{
  "_id": "6a0f5c75acfb0bcc41c596d2",
  "Package": "SynergyLMM",
  "Title": "Statistical Framework for in Vivo Drug Combination Studies",
  "Version": "1.1.3.9000",
  "Authors@R": "c(person(\"Rafael\", \"Romero-Becerra\", , \"rafrombec@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-3935-2647\")),\nperson(\"Zhi\", \"Zhao\", email = \"zhi.zhao@medisin.uio.no\", role = c(\"ctb\")),\nperson(\"Tero\", \"Aittokallio\", email = \"t.a.aittokallio@medisin.uio.no\", role = c(\"ctb\")))",
  "Description": "A framework for evaluating drug combination effects in\npreclinical in vivo studies. 'SynergyLMM' provides functions to\nanalyze longitudinal tumor growth experiments using\nmixed-effects models, perform time-resolved analyses of synergy\nand antagonism, evaluate model diagnostics and performance, and\nassess both post-hoc and a priori statistical power. The\ncalculation of drug combination synergy follows the statistical\nframework provided by Demidenko and Miller (2019,\n<doi:10.1371/journal.pone.0224137>). The implementation and\nanalysis of linear mixed-effect models is based on the methods\ndescribed by Pinheiro and Bates (2000, <doi:10.1007/b98882>),\nand Gałecki and Burzykowski (2013,\n<doi:10.1007/978-1-4614-3900-4>).",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "Config/testthat/edition": "3",
  "LazyData": "true",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/RafRomB/SynergyLMM",
  "BugReports": "https://github.com/RafRomB/SynergyLMM/issues",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "cmake make libicu-dev",
  "Repository": "https://rafromb.r-universe.dev",
  "Date/Publication": "2026-05-21 14:44:13 UTC",
  "RemoteUrl": "https://github.com/rafromb/synergylmm",
  "RemoteRef": "HEAD",
  "RemoteSha": "2b3f7f30698fd782346170dc96a689d8b84e9070",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-21 17:02:29 UTC",
    "User": "root"
  },
  "Author": "Rafael Romero-Becerra [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3935-2647>),\nZhi Zhao [ctb],\nTero Aittokallio [ctb]",
  "Maintainer": "Rafael Romero-Becerra <rafrombec@gmail.com>",
  "MD5sum": "df4c605920222c08ac1623b02ac91cc3",
  "_user": "rafromb",
  "_type": "src",
  "_file": "SynergyLMM_1.1.3.9000.tar.gz",
  "_fileid": "63457056e127d12b071a3adc9c026d09c40662336bb624471d038209df8ed452",
  "_filesize": 6533675,
  "_sha256": "63457056e127d12b071a3adc9c026d09c40662336bb624471d038209df8ed452",
  "_created": "2026-05-21T17:02:29.000Z",
  "_published": "2026-05-21T19:26:45.429Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77251601707,
      "time": 304,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7142309401"
    },
    {
      "job": 77251601585,
      "time": 305,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7142309991"
    },
    {
      "job": 77251601390,
      "time": 335,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7142307376"
    },
    {
      "job": 77251601183,
      "time": 300,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7142296776"
    },
    {
      "job": 77251600937,
      "time": 290,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7142194580"
    },
    {
      "job": 77251600955,
      "time": 130,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7145214874"
    },
    {
      "job": 77251601431,
      "time": 270,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7142296945"
    },
    {
      "job": 77251601818,
      "time": 261,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7142293473"
    },
    {
      "job": 77251601295,
      "time": 276,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7142299546"
    }
  ],
  "_buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/rafromb/synergylmm",
  "_commit": {
    "id": "2b3f7f30698fd782346170dc96a689d8b84e9070",
    "author": "RafRomB <rafrombec@gmail.com>",
    "committer": "RafRomB <rafrombec@gmail.com>",
    "message": "CRAN-SUBMISSION delete\n",
    "time": 1779374653
  },
  "_maintainer": {
    "name": "Rafael Romero-Becerra",
    "email": "rafrombec@gmail.com",
    "login": "rafromb",
