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  "Description": "Fast simulation from ordinary differential equation (ODE)\nbased models typically employed in quantitative pharmacology\nand systems biology.",
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  "Date/Publication": "2026-05-20 02:44:58 UTC",
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    "mrgsim_e",
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      "name": "exBoot",
      "title": "Example input data sets",
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      "fields": [
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      "file": "extran1.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "amt",
        "cmt",
        "time",
        "addl",
        "ii",
        "rate",
        "evid"
      ],
      "rows": 9,
      "table": true,
      "tojson": true
    },
    {
      "name": "extran2",
      "title": "Example input data sets",
      "object": "extran2",
      "file": "extran2.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "time",
        "cmt",
        "evid",
        "amt",
        "addl",
        "ii",
        "rate"
      ],
      "rows": 714,
      "table": true,
      "tojson": true
    },
    {
      "name": "extran3",
      "title": "Example input data sets",
      "object": "extran3",
      "file": "extran3.RData",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "time",
        "cmt",
        "evid",
        "amt",
        "addl",
        "ii",
        "rate",
        "CL",
        "VC",
        "KA"
      ],
      "rows": 714,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "mrgsolve_package",
      "title": "mrgsolve: Simulate from ODE-Based Models",
      "topics": [
        "mrgsolve-package",
        "mrgsolve"
      ]
    },
    {
      "page": "ev_extract",
      "title": "Select columns from an ev object",
      "topics": [
        "$,ev-method",
        "[[,ev-method"
      ]
    },
    {
      "page": "mrgmod_extract",
      "title": "Select parameter values from a model object",
      "topics": [
        "$,mrgmod-method",
        "[,mrgmod-method",
        "[[,mrgmod-method"
      ]
    },
    {
      "page": "aboutsolver",
      "title": "About the lsoda differential equation solver used by mrgsolve",
      "topics": [
        "aboutsolver"
      ]
    },
    {
      "page": "matrix_converters",
      "title": "Coerce R objects to block or diagonal matrices",
      "topics": [
        "as_bmat",
        "as_bmat,ANY-method",
        "as_bmat,data.frame-method",
        "as_bmat,list-method",
        "as_bmat,numeric-method",
        "as_cmat",
        "as_dmat",
        "as_dmat,ANY-method",
        "as_dmat,data.frame-method",
        "as_dmat,list-method",
        "as_dmat,numeric-method"
      ]
    },
    {
      "page": "as_data_set",
      "title": "Create a simulation data set from ev objects or data frames",
      "topics": [
        "as_data_set",
        "as_data_set,data.frame-method",
        "as_data_set,ev-method"
      ]
    },
    {
      "page": "as_deslist",
      "title": "Create a list of designs from a data frame",
      "topics": [
        "as_deslist"
      ]
    },
    {
      "page": "as.ev",
      "title": "Coerce an object to class ev",
      "topics": [
        "as.ev",
        "as.ev,data.frame-method",
        "as.ev,ev-method"
      ]
    },
    {
      "page": "as.list-mrgmod-method",
      "title": "Coerce a model object to list",
      "topics": [
        "as.list,mrgmod-method"
      ]
    },
    {
      "page": "as.list-mrgsims-method",
      "title": "Coerce an mrgsims object to list",
      "topics": [
        "as.list,mrgsims-method"
      ]
    },
    {
      "page": "BLOCK_PARSE",
      "title": "Functions to parse code blocks",
      "topics": [
        "BLOCK_PARSE",
        "CAPTURE",
        "CMT",
        "FIXED",
        "HANDLEMATRIX",
        "INIT",
        "PARAM",
        "THETA"
      ]
    },
    {
      "page": "blocks",
      "title": "Return the code blocks from a model specification file",
      "topics": [
        "blocks",
        "blocks,character-method",
        "blocks,mrgmod-method"
      ]
    },
    {
      "page": "matlist_ops",
      "title": "Operations with matlist objects",
      "topics": [
        "c,matlist-method"
      ]
    },
    {
      "page": "tgrid_ops",
      "title": "Operations with tgrid objects",
      "topics": [
        "*,tgrid,numeric-method",
        "*,tgrids,numeric-method",
        "+,tgrid,numeric-method",
        "+,tgrids,numeric-method",
        "c,tgrid-method",
        "c,tgrids-method",
        "tgrids_*_numeric",
        "tgrids_+_numeric",
        "tgrid_*_numeric",
        "tgrid_+_numeric"
      ]
    },
    {
      "page": "carry_out",
      "title": "Select items to carry into simulated output",
      "topics": [
        "carry.out",
        "carry_out"
