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "dparser", "version": ">= 1.3.1-12", "role": "Imports" }, { "package": "rxode2ll", "version": ">= 2.0.9", "role": "Imports" }, { "package": "data.table", "version": ">= 1.12.4", "role": "Imports" }, { "package": "qs2", "role": "Imports" }, { "package": "vctrs", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Matrix", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "crayon", "role": "Suggests" }, { "package": "curl", "role": "Suggests" }, { "package": "digest", "role": "Suggests" }, { "package": "dplyr", "version": ">= 0.8.0", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "htmltools", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "learnr", "role": "Suggests" }, { "package": "microbenchmark", "role": "Suggests" }, { "package": "nlme", "role": "Suggests" }, { "package": "remotes", "role": "Suggests" }, { "package": "rlang", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "stringi", "role": "Suggests" }, { "package": "symengine", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" }, { "package": "withr", "role": "Suggests" }, { "package": "xgxr", "role": "Suggests" }, { "package": "pillar", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "units", "version": ">= 0.6-0", "role": "Suggests" }, { "package": "rsconnect", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "nlmixr2data", "role": "Suggests" }, { "package": "lifecycle", "role": "Suggests" }, { "package": "kableExtra", "role": "Suggests" }, { "package": "pmxTools", "role": "Suggests" }, { "package": "rootSolve", "role": "Suggests" }, { "package": "memuse", "role": "Suggests" } ], "_owner": "nlmixr2", "_selfowned": true, "_usedby": 19, "_updates": [ { "week": "2025-25", "n": 3 }, { "week": "2025-26", "n": 1 }, { "week": "2025-27", "n": 3 }, { "week": "2025-28", "n": 5 }, { "week": "2025-29", "n": 7 }, { "week": "2025-30", "n": 15 }, { "week": "2025-31", "n": 3 }, { "week": "2025-32", "n": 1 }, { "week": "2025-33", "n": 5 }, { "week": "2025-34", "n": 1 }, { "week": "2025-35", "n": 4 }, { "week": "2025-36", "n": 3 }, { "week": "2025-37", "n": 1 }, { "week": "2025-39", "n": 1 }, { "week": "2025-40", "n": 1 }, { "week": "2025-41", "n": 2 }, { "week": "2025-42", "n": 4 }, { "week": "2025-47", "n": 1 }, { "week": "2025-48", "n": 14 }, { "week": "2025-49", "n": 30 }, { "week": "2025-50", "n": 1 }, { "week": "2026-01", "n": 3 }, { "week": "2026-04", "n": 11 }, { "week": "2026-07", "n": 1 }, { "week": "2026-08", "n": 2 }, { "week": "2026-09", "n": 2 }, { "week": "2026-11", "n": 1 }, { "week": "2026-12", "n": 14 }, { "week": "2026-13", "n": 3 }, { "week": "2026-14", "n": 12 }, { "week": "2026-15", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 10 }, { "week": "2026-19", "n": 17 }, { "week": "2026-20", "n": 18 }, { "week": "2026-21", "n": 28 }, { "week": "2026-22", "n": 22 }, { "week": "2026-23", "n": 9 } ], "_tags": [ { "name": "v4.0.0", "date": "2025-07-16" }, { "name": "v4.0.1", "date": "2025-07-17" }, { "name": "v4.0.2", "date": "2025-07-21" }, { "name": "v4.0.3", "date": "2025-07-24" }, { "name": "v4.1.0", "date": "2025-08-29" }, { "name": "v4.1.1", "date": "2025-10-08" }, { "name": "v5.0.0", "date": "2025-11-27" }, { "name": "v5.0.1", "date": "2025-12-06" }, { "name": "v5.0.2", "date": "2026-03-19" }, { "name": "v5.1.1", "date": "2026-05-27" }, { "name": "v5.1.2", "date": "2026-06-01" } ], "_stars": 60, "_contributors": [ { "user": "mattfidler", "count": 8838, "uuid": 514778 }, { "user": "billdenney", "count": 320, "uuid": 10359931 }, { "user": "wwang-at-github", "count": 68, "uuid": 13064566 }, { "user": "copilot", "count": 27, "uuid": 198982749 }, { "user": "daj025", "count": 7, "uuid": 13022669 }, { "user": "leovuong", "count": 4, "uuid": 92429953 }, { "user": "kestrel99", "count": 3, "uuid": 9568350 }, { "user": "eddelbuettel", "count": 2, "uuid": 673121 }, { "user": "hallowkm", "count": 2, "uuid": 9352362 }, { "user": "s0521", "count": 2, "uuid": 48432488 }, { "user": "claude", "count": 1, "uuid": 81847 }, { "user": "krlmlr", "count": 1, "uuid": 1741643 }, { "user": "timwaterhouse", "count": 1, "uuid": 19149867 } ], "_userbio": { "uuid": 94710774, "type": "organization", "name": "nlmixr2" }, "_downloads": { "count": 3453, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rxode2" }, "_devurl": "https://github.com/nlmixr2/rxode2", "_pkgdown": "https://nlmixr2.github.io/rxode2/", "_searchresults": 1008, "_topics": [ "openblas", "cpp", "openmp" ], "_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/readme.html", "extra/readme.md", "extra/rxode2.html", "manual.pdf" ], "_homeurl": "https://github.com/nlmixr2/rxode2", "_realowner": "nlmixr2", "_cranurl": true, "_releases": [ { "version": "2.0.6", "date": "2022-05-09" }, { "version": "2.0.7", "date": "2022-05-17" }, { "version": "2.0.8", "date": "2022-09-23" }, { "version": "2.0.9", "date": "2022-10-19" }, { "version": "2.0.10", "date": "2022-10-20" }, { "version": "2.0.11", "date": "2022-11-01" }, { "version": "2.0.12", "date": "2023-03-28" }, { "version": "2.0.13", "date": "2023-04-22" }, { "version": "2.0.14", "date": "2023-10-07" }, { "version": "2.1.0", "date": "2023-12-12" }, { "version": "2.1.1", "date": "2023-12-13" }, { "version": "2.1.2", "date": "2024-01-31" }, { "version": "2.1.3", "date": "2024-05-28" }, { "version": "3.0.0", "date": "2024-09-18" }, { "version": "3.0.1", "date": "2024-09-22" }, { "version": "3.0.2", "date": "2024-10-30" }, { "version": "3.0.3", "date": "2024-12-15" }, { "version": "3.0.4", "date": "2025-02-14" }, { "version": "4.0.0", "date": "2025-07-16" }, { "version": "4.0.1", "date": "2025-07-18" }, { "version": "4.0.2", "date": "2025-07-21" }, { "version": "4.0.3", "date": "2025-07-24" }, { "version": "4.1.0", "date": "2025-08-29" }, { "version": "4.1.1", "date": "2025-10-08" }, { "version": "5.0.0", "date": "2025-11-28" }, { "version": "5.0.1", "date": "2025-12-11" }, { "version": "5.0.2", "date": "2026-03-20" }, { "version": "5.1.1", "date": "2026-05-28" }, { "version": "5.1.2", "date": "2026-06-02" } ], "_exports": [ ".assertRenameErrorModelLine", ".cbindOme", ".clearPipe", ".collectWarnings", ".convertId", ".copyUi", ".expandPars", ".extraC", ".extraCnow", ".getErrDist", ".getLastIdLvl", ".getNamedArgumentsToPredDf", ".getWh", ".handleSingleErrTypeNormOrTFoceiBase", ".iniGetAppendArg", ".iniHandleFixOrUnfix", ".iniHandleLine", ".malert", ".matchesLangTemplate", ".minfo", ".modelHandleModelLines", ".msuccess", ".mwarn", ".pipeDfObs", ".pipeDfSub", ".pipeEvents", ".pipeInits", ".pipeKeep", ".pipeNStud", ".pipeNSub", ".pipeOmega", ".pipeParams", ".pipeRx", ".pipeSigma", ".pipeThetaMat", ".quoteCallInfoLines", ".rstudioComplete", ".rxBlankIni", ".rxC", ".rxDocTable", ".rxFromSE", ".rxGetHiBoundaryPred1AndIni", ".rxGetLambdaFromPred1AndIni", ".rxGetLowBoundaryPred1AndIni", ".rxGetPredictionDVTransform", ".rxGetPredictionF", ".rxGetPredictionFTransform", ".rxGetSeed", ".rxGetVarianceForErrorType", ".rxIsLinCmt", ".rxJacobian", ".rxLastCompileSuccess", ".rxLinCmt", ".rxLinCmtGen", ".rxLinNcmt", ".rxode2ptrs", ".rxPrune", ".rxRename", ".rxSEeqUsr", ".rxSens", ".rxSetSeed", ".rxToSE", ".rxTransform", ".rxTransInfo", ".rxWithOptions", ".rxWithSink", ".rxWithSinkBoth", ".rxWithWd", ".s3register", ".solComp2", ".solComp3", ".symengineFs", ".toClassicEvid", ".udfCallFunArg", ".udfEnvReset", ".udfEnvSet", ".udfEnvSetUdf", ".udfExists", ".udfMd5Info", ".uiArg", ".useUtf", ".vecDf", "add.dosing", "add.sampling", "aes", "as_tibble.rxEt", "as.et", "as.ini", "as.model", "as.rxEvid", "as.rxRateDur", "as.rxUi", "assertCompartmentExists", "assertCompartmentName", "assertCompartmentNew", "assertExists", "assertIniDf", "assertParameterValue", "assertRxLinCmt", "assertRxUi", "assertRxUiEstimatedResiduals", "assertRxUiIovNoCor", "assertRxUiMixedOnly", "assertRxUiMuRefOnly", "assertRxUiNoMix", "assertRxUiNormal", "assertRxUiPopulationOnly", "assertRxUiPrediction", "assertRxUiRandomOnIdOnly", "assertRxUiSingleEndpoint", "assertRxUiTransformNormal", "assertRxUnbounded", "assertVariableExists", "assertVariableName", "assertVariableNew", "binomProbs", "bolus", "boxCox", "boxCoxInv", "cvPost", "d2aELU", "d2ELU", "d2ELUa", "d2GELU", "d3GELU", "d4GELU", "dELU", "dELUa", "dfWishart", "dGELU", "dlReLU", "dmexpit", "dPReLU", "dPReLUa", "dPReLUa1", "dReLU", "dSELU", "dsoftplus", "dSwish", "ELU", "erf", "et", "etExpand", "etRbind", "etRep", "etSeq", "etTrans", "eventTable", "evid_", "expand_limits", "expit", "facet_wrap", "findLhs", "forderForceBase", "gammap", "gammapDer", "gammapInv", "gammapInva", "gammaq", "gammaqInv", "gammaqInva", "GELU", "genShinyApp.template", "geom_amt", "geom_cens", "geom_line", "getBaseIniSimModel", "getBaseSimModel", "getBaseSymengineModel", "getRxThreads", "ggplot", "guide_none", "infuse", "infuseDur", "ini", "ini<-", "invWR1d", "is.rxEt", "is.rxSolve", "is.rxStackData", "label_both", "label_context", "label_value", "label_wrap_gen", "linMod", "linMod0", "linModA0", "linModB", "linModB0", "linModD", "linModD0", "linModM", "linModM0", "linToOde", "llikBeta", "llikBinom", "llikCauchy", "llikChisq", "llikExp", "llikF", "llikGamma", "llikGeom", "llikNbinom", "llikNbinomMu", "llikNorm", "llikPois", "llikT", "llikUnif", "llikWeibull", "logit", "logitNormInfo", "lotri", "lowergamma", "lReLU", "meanProbs", "mexpit", "mix", "mlogit", "model", "model<-", "modelExtract", "obs", "odeMethodToInt", "phantom", "phi", "PReLU", "probit", "probitInv", "probitNormInfo", "ReLU", "rinvchisq", "rLKJ1", "rxAllowUnload", "rxAppendModel", "rxAssignControlValue", "rxAssignPtr", "rxbeta", "rxbinom", "rxBlockZeros", "rxC", "rxCat", "rxcauchy", "rxCbindStudyIndividual", "rxChain", "rxChain2", "rxchisq", "rxClean", "rxCombineErrorLines", "rxCompile", "rxCondition", "rxControl", "rxControlUpdateSens", "rxCores", "rxCreateCache", "rxD", "rxDelete", "rxDemoteAddErr", "rxDerived", "rxDeserialize", "rxDfdy", "rxDll", "rxDllLoaded", "rxDynLoad", "rxDynUnload", "rxErrTypeCombine", "rxEtDispatchSolve", "rxEvid", "rxexp", "rxExpandFEta_", "rxExpandGrid", "rxExpandGrid_", "rxExpandIfElse", "rxExpandSens_", "rxExpandSens2_", "rxf", "rxFixPop", "rxFixRes", "rxForget", "rxFromSE", "rxFun", "rxFunParse", "rxgamma", "rxgeom", "rxGetControl", "rxGetDefaultSerialize", "rxGetDistributionSimulationLines", "rxGetLin", "rxGetModel", "rxGetrxode2", "rxGetSeed", "rxGetSerialType_", "rxHtml", "rxIndLinState", "rxIndLinStrategy", "rxInit", "rxInits", "rxIntToBase", "rxIntToLetter", "rxInv", "rxIs", "rxIsCurrent", "rxIsLoaded", "rxLastCompile", "rxLhs", "rxLoad", "rxLoadState", "rxLock", "rxMd5", "rxMemoryEstimate", "rxMemSummary", "rxModels_", "rxModelVars", "rxModelVarsS3", "rxnbinom", "rxnbinomMu", "rxnorm", "rxNorm", "rxnormV", "rxNumLoaded", "rxode", "RxODE", "rxode<-", "RxODE<-", "rxode2", "rxode2<-", "rxode2parse", "rxode2parseAssignPackagesToLoad", "rxode2parseAssignPointerTranslation", "rxode2parseAssignTranslation", "rxode2parseD", "rxode2parseGetPackagesToLoad", "rxode2parseGetPointerAssignment", "rxode2parseGetTranslation", "rxOldQsDes", "rxOptExpr", "rxord", "rxParam", "rxParams", "rxParseErr", "rxParsePk", "rxParsePred", "rxParseSetSilentErr", "rxParseSuppressMsg", "rxPkg", "rxpois", "rxPp", "rxPreferredDistributionName", "rxProgress", "rxProgressAbort", "rxProgressStop", "rxPrune", "rxRateDur", "rxRawToC", "rxReload", "rxRemoveControl", "rxRename", "rxRepR0_", "rxReq", "rxRmFun", "rxRmFunParse", "rxRmvn", "rxS", "rxSaveState", "rxSeedEng", "rxSerialize", "rxSetControl", "rxSetCovariateNamesForPiping", "rxSetIni0", "rxSetPipingAuto", "rxSetProd", "rxSetProgressBar", "rxSetSeed", "rxSetSilentErr", "rxSetSum", "rxSetupIni", "rxSetupScale", "rxShiny", "rxSimThetaOmega", "rxSolve", "rxSolveFree", "rxSolveSetup", "rxSplitPlusQ", "rxStack", "rxState", "rxStateOde", "rxSumProdModel", "rxSupportedFuns", "rxSuppressMsg", "rxSymInvChol", "rxSymInvCholCreate", "rxSymInvCholN", "rxSyncOptions", "rxt", "rxTempDir", "rxTest", "rxTheme", "rxTick", "rxToSE", "rxTrans", "rxUdfUi", "rxUdfUiControl", "rxUdfUiData", "rxUdfUiEst", "rxUdfUiExpr", "rxUdfUiFlag", "rxUdfUiIniDf", "rxUdfUiIniLhs", "rxUdfUiIsValue", "rxUdfUiMv", "rxUdfUiNum", "rxUdfUiParsing", "rxUdfUiReset", "rxUiCompress", "rxUiDecompress", "rxUiDeparse", "rxUiDevelop", "rxUiGet", "rxunif", "rxUnload", "rxUnloadAll", "rxUnlock", "rxUse", "rxValidate", "rxVersion", "rxweibull", "rxWithPreserveSeed", "rxWithSeed", "scale_type", "scale_x_continuous", "scale_x_date", "scale_x_discrete", "scale_y_continuous", "scale_y_date", "scale_y_discrete", "SELU", "setRxThreads", "softplus", "splitBolus", "stat_amt", "stat_cens", "swapMatListWithCube", "Swish", "testCompartmentExists", "testExists", "testIniDf", "testRxLinCmt", "testRxUnbounded", "testVariableExists", "toTrialDuration", "uppergamma", "waiver", "warnRxBounded", "write.template.server", "write.template.ui", "xlab", "yeoJohnson", "yeoJohnsonInv", "ylab", "zeroRe" ], "_datasets": [ { "name": "rxReservedKeywords", "title": "A list and description of rxode2 supported reserved keywords", "object": "rxReservedKeywords", "class": [ "data.frame" ], "fields": [ "Reserved Name", "Meaning", "Alias" ], "rows": 31, "table": true, "tojson": true }, { "name": "rxResidualError", "title": "A description of Rode2 supported residual errors", "object": "rxResidualError", "class": [ "data.frame" ], "fields": [ "Error model", "Functional Form", "Transformation", "code", "addProp", "lhs" ], "rows": 181, "table": true, "tojson": true }, { "name": "rxSyntaxFunctions", "title": "A list and description of Rode supported syntax functions", "object": "rxSyntaxFunctions", "class": [ "data.frame" ], "fields": [ "Function", "Description", "Aliases" ], "rows": 102, "table": true, "tojson": true } ], "_help": [ { "page": "dot-cbindOme", "title": "cbind Ome", "topics": [ ".cbindOme" ] }, { "page": "dot-collectWarnings", "title": "Collect warnings and just warn once.", "topics": [ ".collectWarnings" ] }, { "page": "dot-copyUi", "title": "This copies the rxode2 UI object so it can be modified", "topics": [ ".copyUi" ] }, { "page": "dot-handleSingleErrTypeNormOrTFoceiBase", "title": "Handle the single error for normal or t distributions", "topics": [ ".handleSingleErrTypeNormOrTFoceiBase" ] }, { "page": "dot-matchesLangTemplate", "title": "Check if a language object matches a template language object", "topics": [ ".matchesLangTemplate" ] }, { "page": "dot-modelHandleModelLines", "title": "Handle model lines", "topics": [ ".modelHandleModelLines" ] }, { "page": "dot-quoteCallInfoLines", "title": "Returns quoted call information", "topics": [ ".quoteCallInfoLines" ] }, { "page": "dot-rxLinCmtGen", "title": "Internal function to generate the model variables for a linCmt() model", "topics": [ ".rxLinCmtGen" ] }, { "page": "dot-rxode2ptrs", "title": "Get the rxode2 function pointers", "topics": [ ".rxode2ptrs" ] }, { "page": "dot-rxWithOptions", "title": "Temporarily set options then restore them while running code", "topics": [ ".rxWithOptions" ] }, { "page": "dot-rxWithWd", "title": "Temporarily set options then restore them while running code", "topics": [ ".rxWithWd" ] }, { "page": "dot-toClassicEvid", "title": "This converts NONMEM-style EVIDs to classic RxODE events", "topics": [ ".toClassicEvid" ] }, { "page": "dot-vecDf", "title": "Convert numeric vector to repeated data.frame", "topics": [ ".vecDf" ] }, { "page": "add.dosing", "title": "Add dosing to eventTable", "topics": [ "add.dosing" ] }, { "page": "add.sampling", "title": "Add sampling to eventTable", "topics": [ "add.sampling" ] }, { "page": "as_tibble.rxEt", "title": "Convert to tbl", "topics": [ "as_tibble.rxEt" ] }, { "page": "as.data.table.rxEt", "title": "Convert an event table to a data.table", "topics": [ "as.data.table.rxEt" ] }, { "page": "as.et", "title": "Coerce object to data.frame", "topics": [ "as.et", "as.et.default" ] }, { "page": "as.ini", "title": "Turn into an ini block for initialization", "topics": [ "as.ini", "as.ini.call", "as.ini.character", "as.ini.data.frame", "as.ini.default", "as.ini.lotriFix", "as.ini.matrix" ] }, { "page": "as.model", "title": "Turn into a model expression", "topics": [ "as.model", "as.model.call", "as.model.character", "as.model.default", "as.model.list" ] }, { "page": "as.rxUi", "title": "As rxode2 ui", "topics": [ "as.rxUi", "as.rxUi.default", "as.rxUi.function", "as.rxUi.rxModelVars", "as.rxUi.rxode2", "as.rxUi.rxode2tos", "as.rxUi.rxUi" ] }, { "page": "assertCompartmentExists", "title": "Verify that the compartment exists in a model", "concept": [ "Assertions" ], "topics": [ "assertCompartmentExists", "testCompartmentExists" ] }, { "page": "assertCompartmentName", "title": "Verify that a value is a valid nlmixr2 compartment name", "concept": [ "Assertions" ], "topics": [ "assertCompartmentName", "assertExists", "assertParameterValue", "assertVariableName", "testExists" ] }, { "page": "assertCompartmentNew", "title": "Verify that a compartment would be new to the model", "concept": [ "Assertions" ], "topics": [ "assertCompartmentNew" ] }, { "page": "assertRxUi", "title": "Assert properties of the rxUi models", "concept": [ "Assertions" ], "topics": [ "assertRxUi", "assertRxUiEstimatedResiduals", "assertRxUiIovNoCor", "assertRxUiMixedOnly", "assertRxUiMuRefOnly", "assertRxUiNoMix", "assertRxUiNormal", "assertRxUiPopulationOnly", "assertRxUiPrediction", "assertRxUiRandomOnIdOnly", "assertRxUiSingleEndpoint", "assertRxUiTransformNormal" ] }, { "page": "assertVariableExists", "title": "Assert a variable exists in the model", "concept": [ "Assertions" ], "topics": [ "assertVariableExists", "testVariableExists" ] }, { "page": "assertVariableNew", "title": "Assert a variable would be new to the model", "concept": [ "Assertions" ], "topics": [ "assertVariableNew" ] }, { "page": "binomProbs", "title": "Calculate expected confidence bands with binomial sampling distribution", "topics": [ "binomProbs", "binomProbs.default" ] }, { "page": "bolus", "title": "Administer a bolus dose inside a rxode2 model", "topics": [ "bolus" ] }, { "page": "boxCox", "title": "boxCox/yeoJohnson and inverse boxCox/yeoJohnson functions", "topics": [ "boxCox", "boxCoxInv", "yeoJohnson", "yeoJohnsonInv" ] }, { "page": "cvPost", "title": "Sample a covariance Matrix from the Posterior Inverse Wishart distribution.", "topics": [ "cvPost" ] }, { "page": "dELU", "title": "Derivatives of the Exponential Linear Unit (ELU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "d2aELU", "d2ELU", "d2ELUa", "dELU", "dELUa" ] }, { "page": "dfWishart", "title": "This uses simulations to match the rse", "topics": [ "dfWishart" ] }, { "page": "dGELU", "title": "Derivatives of GELU", "concept": [ "Activation Functions" ], "topics": [ "d2GELU", "d3GELU", "d4GELU", "dGELU" ] }, { "page": "dlReLU", "title": "Derivative of Leaky ReLU activation function", "concept": [ "Activation Functions" ], "topics": [ "dlReLU" ] }, { "page": "dPReLU", "title": "Derivatives