    "orcid": "0000-0003-3935-2647",
    "description": "",
    "uuid": 104798320
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.0",
      "role": "Depends"
    },
    {
      "package": "magrittr",
      "version": ">= 2.0.3",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "version": ">= 1.1.4",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.5.1",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "version": ">= 1.1.3",
      "role": "Imports"
    },
    {
      "package": "nlme",
      "version": ">= 3.1-165",
      "role": "Imports"
    },
    {
      "package": "nlmeU",
      "role": "Imports"
    },
    {
      "package": "fBasics",
      "role": "Imports"
    },
    {
      "package": "car",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "performance",
      "role": "Imports"
    },
    {
      "package": "lattice",
      "role": "Imports"
    },
    {
      "package": "marginaleffects",
      "role": "Imports"
    },
    {
      "package": "clubSandwich",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "rafromb",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 6
    },
    {
      "week": "2025-23",
      "n": 31
    },
    {
      "week": "2025-24",
      "n": 1
    },
    {
      "week": "2025-26",
      "n": 5
    },
    {
      "week": "2025-27",
      "n": 6
    },
    {
      "week": "2025-28",
      "n": 5
    },
    {
      "week": "2025-29",
      "n": 3
    },
    {
      "week": "2025-30",
      "n": 5
    },
    {
      "week": "2025-31",
      "n": 15
    },
    {
      "week": "2025-34",
      "n": 7
    },
    {
      "week": "2025-40",
      "n": 15
    },
    {
      "week": "2025-41",
      "n": 1
    },
    {
      "week": "2025-47",
      "n": 8
    },
    {
      "week": "2025-48",
      "n": 2
    },
    {
      "week": "2026-20",
      "n": 4
    },
    {
      "week": "2026-21",
      "n": 3
    }
  ],
  "_tags": [
    {
      "name": "v1.1.0",
      "date": "2025-07-29"
    },
    {
      "name": "v1.1.2",
      "date": "2025-11-20"
    },
    {
      "name": "v1.1.3",
      "date": "2026-05-11"
    }
  ],
  "_stars": 3,
  "_contributors": [
    {
      "user": "rafromb",
      "count": 328,
      "uuid": 104798320
    },
    {
      "user": "zhizuio",
      "count": 3,
      "uuid": 39630023
    },
    {
      "user": "teunbrand",
      "count": 1,
      "uuid": 49372158
    }
  ],
  "_userbio": {
    "uuid": 104798320,
    "type": "user",
    "name": "Rafael Romero-Becerra"
  },
  "_downloads": {
    "count": 291,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SynergyLMM"
  },
  "_devurl": "https://github.com/rafromb/synergylmm",
  "_searchresults": 4,
  "_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/SynergyLMM.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/rafromb/synergylmm",
  "_realowner": "rafromb",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.0",
      "date": "2025-02-06"
    },
    {
      "version": "1.0.1",
      "date": "2025-02-07"
    },
    {
      "version": "1.1.0",
      "date": "2025-08-01"
    },
    {
      "version": "1.1.1",
      "date": "2025-08-22"
    },
    {
      "version": "1.1.2",
      "date": "2025-11-20"
    },
    {
      "version": "1.1.3",
      "date": "2026-05-12"
    }
  ],
  "_exports": [
    "%>%",
    "APrioriPwr",
    "CookDistance",
    "getRTV",
    "lmmModel",
    "lmmModel_estimates",
    "lmmSynergy",
    "logLikSubjectDisplacements",
    "ObsvsPred",
    "plot_lmmModel",
    "plot_lmmSynergy",
    "plot_ObsvsPred",
    "plot_ranefDiagnostics",
    "plot_residDiagnostics",
    "plot_SynergyLMM",
    "PostHocPwr",
    "Pwr",
    "PwrSampleSize",
    "PwrTime",
    "ranefDiagnostics",
    "residDiagnostics",
    "simulateTumorGrowth"
  ],
  "_datasets": [
    {
      "name": "grwth_data",
      "title": "Example Tumor Growth Data",
      "object": "grwth_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "subject",
        "Time",
        "Treatment",
        "TumorVolume"
      ],
      "rows": 352,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "APrioriPwr",