      ]
    },
    {
      "page": "check_data_names",
      "title": "Check input data set names against model parameters",
      "topics": [
        "check_data_names"
      ]
    },
    {
      "page": "cmtn",
      "title": "Get the compartment number from a compartment name",
      "topics": [
        "cmtn",
        "cmtn,mrgmod-method"
      ]
    },
    {
      "page": "code",
      "title": "Extract the code from a model",
      "topics": [
        "code"
      ]
    },
    {
      "page": "collapse_matrix",
      "title": "Collapse the matrices of a matlist object",
      "topics": [
        "collapse_matrix"
      ]
    },
    {
      "page": "collapse_matrices",
      "title": "Collapse OMEGA or SIGMA matrix lists",
      "topics": [
        "collapse_omega",
        "collapse_sigma"
      ]
    },
    {
      "page": "custom_tol",
      "title": "Customize tolerances for specific compartments",
      "topics": [
        "custom_atol",
        "custom_rtol",
        "custom_tol"
      ]
    },
    {
      "page": "data_set",
      "title": "Select a data set for simulation",
      "topics": [
        "data_set",
        "data_set,mrgmod,ANY-method",
        "data_set,mrgmod,data.frame-method",
        "data_set,mrgmod,ev-method"
      ]
    },
    {
      "page": "design",
      "title": "Set observation designs for the simulation",
      "topics": [
        "design"
      ]
    },
    {
      "page": "details",
      "title": "Extract model details",
      "topics": [
        "details"
      ]
    },
    {
      "page": "dsl_preprocess",
      "title": "DSL preprocessing functions",
      "topics": [
        "convert_fort_if",
        "convert_pow",
        "convert_semicolons",
        "dsl_preprocess",
        "warn_int_div"
      ]
    },
    {
      "page": "env_eval",
      "title": "Re-evaluate the code in the ENV block",
      "topics": [
        "env_eval"
      ]
    },
    {
      "page": "env_get",
      "title": "Return model environment or objects from the model environment",
      "topics": [
        "env_get",
        "env_get.mrgmod",
        "env_get.mrgsims",
        "env_get_env",
        "env_get_env.mrgmod",
        "env_get_env.mrgsims",
        "env_get_obj"
      ]
    },
    {
      "page": "env_ls",
      "title": "List objects in the model environment",
      "topics": [
        "env_ls"
      ]
    },
    {
      "page": "env_update",
      "title": "Update objects in model environment",
      "topics": [
        "env_update"
      ]
    },
    {
      "page": "ev",
      "title": "Event objects for simulating PK and other interventions",
      "topics": [
        "ev",
        "ev,ev-method",
        "ev,missing-method",
        "ev,mrgmod-method"
      ]
    },
    {
      "page": "ev_assign",
      "title": "Replicate a list of events into a data set",
      "topics": [
        "assign_ev",
        "ev_assign"
      ]
    },
    {
      "page": "ev_days",
      "title": "Schedule dosing events on days of the week",
      "topics": [
        "ev_days"
      ]
    },
    {
      "page": "ev_rep",
      "title": "Replicate an event object",
      "topics": [
        "ev_rep"
      ]
    },
    {
      "page": "ev_repeat",
      "title": "Repeat a block of dosing events",
      "topics": [
        "ev_repeat"
      ]
    },
    {
      "page": "ev_rx",
      "title": "Create intervention objects from Rx input",
      "topics": [
        "ev_rx",
        "ev_rx,character,missing-method",
        "ev_rx,mrgmod,character-method",
        "parse_rx"
      ]
    },
    {
      "page": "ev_seq",
      "title": "Schedule a series of event objects",
      "topics": [
        "ev_seq",
        "seq.ev"
      ]
    },
    {
      "page": "evd",
      "title": "Create an event object with data-like names",
      "topics": [
        "as.evd",
        "evd",
        "evd,ev-method",
        "evd,missing-method",
        "evd,mrgmod-method"
      ]
    },
    {
      "page": "exdatasets",
      "title": "Example input data sets",
      "topics": [
        "exBoot",
        "exdatasets",
        "exidata",
        "exTheoph",
        "extran1",
        "extran2",
        "extran3"
      ]
    },
    {
      "page": "expand_observations",
      "title": "Insert observations into a data set",
      "topics": [
        "expand_observations"
      ]
    },
    {
      "page": "expand.idata",
      "title": "Create template data sets for simulation",
      "topics": [
        "evd_expand",
        "ev_expand",
        "expand.ev",
        "expand.evd",
        "expand.idata"
      ]
    },
    {
      "page": "get_tol",
      "title": "Extract rtol and atol information from a model object",
      "topics": [
        "get_tol",
        "get_tol_list"
      ]
    },
    {
      "page": "idata_set",
      "title": "Select a idata set for simulation",
      "topics": [
