{
  "_id": "6a1d35de1d7bb097a0a3cdd7",
  "Package": "clinDR",
  "Version": "2.5.2",
  "Date": "2025-09-30",
  "Title": "Simulation and Analysis Tools for Clinical Dose Response\nModeling",
  "Authors@R": "c(person(\"Neal\",\"Thomas\",role=c(\"aut\",\"cre\"),\nemail=\"snthomas99@gmail.com\",comment=c(ORCID = '0000-0002-1915-8487')),\nperson(\"Jing\",\"Wu\",role=\"aut\",\nemail=\"Jing_Wu@uri.edu\"),\nperson(\"Mike K.\",\"Smith\",role=\"aut\",\nemail=\"mike.k.smith@pfizer.com\"))",
  "Maintainer": "Neal Thomas <snthomas99@gmail.com>",
  "Description": "Bayesian and ML Emax model fitting, graphics and\nsimulation for clinical dose response.  The summary data from\nthe dose response meta-analyses in Thomas, Sweeney, and\nSomayaji (2014) <doi:10.1080/19466315.2014.924876> and Thomas\nand Roy (2016) <doi:10.1080/19466315.2016.1256229> Wu,\nBanerjee, Jin, Menon, Martin, and Heatherington(2017)\n<doi:10.1177/0962280216684528> are included in the package. The\nprior distributions for the Bayesian analyses default to the\nposterior predictive distributions derived from these\nreferences.",
  "License": "GPL (>= 2)",
  "NeedsCompilation": "no",
  "Author": "Neal Thomas [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-1915-8487>), Jing Wu [aut], Mike\nK. Smith [aut]",
  "Packaged": {
    "Date": "2026-06-01 07:11:43 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev zlib1g-dev",
  "Repository": "https://snthomas99.r-universe.dev",
  "Date/Publication": "2025-10-02 19:30:02 UTC",
  "RemoteUrl": "https://github.com/cran/clinDR",
  "RemoteRef": "HEAD",
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  "_user": "snthomas99",
  "_type": "src",
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  "_created": "2026-06-01T07:11:43.000Z",
  "_published": "2026-06-01T07:33:50.151Z",
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    "author": "Neal Thomas <snthomas99@gmail.com>",
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    "message": "version 2.5.2\n",
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    "email": "snthomas99@gmail.com",
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    "uuid": 10768225,
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  "_dependencies": [
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    {
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  "_rbuild": "4.6.0",
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
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    "extra/contents.json",
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  "_realowner": "snthomas99",
  "_cranurl": false,
  "_releases": [
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    },
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    },
    {
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  "_exports": [
    "bpchkMonoEmax",
    "checkMonoEmax",
    "coef.emaxsim",
    "coef.emaxsimB",
    "coef.fitEmax",
    "coef.fitEmaxB",
    "compileStanModels",
    "DRDensityPlot",
    "emaxalt",
    "emaxfun",
    "emaxPrior.control",
    "emaxsim",
    "emaxsimB",
    "fitEmax",
    "fitEmaxB",
    "FixedMean",
    "mcmc.control",
    "nllogis",
    "plot.emaxsim",
    "plot.emaxsimB",
    "plot.emaxsimBobj",
    "plot.emaxsimobj",
    "plot.fitEmax",
    "plot.fitEmaxB",
    "plot.plotB",
    "plotB",
    "plotBdensity",
    "plotD",
    "predict.emaxalt",
    "predict.emaxsim",
    "predict.emaxsimB",
    "predict.emaxsimBobj",
    "predict.emaxsimobj",
    "predict.fitEmax",
    "predict.fitEmaxB",
    "print.emaxPrior",
    "print.emaxsim",
    "print.emaxsimB",
    "print.emaxsimBobj",
    "print.emaxsimobj",
    "print.fitEmax",
    "print.fitEmaxB",
    "prior.control",
    "RandEmax",
    "randomEmax",
    "runSimulations",
    "SeEmax",
    "selEstan",
    "showStanModels",
    "sigma.emaxsim",
    "sigma.emaxsimB",
    "sigma.fitEmax",
    "sigma.fitEmaxB",
    "solveDose",
    "solveEmax",
    "startEmax",
    "summary.emaxsim",
    "summary.emaxsimB",
    "summary.emaxsimBobj",