      "title": "_A Priori_ Synergy Power Analysis Based on Variability and Drug Effect",
      "topics": [
        "APrioriPwr"
      ]
    },
    {
      "page": "CookDistance",
      "title": "Cook's distance for individual subjects",
      "topics": [
        "CookDistance"
      ]
    },
    {
      "page": "getRTV",
      "title": "Helper function to calculate the relative tumor volume from an imput data frame of tumor growth",
      "topics": [
        "getRTV"
      ]
    },
    {
      "page": "grwth_data",
      "title": "Example Tumor Growth Data",
      "topics": [
        "grwth_data"
      ]
    },
    {
      "page": "lmmModel",
      "title": "Linear Mixed Effect Model for Tumor Growth",
      "topics": [
        "lmmModel"
      ]
    },
    {
      "page": "lmmModel_estimates",
      "title": "Get estimates from a linear mixed model of tumor growth data",
      "topics": [
        "lmmModel_estimates",
        "lmmModel_estimates.explme",
        "lmmModel_estimates.gompertzlme"
      ]
    },
    {
      "page": "lmmSynergy",
      "title": "Synergy calculation using linear-mixed and non-linear mixed-effect models",
      "topics": [
        "lmmSynergy",
        "lmmSynergy.explme",
        "lmmSynergy.gompertzlme"
      ]
    },
    {
      "page": "logLikSubjectDisplacements",
      "title": "Likelihood displacements for the model",
      "topics": [
        "logLikSubjectDisplacements"
      ]
    },
    {
      "page": "ObsvsPred",
      "title": "Observed vs predicted values and performance of the model",
      "topics": [
        "ObsvsPred"
      ]
    },
    {
      "page": "plot_lmmModel",
      "title": "Plotting of tumor growth data from a fitted model",
      "topics": [
        "plot_lmmModel"
      ]
    },
    {
      "page": "plot_lmmSynergy",
      "title": "Plotting synergy results",
      "topics": [
        "plot_lmmSynergy"
      ]
    },
    {
      "page": "plot_ObsvsPred",
      "title": "Plots of Observed vs Predicted Values",
      "topics": [
        "plot_ObsvsPred"
      ]
    },
    {
      "page": "plot_ranefDiagnostics",
      "title": "Plots for random effects diagnostics",
      "topics": [
        "plot_ranefDiagnostics"
      ]
    },
    {
      "page": "plot_residDiagnostics",
      "title": "Plots for residuals diagnostics",
      "topics": [
        "plot_residDiagnostics"
      ]
    },
    {
      "page": "plot_SynergyLMM",
      "title": "Plotting SynergyLMM results",
      "topics": [
        "plot_SynergyLMM"
      ]
    },
    {
      "page": "PostHocPwr",
      "title": "Post hoc power calculation based on simulations of the synergy evaluation using LMM.",
      "topics": [
        "PostHocPwr"
      ]
    },
    {
      "page": "Pwr",
      "title": "Calculates power based on a model fit",
      "topics": [
        "Pwr"
      ]
    },
    {
      "page": "Pwr.lme",
      "title": "Performs power calculations",
      "topics": [
        "Pwr.lme"
      ]
    },
    {
      "page": "PwrSampleSize",
      "title": "_A Priori_ Synergy Power Analysis Based on Sample Size",
      "topics": [
        "PwrSampleSize"
      ]
    },
    {
      "page": "PwrTime",
      "title": "_A Priori_ Synergy Power Analysis Based on Time",
      "topics": [
        "PwrTime"
      ]
    },
    {
      "page": "ranefDiagnostics",
      "title": "Diagnostics of random effects of the linear mixed model",
      "topics": [
        "ranefDiagnostics"
      ]
    },
    {
      "page": "residDiagnostics",
      "title": "Diagnostics of residuals of the linear mixed model",
      "topics": [
        "residDiagnostics"
      ]
    },
    {
      "page": "simulateTumorGrowth",
      "title": "Helper function to simulate tumor growth data for a two-drug combination experiment.",
      "topics": [
        "simulateTumorGrowth"
      ]
    }
  ],
  "_pkglogo": "https://github.com/rafromb/synergylmm/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/rafromb/synergylmm/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "bayestestR",
    "boot",
    "broom",
    "car",
    "carData",
    "checkmate",