Parametric ReLU Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dPReLU", "dPReLUa", "dPReLUa1" ] }, { "page": "dReLU", "title": "Derivative of the Rectified Linear Unit (ReLU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dReLU" ] }, { "page": "dSELU", "title": "Derivative of the Scaled Exponential Linear Unit (SELU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dSELU" ] }, { "page": "dsoftplus", "title": "Default Softplus Activation Function", "concept": [ "Activation Functions" ], "topics": [ "d2softplus", "d3softplus", "d4softplus", "dsoftplus" ] }, { "page": "dSwish", "title": "Derivative of the Swish Activation Function", "concept": [ "Activation Functions" ], "topics": [ "dSwish" ] }, { "page": "ELU", "title": "Exponential Linear Unit (ELU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "ELU" ] }, { "page": "erf", "title": "Error function", "topics": [ "erf" ] }, { "page": "et", "title": "Event Table Function", "topics": [ "et", "et.default", "et.function", "et.rxode2", "et.rxParams", "et.rxSolve", "et.rxUi" ] }, { "page": "etExpand", "title": "Expand additional doses", "topics": [ "etExpand" ] }, { "page": "etRbind", "title": "Combining event tables", "topics": [ "etRbind", "rbind.rxEt" ] }, { "page": "etRep", "title": "Repeat an rxode2 event table", "topics": [ "etRep", "rep.rxEt" ] }, { "page": "etSeq", "title": "Sequence of event tables", "topics": [ "etSeq", "seq.rxEt" ] }, { "page": "eventTable", "title": "Create an event table object", "concept": [ "Nonlinear regression", "Pharmacodynamics (PD)", "Pharmacokinetics (PK)", "ordinary differential equations" ], "topics": [ "eventTable" ] }, { "page": "evid_", "title": "Push a future dose or observation event from within an rxode2 model", "topics": [ "evid_" ] }, { "page": "gammap", "title": "Gammap: normalized lower incomplete gamma function", "topics": [ "gammap" ] }, { "page": "gammapDer", "title": "gammapDer: derivative of gammap", "topics": [ "gammapDer" ] }, { "page": "gammapInv", "title": "gammapInv and gammapInva: Inverses of normalized gammap function", "topics": [ "gammapInv", "gammapInva" ] }, { "page": "gammaq", "title": "Gammaq: normalized upper incomplete gamma function", "topics": [ "gammaq" ] }, { "page": "gammaqInv", "title": "gammaqInv and gammaqInva: Inverses of normalized gammaq function", "topics": [ "gammaqInv", "gammaqInva" ] }, { "page": "GELU", "title": "GELU activation function", "concept": [ "Activation Functions" ], "topics": [ "GELU" ] }, { "page": "genShinyApp.template", "title": "Generate an example (template) of a dosing regimen shiny app", "concept": [ "PK/PD", "pharmacometrics" ], "topics": [ "genShinyApp.template", "write.template.server", "write.template.ui" ] }, { "page": "getRxThreads", "title": "Get/Set the number of threads that rxode2 uses", "topics": [ "getRxThreads", "rxCores", "setRxThreads" ] }, { "page": "infuse", "title": "Administer a infusion (with rate being fixed) inside a rxode2 model", "topics": [ "infuse" ] }, { "page": "infuseDur", "title": "Administer a infusion (with duration being fixed) inside a rxode2 model", "topics": [ "infuseDur" ] }, { "page": "ini", "title": "Ini block for rxode2/nlmixr models", "concept": [ "Initial conditions" ], "topics": [ "ini", "ini.default", "ini.rxUi" ] }, { "page": "ini-set", "title": "Assign the ini block in the rxode2 related object", "topics": [ "ini<-" ] }, { "page": "is.rxEt", "title": "Check if object is an rxEt event table", "topics": [ "is.rxEt" ] }, { "page": "is.rxStackData", "title": "Return if the object can be stacked", "topics": [ "is.rxStackData" ] }, { "page": "linMod", "title": "Linear model to replace in rxode2 ui model", "concept": [ "User functions" ], "topics": [ "linMod", "linMod0", "linModA", "linModA0", "linModB", "linModB0", "linModD", "linModD0", "linModM", "linModM0" ] }, { "page": "linToOde", "title": "Convert linCmt rxUi models to ODE rxUi models", "topics": [ "linToOde" ] }, { "page": "llikBeta", "title": "Calculate the log likelihood of the binomial function (and its derivatives)", "topics": [ "llikBeta" ] }, { "page": "llikBinom", "title": "Calculate the log likelihood of the binomial function (and its derivatives)", "topics": [ "llikBinom" ] }, { "page": "llikCauchy", "title": "log likelihood of Cauchy distribution and it's derivatives (from stan)", "topics": [ "llikCauchy" ] }, { "page": "llikChisq", "title": "log likelihood and derivatives for chi-squared distribution", "topics": [ "llikChisq" ] }, { "page": "llikExp", "title": "log likelihood and derivatives for exponential distribution", "topics": [ "llikExp" ] }, { "page": "llikF", "title": "log likelihood and derivatives for F distribution", "topics": [ "llikF" ] }, { "page": "llikGamma", "title": "log likelihood and derivatives for Gamma distribution", "topics": [ "llikGamma" ] }, { "page": "llikGeom", "title": "log likelihood and derivatives for Geom distribution", "topics": [ "llikGeom" ] }, { "page": "llikNbinom", "title": "Calculate the log likelihood of the negative binomial function (and its derivatives)", "topics": [ "llikNbinom" ] }, { "page": "llikNbinomMu", "title": "Calculate the log likelihood of the negative binomial function (and its derivatives)", "topics": [ "llikNbinomMu" ] }, { "page": "llikNorm", "title": "Log likelihood for normal distribution", "topics": [ "llikNorm" ] }, { "page": "llikPois", "title": "log-likelihood for the Poisson distribution", "topics": [ "llikPois" ] }, { "page": "llikT", "title": "Log likelihood of T and it's derivatives (from stan)", "topics": [ "llikT" ] }, { "page": "llikUnif", "title": "log likelihood and derivatives for Unif distribution", "topics": [ "llikUnif" ] }, { "page": "llikWeibull", "title": "log likelihood and derivatives for Weibull distribution", "topics": [ "llikWeibull" ] }, { "page": "logit", "title": "logit and inverse logit (expit) functions", "topics": [ "expit", "logit", "logitNormInfo", "probitNormInfo" ] }, { "page": "lowergamma", "title": "lowergamma: upper incomplete gamma function", "topics": [ "lowergamma" ] }, { "page": "lReLU", "title": "Leaky ReLU activation function", "concept": [ "Activation Functions" ], "topics": [ "lReLU" ] }, { "page": "meanProbs", "title": "Calculate expected confidence bands or prediction intreval with normal or t