    "summary.emaxsimobj",
    "summary.fitEmax",
    "summary.fitEmaxB",
    "targetBeta",
    "targetCI",
    "targetD",
    "update.emaxsimobj",
    "vcov.emaxsim",
    "vcov.fitEmax"
  ],
  "_datasets": [
    {
      "name": "metaData",
      "title": "Dose response data from several published meta-analyses",
      "object": "metaData",
      "file": "metaData.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "taid",
        "protid",
        "drugid",
        "gname",
        "bname",
        "drugtype",
        "route",
        "routeShort",
        "oralForm",
        "fdaapproved",
        "metasource",
        "protno",
        "nctno",
        "protyear",
        "design",
        "actcomp",
        "etype",
        "poptype",
        "primsource",
        "primtype",
        "primtime",
        "timeunit",
        "indication",
        "broadta",
        "endpointLong",
        "endpointShort",
        "dose",
        "regimen",
        "tload",
        "nload",
        "primregimen",
        "rslt",
        "se",
        "sd",
        "lcl",
        "ucl",
        "alpha",
        "sampsize",
        "ittsize",
        "pmiss"
      ],
      "rows": 1797,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "clinDR-package",
      "title": "Bayesian and maximum likelihood Emax model fitting, graphics and simulation for clinical dose response.",
      "topics": [
        "clinDR-package"
      ]
    },
    {
      "page": "Brextract",
      "title": "Extract a simulation from the output of emaxsim",
      "topics": [
        "[.emaxsim"
      ]
    },
    {
      "page": "BrextractB",
      "title": "Extract a simulation from the output of emaxsimB",
      "topics": [
        "[.emaxsimB"
      ]
    },
    {
      "page": "bpchkMonoEmax",
      "title": "Bayes posterior predictive test for Emax (monotone) model fit",
      "topics": [
        "bpchkMonoEmax"
      ]
    },
    {
      "page": "checkMonoEmax",
      "title": "Bayes posterior predictive test for Emax (monotone) model fit",
      "topics": [
        "checkMonoEmax"
      ]
    },
    {
      "page": "coef",
      "title": "Extract Emax model parameter estimates",
      "topics": [
        "coef.emaxsim",
        "coef.emaxsimB",
        "coef.fitEmax",
        "coef.fitEmaxB"
      ]
    },
    {
      "page": "compileStanModels",
      "title": "Compile 'rstan' Emax models after package 'clinDR' is installed",
      "topics": [
        "compileStanModels"
      ]
    },
    {
      "page": "DRDensityPlot",
      "title": "Plot Bayes or confidence interval density contours over a grid of points (usually dose or time)",
      "topics": [
        "DRDensityPlot"
      ]
    },
    {
      "page": "emaxalt",
      "title": "Fit 4- or 3-parameter Emax model substituting simpler curves if convergence not achieved.",
      "topics": [
        "emaxalt"
      ]
    },
    {
      "page": "emaxfun",
      "title": "Vectorized versions of the hyperbolic and sigmoidal Emax models",
      "topics": [
        "emaxfun"
      ]
    },
    {
      "page": "emaxPrior.control",
      "title": "Set the parameters of the prior distribution for the Emax model implemented in 'fitEmaxB'.",
      "topics": [
        "emaxPrior.control"
      ]
    },
    {
      "page": "emaxsim",
      "title": "Simulate Emax maximum likelihood estimation",
      "topics": [
        "emaxsim"
      ]
    },
    {
      "page": "emaxsimB",
      "title": "Simulate Emax Bayesian estimation",
      "topics": [
        "emaxsimB"
      ]
    },
    {
      "page": "emaxsolve",
      "title": "Solve Emax function for target value",
      "topics": [
        "solveDose",
        "solveEmax"
      ]
    },
    {
      "page": "fitEmax",
      "title": "ML fit of hyperbolic or sigmoidal Emax models to continuous/binary dose response data.",
      "topics": [
        "fitEmax"
      ]
    },
    {
      "page": "fitEmaxB",
      "title": "Bayesian fit of hyperbolic or sigmoidal Emax models to continuous/binary dose response data.",