    "cli",
    "clubSandwich",
    "colorspace",
    "cowplot",
    "cpp11",
    "data.table",
    "datawizard",
    "Deriv",
    "doBy",
    "dplyr",
    "farver",
    "fBasics",
    "forecast",
    "Formula",
    "fracdiff",
    "generics",
    "ggplot2",
    "glue",
    "gss",
    "gtable",
    "insight",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "lme4",
    "lmtest",
    "magrittr",
    "marginaleffects",
    "MASS",
    "Matrix",
    "MatrixModels",
    "mgcv",
    "microbenchmark",
    "minqa",
    "modelr",
    "nlme",
    "nlmeU",
    "nloptr",
    "nnet",
    "numDeriv",
    "pbkrtest",
    "performance",
    "pillar",
    "pkgconfig",
    "purrr",
    "quantreg",
    "R6",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "S7",
    "sandwich",
    "scales",
    "SparseM",
    "spatial",
    "stabledist",
    "stringi",
    "stringr",
    "survival",
    "tibble",
    "tidyr",
    "tidyselect",
    "timeDate",
    "timeSeries",
    "urca",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "SynergyLMM.Rmd",
      "filename": "SynergyLMM.html",
      "title": "SynergyLMM - Guided Tutorial",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "0. Recommended Workflow",
        "1. Data Upload and Model Fit",
        "1.1 Exponential Model Fitting",
        "1.2 Gompertz Model Fitting",
        "1.3 Model Estimates",
        "2. Model Diagnostics",
        "2.1 Random Effects Diagnostics",
        "2.2 Residual Diagnostics",
        "2.3 Solutions for Violations of Model Diagnostics",
        "2.4 Model Performance",
        "2.5 Influential Diagnostics",
        "3. Synergy Analysis",
        "4. Power Analysis",
        "4.1 Post Hoc Power Analysis",
        "4.2 A Priori Power Analysis",
        "Sample Size Power Analysis",
        "Time Power Analysis",
        "Variability Power Analysis",
        "5. Citation"
      ],
      "created": "2024-11-11 15:19:58",
      "modified": "2025-11-20 10:57:00",
      "commits": 12
    }
  ],
  "_score": 5.681241237375588,
  "_indexed": true,
  "_nocasepkg": "synergylmm",
  "_universes": [
    "rafromb"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1.3.9000",
      "date": "2026-05-21T17:05:15.000Z",
      "distro": "noble",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "5a6cebceab8d4db0c7c2202260c9e7480476d43fc6a5ac5bafe3553faf13b1ce",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.1.3.9000",
      "date": "2026-05-21T17:05:21.000Z",
      "distro": "noble",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "b7cfeaa9b012d7328284560061ddda59bc5407b9c91ce7b7d8e8a155e2b43d8f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1.3.9000",
      "date": "2026-05-21T17:05:34.000Z",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "f030372b278435aa86988cc106f55040f212c8f29a7bd3eaef0c509836ffd3a6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.1.3.9000",
      "date": "2026-05-21T17:05:04.000Z",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "b2485f427e0a3aa067d2d17b344a4141e750a24913d2c1ca27ca7ba696b88d1c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1.3.9000",
      "date": "2026-05-21T19:26:28.000Z",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "fa15ac0df505db3a8e648214098ac957598f85f497f4027e563717853752c951",
      "status": "success",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1.3.9000",
      "date": "2026-05-21T17:04:12.000Z",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "ab729d4b5633ee0d215cc60c09a67ae0a773c0b57fc98adccf9af84ff9b0cd92",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1.3.9000",
      "date": "2026-05-21T17:04:07.000Z",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "304825ddd095adddf345451fbf8fc27a36a2e0fa1b412f89b828b85f3bef6d67",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.1.3.9000",
      "date": "2026-05-21T17:04:14.000Z",
      "commit": "2b3f7f30698fd782346170dc96a689d8b84e9070",
      "fileid": "b90deae6ea68fd9d3d5fb61b84501cfe05fa10bd882df6bffa5a2c30e130d585",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/rafromb/actions/runs/26240588065"
    }
  ]
}