sampling distribution", "topics": [ "meanProbs", "meanProbs.default" ] }, { "page": "mexpit", "title": "mexpit - Convert log-scale numbers to probabilities", "topics": [ "dmexpit", "mexpit" ] }, { "page": "mix", "title": "Specify a mixture model of variables", "topics": [ "mix" ] }, { "page": "mlogit", "title": "mlogit - Convert multiple probabilities to log-scale numbers", "topics": [ "mlogit" ] }, { "page": "model", "title": "Model block for rxode2/nlmixr models", "topics": [ "model", "model.default", "model.function", "model.rxModelVars", "model.rxode2", "model.rxUi" ] }, { "page": "model-set", "title": "Assign the model block in the rxode2 related object", "topics": [ "model<-" ] }, { "page": "modelExtract", "title": "Extract model lines from a rxui model", "topics": [ "modelExtract", "modelExtract.default", "modelExtract.function", "modelExtract.rxModelVars", "modelExtract.rxode2", "modelExtract.rxUi" ] }, { "page": "multiply", "title": "Multiply dose the rxode2 system in the model", "topics": [ "multiply" ] }, { "page": "obs", "title": "Add observations to a model", "topics": [ "obs" ] }, { "page": "odeMethodToInt", "title": "Conversion between character and integer ODE integration methods for rxode2", "topics": [ "odeMethodToInt" ] }, { "page": "phantom", "title": "Administer a phantom/transit dose inside a rxode2 model", "topics": [ "phantom" ] }, { "page": "phi", "title": "Cumulative distribution of standard normal", "topics": [ "phi" ] }, { "page": "plot.rxSolve", "title": "Plot rxode2 objects", "concept": [ "rxode2 plotting" ], "topics": [ "plot.rxSolve", "plot.rxSolveConfint1", "plot.rxSolveConfint2" ] }, { "page": "PReLU", "title": "Parametric ReLU Activation Function", "concept": [ "Activation Functions" ], "topics": [ "PReLU" ] }, { "page": "print.rxModelVars", "title": "Print Values", "topics": [ "print.rxModelVars" ] }, { "page": "probit", "title": "probit and inverse probit functions", "topics": [ "probit", "probitInv" ] }, { "page": "ReLU", "title": "Rectified Linear Unit (ReLU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "ReLU" ] }, { "page": "replace", "title": "Replace dose the rxode2 system in the model", "topics": [ "replace" ] }, { "page": "reset", "title": "Reset the rxode2 system in the model", "topics": [ "reset" ] }, { "page": "rinvchisq", "title": "Scaled Inverse Chi Squared distribution", "topics": [ "rinvchisq" ] }, { "page": "rxAllowUnload", "title": "Allow unloading of dlls", "topics": [ "rxAllowUnload" ] }, { "page": "rxAppendModel", "title": "Append two rxui models together", "topics": [ "rxAppendModel" ] }, { "page": "rxAssignControlValue", "title": "Assign Control Variable", "topics": [ "rxAssignControlValue" ] }, { "page": "rxAssignPtr", "title": "Assign pointer based on model variables", "topics": [ "rxAssignPtr" ] }, { "page": "rxbeta", "title": "Simulate beta variable from threefry generator", "topics": [ "rxbeta" ] }, { "page": "rxbinom", "title": "Simulate Binomial variable from threefry generator", "topics": [ "rxbinom" ] }, { "page": "rxcauchy", "title": "Simulate Cauchy variable from threefry generator", "topics": [ "rxcauchy" ] }, { "page": "rxCbindStudyIndividual", "title": "Bind the study parameters and individual parameters", "topics": [ "rxCbindStudyIndividual" ] }, { "page": "rxchisq", "title": "Simulate chi-squared variable from threefry generator", "topics": [ "rxchisq" ] }, { "page": "rxClean", "title": "Cleanup anonymous DLLs by unloading them", "topics": [ "rxClean" ] }, { "page": "rxCompile", "title": "Compile a model if needed", "topics": [ "rxCompile", "rxCompile.character", "rxCompile.rxDll", "rxCompile.rxModelVars", "rxCompile.rxode2" ] }, { "page": "rxControlUpdateSens", "title": "This updates the tolerances based on the sensitivity equations", "topics": [ "rxControlUpdateSens" ] }, { "page": "rxCreateCache", "title": "This will create the cache directory for rxode2 to save between sessions", "topics": [ "rxCreateCache" ] }, { "page": "rxD", "title": "Add to rxode2's derivative tables", "topics": [ "rxD" ] }, { "page": "rxDelete", "title": "Delete the DLL for the model", "topics": [ "rxDelete" ] }, { "page": "rxDerived", "title": "Calculate derived parameters for the 1-, 2-, and 3- compartment linear models.", "topics": [ "rxDerived" ] }, { "page": "rxDfdy", "title": "Jacobian and parameter derivatives", "concept": [ "Query model information" ], "topics": [ "rxDfdy" ] }, { "page": "rxEtDispatchSolve", "title": "Dispatch solve to 'rxode2' solve", "topics": [ "rxEtDispatchSolve", "rxEtDispatchSolve.default" ] }, { "page": "rxEvid", "title": "EVID formatting for tibble and other places.", "topics": [ "as.character.rxEvid", "as.rxEvid", "c.rxEvid", "c.rxRateDur", "format.rxEvid", "format.rxRateDur", "print.rxEvid", "rxEvid", "units<-.rxEvid", "[.rxEvid", "[[.rxEvid" ] }, { "page": "rxexp", "title": "Simulate exponential variable from threefry generator", "topics": [ "rxexp" ] }, { "page": "rxf", "title": "Simulate F variable from threefry generator", "topics": [ "rxf" ] }, { "page": "rxFixPop", "title": "Apply the fixed population estimated parameters", "topics": [ "rxFixPop" ] }, { "page": "rxFixRes", "title": "Literally fix residual parameters", "topics": [ "rxFixRes" ] }, { "page": "rxFun", "title": "Add/Create C functions for use in rxode2", "topics": [ "rxFun", "rxRmFun" ] }, { "page": "rxgamma", "title": "Simulate gamma variable from threefry generator", "topics": [ "rxgamma" ] }, { "page": "rxgeom", "title": "Simulate geometric variable from threefry generator", "topics": [ "rxgeom" ] }, { "page": "rxGetControl", "title": "rxGetControl option from ui", "topics": [ "rxGetControl" ] }, { "page": "rxGetDefaultSerialize", "title": "Get the Default Serialization Type", "topics": [ "rxGetDefaultSerialize" ] }, { "page": "rxGetLin", "title": "Get the linear compartment model true function", "topics": [ "rxGetLin" ] }, { "page": "rxGetrxode2", "title": "Get rxode2 model from object", "topics": [ "rxGetrxode2" ] }, { "page": "rxGetSeed", "title": "Get the rxode2 seed", "topics": [ "rxGetSeed" ] }, { "page": "rxHtml", "title": "Format rxSolve and related objects as html.", "topics": [ "rxHtml", "rxHtml.rxSolve" ] }, { "page": "rxIndLinState", "title": "Set the preferred factoring by state", "topics": [ "rxIndLinState" ] }, { "page": "rxIndLinStrategy", "title": "This sets the inductive linearization strategy for matrix building", "topics": [ "rxIndLinStrategy" ] }, { "page": "rxIntToBase", "title": "Convert a positive base", "topics": [ "rxIntToBase" ] }, { "page": "rxIntToLetter", "title": "Convert a positive integer to a letter series", "topics": [ "rxIntToLetter" ] }, { "page": "rxInv", "title": "Invert matrix using RcppArmadillo.", "topics": [ "rxInv" ] }, { "page": "rxIsCurrent", "title": "Checks if the rxode2 object was built with the current build", "topics": [ "rxIsCurrent" ] }, { "page": "rxLastCompile", "title": "Get the last compiled model information as alist", "topics": [ "rxLastCompile" ] }, { "page": "rxLhs", "title": "Left handed Variables", "concept": [ "Query model information" ], "topics": [ "rxLhs" ] }, { "page": "rxLock", "title": "Lock/unlocking of rxode2 dll file", "topics": [ "rxLock", "rxUnlock" ] }, { "page": "rxMemoryEstimate", "title": "Estimate memory required by rxSolve() for a given dataset and model", "topics": [ "rxMemoryEstimate" ] }, { "page": "rxMemSummary", "title": "Create a per-ID event summary for memory estimation", "topics": [ "rxMemSummary" ] }, { "page": "rxnbinom", "title": "Simulate Binomial variable from threefry generator", "topics": [ "rxnbinom", "rxnbinomMu" ] }, { "page": "rxNorm", "title": "Get the normalized model", "topics": [ "rxNorm" ] }, { "page": "rxnormV", "title": "Simulate random normal variable from threefry generator", "topics": [ "rxnorm", "rxnormV" ] }, { "page": "rxNumLoaded", "title": "Get the number of loaded rxode2 DLLs", "topics": [ "rxNumLoaded" ] }, { "page": "rxode2", "title": "Create an ODE-based model specification", "concept": [ "Nonlinear regression", "ODE models", "Ordinary differential equations", "Pharmacodynamics (PD)", "Pharmacokinetics (PK)" ], "topics": [ "RxODE", "rxode", "rxode2" ] }, { "page": "rxode2-set", "title": "Set the function body of an rxUi object while retaining other object information (like data)", "topics": [ "rxode2<-", "rxode2<-.default", "rxode2<-.function", "RxODE<-", "rxode<-" ] }, { "page": "rxode2parse", "title": "Internal translation to get model variables list", "topics": [ "rxode2parse" ] }, { "page": "rxode2parseAssignTranslation", "title": "This assigns the c level linkages for a roxde2 model", "topics": [ "rxode2parseAssignTranslation" ] }, { "page": "rxode2parseD", "title": "This gives the derivative table for rxode2", "topics": [ "rxode2parseD" ] }, { "page": "rxode2parseAssignPackagesToLoad", "title": "Control the packages that are loaded when a 'rxode2' model dll is loaded", "topics": [ "rxode2parseAssignPackagesToLoad", "rxode2parseGetPackagesToLoad" ] }, { "page": "rxode2parseGetPointerAssignment", "title": "This function gets the currently assigned function pointer assignments", "topics": [ "rxode2parseGetPointerAssignment" ] }, { "page": "rxode2parseGetTranslation", "title": "This function gets the currently assigned translations", "topics": [ "rxode2parseGetTranslation" ] }, { "page": "rxOptExpr", "title": "Optimize rxode2 for computer evaluation", "topics": [ "rxOptExpr" ] }, { "page": "rxord", "title": "Simulate ordinal value", "topics": [ "rxord" ] }, { "page": "rxParams", "title": "Parameters specified by the model", "concept": [ "Query model information" ], "topics": [ "rxParam", "rxParams", "rxParams.rxEt", "rxParams.rxode2", "rxParams.rxSolve" ] }, { "page": "rxParseSuppressMsg", "title": "Respect suppress messages", "topics": [ "rxParseSuppressMsg" ] }, { "page": "rxPkg", "title": "Creates a package from compiled rxode2 models", "topics": [ "rxPkg" ] }, { "page": "rxpois", "title": "Simulate random Poisson variable from threefry generator", "topics": [ "rxpois" ] }, { "page": "rxPp", "title": "Simulate a from a Poisson process", "topics": [ "rxPp" ] }, { "page": "rxPreferredDistributionName", "title": "Change distribution name to the preferred distribution name term", "topics": [ "rxPreferredDistributionName" ] }, { "page": "rxProgress", "title": "rxode2 progress bar functions", "topics": [ "rxProgress", "rxProgressAbort", "rxProgressStop", "rxTick" ] }, { "page": "rxRateDur", "title": "Creates a rxRateDur object", "topics": [ "as.character.rxRateDur", "as.rxRateDur", "rxRateDur", "[.rxRateDur", "[[.rxRateDur" ] }, { "page": "rxRemoveControl", "title": "rxRemoveControl options for UI object", "topics": [ "rxRemoveControl" ] }, { "page": "rxRename", "title": "Rename items inside of a 'rxode2' ui model", "topics": [ ".rxRename", "rename.function", "rename.rxUi", "rxRename", "rxRename.default", "rxRename.function", "rxRename.rxUi" ] }, { "page": "rxReservedKeywords", "title": "A list and description of rxode2 supported reserved keywords", "topics": [ "rxReservedKeywords" ] }, { "page": "rxResidualError", "title": "A description of Rode2 supported residual errors", "topics": [ "rxResidualError" ] }, { "page": "rxRmvn", "title": "Simulate from a (truncated) multivariate normal", "topics": [ "rxRmvn" ] }, { "page": "rxS", "title": "Load a model into a symengine environment", "topics": [ "rxS" ] }, { "page": "rxSetControl", "title": "rxSetControl options for UI object", "topics": [ "rxSetControl" ] }, { "page": "rxSetCovariateNamesForPiping", "title": "Assign covariates for piping", "topics": [ "rxSetCovariateNamesForPiping" ] }, { "page": "rxSetIni0", "title": "Set Initial conditions to time zero instead of the first observed/dosed time", "topics": [ "rxSetIni0" ] }, { "page": "rxSetPipingAuto", "title": "Set the variables for the model piping automatic covarite selection", "topics": [ "rxSetPipingAuto" ] }, { "page": "rxSetProd", "title": "Defunct setting of product", "topics": [ "rxSetProd" ] }, { "page": "rxSetProgressBar", "title": "Set timing for progress bar", "topics": [ "rxSetProgressBar" ] }, { "page": "rxSetSeed", "title": "Set the parallel seed for rxode2 random number generation", "topics": [ "rxSetSeed" ] }, { "page": "rxSetSum", "title": "Defunct setting of sum", "topics": [ "rxSetSum" ] }, { "page": "rxShiny", "title": "Use Shiny to help develop an rxode2 model", "topics": [ "rxShiny", "rxShiny.default", "rxShiny.rxSolve" ] }, { "page": "rxSimThetaOmega", "title": "Simulate Parameters from a Theta/Omega specification", "topics": [ "rxSimThetaOmega" ] }, { "page": "rxSolve", "title": "Options, Solving & Simulation of an ODE/solved system", "topics": [ "predict.function", "predict.rxEt", "predict.rxode2", "predict.rxParams", "predict.rxSolve", "predict.rxUi", "rxControl", "rxSolve", "rxSolve.default", "rxSolve.function", "rxSolve.nlmixr2FitCore", "rxSolve.nlmixr2FitData", "rxSolve.rxode2tos", "rxSolve.rxSolve", "rxSolve.rxUi", "simulate.rxode2", "simulate.rxParams", "simulate.rxSolve", "solve.function", "solve.rxEt", "solve.rxode2", "solve.rxParams", "solve.rxSolve", "solve.rxUi", "update.rxSolve" ] }, { "page": "rxStack", "title": "Stack a solved object for things like default ggplot2 plot", "topics": [ "rxStack" ] }, { "page": "rxState", "title": "State variables", "concept": [ "Query model information" ], "topics": [ "rxState" ] }, { "page": "rxStateOde", "title": "Get the ODE states only", "topics": [ "rxStateOde" ] }, { "page": "rxSumProdModel", "title": "Recast model in terms of sum/prod", "topics": [ "rxSumProdModel" ] }, { "page": "rxSupportedFuns", "title": "Get list of supported functions", "topics": [ "rxSupportedFuns" ] }, { "page": "rxSuppressMsg", "title": "Respect suppress messages", "topics": [ "rxSuppressMsg" ] }, { "page": "rxSymInvChol", "title": "Get Omega^-1 and derivatives", "topics": [ "rxSymInvChol" ] }, { "page": "rxSyncOptions", "title": "Sync options with rxode2 variables", "topics": [ "rxSyncOptions" ] }, { "page": "rxSyntaxFunctions", "title": "A list and description of Rode supported syntax functions", "topics": [ "rxSyntaxFunctions" ] }, { "page": "rxt", "title": "Simulate student t variable from threefry generator", "topics": [ "rxt" ] }, { "page": "rxTempDir", "title": "Get the rxode2 temporary directory", "topics": [ "rxTempDir" ] }, { "page": "rxTheme", "title": "rxTheme is the ggplot2 theme for rxode2 plots", "concept": [ "rxode2 plotting" ], "topics": [ "rxTheme" ] }, { "page": "rxToSE", "title": "rxode2 to symengine environment", "topics": [ ".rxFromSE", ".rxToSE", "rxFromSE", "rxToSE" ] }, { "page": "rxTrans", "title": "Translate the model to C code if needed", "topics": [ "rxTrans", "rxTrans.character", "rxTrans.default" ] }, { "page": "rxUdfUiControl", "title": "Return the control that is being processed or setup control for processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiControl" ] }, { "page": "rxUdfUiData", "title": "Return the data.frame that is being processed or setup data.frame for processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiData" ] }, { "page": "rxUdfUiEst", "title": "Return the current estimation method for the UI processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiEst" ] }, { "page": "rxUdfUiExpr", "title": "Give the expression as a compressed model or expression", "topics": [ "rxUdfUiExpr" ] }, { "page": "rxUdfUiFlag", "title": "Is the expression actually a flag that can be used in the rxUdfUi functions?", "topics": [ "rxUdfUiFlag" ] }, { "page": "rxUdfUiIniDf", "title": "Get the rxode2 iniDf of the current UI being processed (or return NULL)", "topics": [ "rxUdfUiIniDf" ] }, { "page": "rxUdfUiIniLhs", "title": "Return the lhs parsed language expression", "concept": [ "User functions" ], "topics": [ "rxUdfUiIniLhs" ] }, { "page": "rxUdfUiIsValue", "title": "Is the expression actually equal to a value?", "topics": [ "rxUdfUiIsValue" ] }, { "page": "rxUdfUiMv", "title": "Return the model variables that is being processed or setup model variables for processing", "concept": [ "User functions" ], "topics": [ "rxUdfUiMv" ] }, { "page": "rxUdfUiNum", "title": "This gives the current number in the ui of the particular function being called.", "concept": [ "User functions" ], "topics": [ "rxUdfUiNum" ] }, { "page": "rxUdfUiParsing", "title": "Returns if the current ui function is being parsed", "concept": [ "User functions" ], "topics": [ "rxUdfUiParsing" ] }, { "page": "rxUiDecompress", "title": "Compress/Decompress 'rxode2' ui", "topics": [ "rxUiCompress", "rxUiDecompress" ] }, { "page": "rxUiDeparse", "title": "This is a generic function for deparsing certain objects when printing out a rxode2 object. Currently it is used for any meta-information", "topics": [ "rxUiDeparse", "rxUiDeparse.default", "rxUiDeparse.lotriFix", "rxUiDeparse.rxControl" ] }, { "page": "rxUiDevelop", "title": "rxUiDevelop - Enable/Disable rxUi development. Here all $ completions are given", "topics": [ "rxUiDevelop" ] }, { "page": "rxUiGet", "title": "S3 for getting information from UI model", "topics": [ "rxUiGet", "rxUiGet.allCovs", "rxUiGet.cmtLines", "rxUiGet.covLhs", "rxUiGet.default", "rxUiGet.dvidLine", "rxUiGet.etaLhs", "rxUiGet.fun", "rxUiGet.funPartsDigest", "rxUiGet.funPrint", "rxUiGet.funTxt", "rxUiGet.ini", "rxUiGet.iniFun", "rxUiGet.interpLines", "rxUiGet.levelLhs", "rxUiGet.levels", "rxUiGet.lhsCov", "rxUiGet.lhsEta", "rxUiGet.lhsTheta", "rxUiGet.lhsVar", "rxUiGet.lstChr", "rxUiGet.md5", "rxUiGet.model", "rxUiGet.modelDesc", "rxUiGet.modelFun", "rxUiGet.multipleEndpoint", "rxUiGet.muRefTable", "rxUiGet.omega", "rxUiGet.paramsLine", "rxUiGet.props", "rxUiGet.sha1", "rxUiGet.simulationIniModel", "rxUiGet.simulationModel", "rxUiGet.simulationSigma", "rxUiGet.splitDose", "rxUiGet.splitDoseLines", "rxUiGet.state", "rxUiGet.stateDf", "rxUiGet.statePropDf", "rxUiGet.symengineModelNoPrune", "rxUiGet.symengineModelPrune", "rxUiGet.theta", "rxUiGet.thetaLhs", "rxUiGet.thetaLower", "rxUiGet.thetaUpper", "rxUiGet.varLhs" ] }, { "page": "rxunif", "title": "Simulate uniform variable from threefry generator", "topics": [ "rxunif" ] }, { "page": "rxUnloadAll", "title": "Unloads all rxode2 compiled DLLs", "topics": [ "rxUnloadAll" ] }, { "page": "rxUse", "title": "Use model object in your package", "topics": [ "rxUse" ] }, { "page": "rxValidate", "title": "Validate rxode2 This allows easy validation/qualification of nlmixr by running the testing suite on your system.", "topics": [ "rxTest", "rxValidate" ] }, { "page": "rxweibull", "title": "Simulate Weibull variable from threefry generator", "topics": [ "rxweibull" ] }, { "page": "rxWithSeed", "title": "Preserved seed and possibly set the seed", "topics": [ "rxWithPreserveSeed", "rxWithSeed" ] }, { "page": "SELU", "title": "Scaled Exponential Linear Unit (SELU) Activation Function", "concept": [ "Activation Functions" ], "topics": [ "SELU" ] }, { "page": "softplus", "title": "Softplus Activation Function", "concept": [ "Activation Functions" ], "topics": [ "softplus" ] }, { "page": "splitBolus", "title": "Split bolus doses across compartments inside an rxode2 model", "topics": [ "splitBolus" ] }, { "page": "stat_amt", "title": "Dosing/Amt geom/stat", "topics": [ "geom_amt", "stat_amt" ] }, { "page": "stat_cens", "title": "Censoring geom/stat", "topics": [ "geom_cens", "stat_cens" ] }, { "page": "summary.rxode2", "title": "Print expanded information about the rxode2 object.", "topics": [ "summary.rxode2" ] }, { "page": "swapMatListWithCube", "title": "Swaps the matrix list with a cube", "topics": [ "swapMatListWithCube" ] }, { "page": "Swish", "title": "Switch Activation Function", "concept": [ "Activation Functions" ], "topics": [ "Swish" ] }, { "page": "testIniDf", "title": "This function tests if this object is a iniDf as needed by the UI", "concept": [ "Assertions" ], "topics": [ "assertIniDf", "testIniDf" ] }, { "page": "testRxLinCmt", "title": "Test if rxode2 uses linear solved systems", "topics": [ "assertRxLinCmt", "testRxLinCmt" ] }, { "page": "testRxUnbounded", "title": "Test if the rxode2 model has any parameters with user defined boundaries", "concept": [ "Assertions" ], "topics": [ "assertRxUnbounded", "testRxUnbounded", "warnRxBounded" ] }, { "page": "toTrialDuration", "title": "Convert event data to trial duration data A helper function to create a custom event table. The observation time will start from the first event time (baseline) and end at trial duration. The interval is the spacing between each observation.", "topics": [ "toTrialDuration" ] }, { "page": "update.rxUi", "title": "Update for rxUi", "topics": [ "update.rxUi" ] }, { "page": "uppergamma", "title": "uppergamma: upper incomplete gamma function", "topics": [ "uppergamma" ] }, { "page": "zeroRe", "title": "Set random effects and residual error to zero", "concept": [ "Initial conditions" ], "topics": [ "zeroRe" ] } ], "_pkglogo": "https://github.com/nlmixr2/rxode2/raw/HEAD/logo.png", "_readme": "https://github.com/nlmixr2/rxode2/raw/HEAD/README.md", "_rundeps": [ "armadillo4r", "backports", "BH", "cachem", "checkmate", "cli", "cpp11", "cpp4r", "crayon", "data.table", "desc", "digest", "dparser", "farver", "fastmap", "ggplot2", "glue", "gtable", "inline", "isoband", "labeling", "lifecycle", "lotri", "memoise", "PreciseSums", "qs2", "R6", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "RcppParallel", "rex", "rlang", "rxode2ll", "S7", "scales", "sitmo", "StanHeaders", "stringfish", "sys", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "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" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "rxode2-syntax.Rmd", "filename": "rxode2-syntax.html", "title": "rxode2 ODE solving syntax", "engine": "knitr::rmarkdown_notangle", "headings": [ "Introduction", "Creating rxode2 models", "Syntax", "Note", "Example model", "Example", "Interface and data handling between R and the generated C code" ], "created": "2021-12-01 07:08:21", "modified": "2026-04-28 22:17:08", "commits": 7 } ], "_score": 12.444899073925239, "_indexed": true, "_nocasepkg": "rxode2", "_universes": [ "nlmixr2", "mattfidler" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "5.1.2", "date": "2026-06-06T15:27:06.000Z", "distro": "noble", "arch": "aarch64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "9aad8565bcd6217b67ed90cf194c96f536e11139f52959a3bac73b71a3f85eb6", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.7.0", "os": "linux", "version": "5.1.2", "date": "2026-06-06T15:27:33.000Z", "distro": "noble", "arch": "x86_64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "660a80d491bdceeb39d70a2ef2c20e639380486ffb401b14d9215bcb18d5d137", "status": "failure", "check": "ERROR", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.6.0", "os": "linux", "version": "5.1.2", "date": "2026-06-06T15:26:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "a82626a84d53f8af3e53b8f029a281f9291fb8ef39ba47fef654bcb737fa81d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.6.0", "os": "linux", "version": "5.1.2", "date": "2026-06-06T15:26:50.000Z", "distro": "noble", "arch": "x86_64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "87054914244051c40d8bd364c661e8081ac3821a80110133404bdcdf2f3d169b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.5.3", "os": "mac", "version": "5.1.2", "date": "2026-06-06T15:25:44.000Z", "arch": "aarch64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "77a05e871c66bbcb5c44bd93bcba3020bc0faaedfeae97b490f1219a918199a6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.5.3", "os": "mac", "version": "5.1.2", "date": "2026-06-06T15:27:25.000Z", "arch": "x86_64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "b80f0039ce47875498163380ea58db186d08519bc7e928b8eb9deb8b7b1f9648", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.6.0", "os": "mac", "version": "5.1.2", "date": "2026-06-06T15:25:42.000Z", "arch": "aarch64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "c1c121f89a1abd4fc93c04b6428fa167368f804f367e13453952a9440d4ffe59", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.6.0", "os": "mac", "version": "5.1.2", "date": "2026-06-06T15:28:33.000Z", "arch": "x86_64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "8d968d2380097e9d7cb224b19d308baf65c7517a67693da2e95b77e0691b9b0f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.7.0", "os": "win", "version": "5.1.2", "date": "2026-06-06T15:25:59.000Z", "arch": "x86_64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "52eee12f4a4effd27b1460e036d6f8abe73c6ef05cd078aff7ce9b6fad49eaed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.5.3", "os": "win", "version": "5.1.2", "date": "2026-06-06T15:26:01.000Z", "arch": "x86_64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "48cd1f0822377ebacc419335b767817daf72de54bd15eca20a84319f2389f4c2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" }, { "r": "4.6.0", "os": "win", "version": "5.1.2", "date": "2026-06-06T15:26:15.000Z", "arch": "x86_64", "commit": "50e853ec1c1742e4f03b14b432f2a250de423128", "fileid": "8b81bdd95b0b3c48f7f30fdfaff263123dbb0624b3cf23f880b846755f1e572f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/nlmixr2/actions/runs/27065897517" } ] }