      "topics": [
        "fitEmaxB"
      ]
    },
    {
      "page": "FixedMean",
      "title": "Fixed means (proportions) random data constructor for emaxsim for continuous or binary data",
      "topics": [
        "FixedMean"
      ]
    },
    {
      "page": "mcmc.control",
      "title": "Settings for 'restan' execution in function 'fitEmaxB'",
      "topics": [
        "mcmc.control"
      ]
    },
    {
      "page": "metaData",
      "title": "Dose response data from several published meta-analyses",
      "topics": [
        "metaData"
      ]
    },
    {
      "page": "nllogis",
      "title": "The negative log likelihood function for a 3- or 4- parameter Emax model on the logit scale for binary dose response.",
      "topics": [
        "nllogis"
      ]
    },
    {
      "page": "plot.emaxsim",
      "title": "Plot the output of emaxsim",
      "topics": [
        "plot.emaxsim"
      ]
    },
    {
      "page": "plot.emaxsimB",
      "title": "Plot the output of emaxsimB",
      "topics": [
        "plot.emaxsimB"
      ]
    },
    {
      "page": "plot.emaxsimBobj",
      "title": "Plot dose response from a data set generated by emaxsimB",
      "topics": [
        "plot.emaxsimBobj"
      ]
    },
    {
      "page": "plot.emaxsimobj",
      "title": "Plot dose response from a data set generated by emaxsim",
      "topics": [
        "plot.emaxsimobj"
      ]
    },
    {
      "page": "plot.fitEmax",
      "title": "Plot a Emax model and dose group means.",
      "topics": [
        "plot.fitEmax"
      ]
    },
    {
      "page": "plot.fitEmaxB",
      "title": "Plot a Emax model and dose group means.",
      "topics": [
        "plot.fitEmaxB"
      ]
    },
    {
      "page": "plot.plotB",
      "title": "Plot Bayes dose response curve and dose group means",
      "topics": [
        "plot.plotB"
      ]
    },
    {
      "page": "plotB",
      "title": "Plot Bayes dose response curve and dose group means",
      "topics": [
        "plotB"
      ]
    },
    {
      "page": "plotBdensity",
      "title": "Density plot displaying Bayes prior or posterior dose response",
      "topics": [
        "plotBdensity"
      ]
    },
    {
      "page": "plotD",
      "title": "Basic plot of dose group means",
      "topics": [
        "plotD"
      ]
    },
    {
      "page": "predict.emaxalt",
      "title": "Mean response and SE for specified doses for a simulated object output by function emaxalt",
      "topics": [
        "predict.emaxalt"
      ]
    },
    {
      "page": "predict.emaxsim",
      "title": "Mean response and SE for specified doses for each replicate data set in an emaxsim object",
      "topics": [
        "predict.emaxsim"
      ]
    },
    {
      "page": "predict.emaxsimB",
      "title": "Mean response and SE for each replicate data set in an emaxsimB object",
      "topics": [
        "predict.emaxsimB"
      ]
    },
    {
      "page": "predict.emaxsimBobj",
      "title": "Mean response estimates (posterior means) and SE (posterior SD) for specified doses for a simulated emaxsimBobj object",
      "topics": [
        "predict.emaxsimBobj"
      ]
    },
    {
      "page": "predict.emaxsimobj",
      "title": "Mean response and SE for specified doses for a simulated emaxsimobj object",
      "topics": [
        "predict.emaxsimobj"
      ]
    },
    {
      "page": "predict.fitEmax",
      "title": "Estimated mean/proportion and confidence intervals derived from the maximum likelihood fit of a 3- or 4- parameter Emax model.",
      "topics": [
        "predict.fitEmax"
      ]
    },
    {
      "page": "predict.fitEmaxB",
      "title": "Estimated mean and posterior intervals derived from a Bayesian hyperbolic or sigmiodial Emax model.",
      "topics": [
        "predict.fitEmaxB"
      ]
    },
    {
      "page": "print.emaxsim",
      "title": "Print simulation output from emaxsim",
      "topics": [
        "print.emaxsim"
      ]
    },
    {
      "page": "print.emaxsimB",
      "title": "Print simulation output from emaxsimB",
      "topics": [
        "print.emaxsimB"
      ]
    },
    {
      "page": "print.emaxsimBobj",
      "title": "Print a summary of the fitted Emax model",
      "topics": [
        "print.emaxsimBobj"
      ]
    },
    {
      "page": "print.emaxsimobj",
      "title": "Print a data set generated by emaxsim",
      "topics": [
        "print.emaxsimobj"
      ]
    },
    {
      "page": "print.fitEmax",
      "title": "Print a summary of the fitted Emax model",
      "topics": [
        "print.fitEmax"
      ]
    },
    {
      "page": "print.fitEmaxB",
      "title": "Print a summary of the fitted Bayesian Emax model",
      "topics": [
        "print.fitEmaxB"
      ]
    },
    {
      "page": "print.emaxPrior",
      "title": "Print protocol or sap text describing the prior distribution for the model parameters of the input emaxPrior object",
      "topics": [
        "print.emaxPrior"
      ]
    },
    {
      "page": "prior.control",
      "title": "Set the parameters of the prior distribution for the Emax model implemented in 'fitEmaxB'.",
      "topics": [
        "prior.control"
      ]
    },
    {
      "page": "RandEmax",
      "title": "Random data constructor function for emaxsim creating random parameters for an Emax model for continuous or binary data.",
      "topics": [
        "RandEmax"
      ]
    },
    {
      "page": "randomEmax",
      "title": "Random data constructor function for emaxsim(B) creating random parameters for an Emax model for continuous or binary data.",
      "topics": [
        "randomEmax"
      ]
    },
    {
      "page": "runSimulations",
      "title": "Shiny app for function 'emaxsim(B)'",
      "topics": [
        "runSimulations"
      ]
    },
    {
      "page": "SeEmax",
      "title": "Asymptotic SE for dose response estimates from a 3- or 4- parameter Emax model",
      "topics": [
        "SeEmax"
      ]
    },
    {
      "page": "selEstan",
      "title": "Select a pre-compiled 'rstan' Emax model",
      "topics": [
        "selEstan"
      ]
    },
    {
      "page": "showStanModels",
      "title": "Display 'STAN' model code.",
      "topics": [
        "showStanModels"
      ]
    },
    {
      "page": "sigma",
      "title": "Extract Emax model residual SD estimates",
      "topics": [
        "sigma.emaxsim",
        "sigma.emaxsimB",
        "sigma.fitEmax",
        "sigma.fitEmaxB"
      ]
    },
    {
      "page": "startEmax",
      "title": "Compute starting parameter values for the 3- or 4- Emax model.",
      "topics": [
        "startEmax"
      ]
    },
    {
      "page": "summary.emaxsim",
      "title": "Summary of output of emaxsim",
      "topics": [
        "summary.emaxsim"
      ]
    },
    {
      "page": "summary.emaxsimB",
      "title": "Summary of output of emaxsimB",
      "topics": [
        "summary.emaxsimB"
      ]
    },
    {
      "page": "summary.emaxsimBobj",
      "title": "Summarize Emax fit to a data set generated by emaxsimB",
      "topics": [
        "summary.emaxsimBobj"
      ]
    },
    {
      "page": "summary.emaxsimobj",
      "title": "Summarize Emax fit to a data set generated by emaxsim",
      "topics": [
        "summary.emaxsimobj"
      ]
    },
    {
      "page": "summary.fitEmax",
      "title": "Print a summary of the fitted Emax model",
      "topics": [
        "summary.fitEmax"
      ]
    },
    {
      "page": "summary.fitEmaxB",
      "title": "Print a summary of the fitted Bayesian Emax model",
      "topics": [
        "summary.fitEmaxB"
      ]
    },
    {
      "page": "targetBeta",
      "title": "Find a scaled Beta distribution matching specified probabilities",
      "topics": [
        "targetBeta"
      ]
    },
    {
      "page": "targetCI",
      "title": "Compute the dose with confidence interval exceeding a target change from placebo for each simulated example in an emaxsim object.",
      "topics": [
        "targetCI"
      ]
    },
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