        "idata_set",
        "idata_set,mrgmod,ANY-method",
        "idata_set,mrgmod,data.frame-method"
      ]
    },
    {
      "page": "init",
      "title": "Methods for working with the model compartment list",
      "topics": [
        "init",
        "init,ANY-method",
        "init,list-method",
        "init,missing-method",
        "init,mrgmod-method",
        "init,mrgsims-method"
      ]
    },
    {
      "page": "inventory",
      "title": "Check whether all required parameters needed in a model are present in an object",
      "topics": [
        "inventory"
      ]
    },
    {
      "page": "is.mrgmod",
      "title": "Check if an object is a model object",
      "topics": [
        "is.mrgmod"
      ]
    },
    {
      "page": "is.mrgsims",
      "title": "Check if an object is mrgsims output",
      "topics": [
        "is.mrgsims"
      ]
    },
    {
      "page": "knobs",
      "title": "DEFUNCT: Run sensitivity analysis on model settings",
      "topics": [
        "knobs"
      ]
    },
    {
      "page": "lctran",
      "title": "Change the case of nmtran-like data items",
      "topics": [
        "lctran",
        "lctran.data.frame",
        "lctran.ev",
        "uctran",
        "uctran.data.frame",
        "uctran.ev"
      ]
    },
    {
      "page": "loadso",
      "title": "Load the model shared object",
      "topics": [
        "loadso",
        "loadso.mrgmod"
      ]
    },
    {
      "page": "matrix_helpers",
      "title": "Create matrices from vector input",
      "topics": [
        "bmat",
        "cmat",
        "dmat",
        "matrix_helpers"
      ]
    },
    {
      "page": "mcode",
      "title": "Write, compile, and load model code",
      "topics": [
        "mcode",
        "mcode_cache"
      ]
    },
    {
      "page": "mcRNG",
      "title": "Set RNG to use L'Ecuyer-CMRG",
      "topics": [
        "mcRNG"
      ]
    },
    {
      "page": "modlib",
      "title": "Internal model library",
      "topics": [
        "modlib"
      ]
    },
    {
      "page": "modlib_details",
      "title": "modlib: PK/PD Model parameters, compartments, and output variables",
      "topics": [
        "modlib_details"
      ]
    },
    {
      "page": "modlib_pk",
      "title": "modlib: Pharmacokinetic models",
      "topics": [
        "modlib_pk"
      ]
    },
    {
      "page": "modlib_pkpd",
      "title": "modlib: Pharmacokinetic / pharmacodynamic models",
      "topics": [
        "modlib_pkpd"
      ]
    },
    {
      "page": "modlib_tmdd",
      "title": "modlib: Target mediated disposition model",
      "topics": [
        "modlib_tmdd"
      ]
    },
    {
      "page": "modlib_viral",
      "title": "modlib: HCV viral dynamics models",
      "topics": [
        "modlib_viral"
      ]
    },
    {
      "page": "mread",
      "title": "Read a model specification file",
      "topics": [
        "mread",
        "mread_cache",
        "mread_file"
      ]
    },
    {
      "page": "mread_yaml",
      "title": "Read a model from yaml format",
      "topics": [
        "mread_yaml",
        "yaml_to_cpp"
      ]
    },
    {
      "page": "mrgsim",
      "title": "Simulate from a model object",
      "topics": [
        "do_mrgsim",
        "mrgsim",
        "mrgsim_df"
      ]
    },
    {
      "page": "mrgsim_q",
      "title": "Simulate from a model object with quicker turnaround",
      "topics": [
        "mrgsim_q"
      ]
    },
    {
      "page": "mrgsim_variants",
      "title": "mrgsim variant functions",
      "topics": [
        "mrgsim_0",
        "mrgsim_d",
        "mrgsim_di",
        "mrgsim_e",
        "mrgsim_ei",
        "mrgsim_i",
        "mrgsim_variants"
      ]
    },
    {
      "page": "mrgsims_dplyr",
      "title": "Methods for handling output with dplyr verbs",
      "topics": [
        "as.tbl.mrgsims",
        "as_data_frame.mrgsims",
        "as_tibble.mrgsims",
        "distinct.mrgsims",
        "do.mrgsims",
        "filter.mrgsims",
        "group_by.mrgsims",
        "mrgsims_dplyr",
        "mutate.mrgsims",
        "pull.mrgsims",
        "select.mrgsims",
        "slice.mrgsims",
        "summarise.each",
        "summarise.mrgsims"
      ]
    },
    {
      "page": "mrgsims_modify",
      "title": "Methods for modifying mrgsims objects",
      "topics": [
        "filter_sims",
        "mrgsims_modify",
        "mutate_sims",
        "select_sims"
      ]
    },
    {
      "page": "ev_dplyr",
      "title": "dplyr verbs for event objects",
      "topics": [
        "filter.ev",
        "mutate.ev",
        "select.ev"
      ]
    },
    {
      "page": "mwrite_cpp",
      "title": "Write a model to native mrgsolve format",
      "topics": [
        "mwrite_cpp"
      ]
    },
    {
      "page": "mwrite_yaml",
      "title": "Write model code to yaml format",
      "topics": [
        "mwrite_yaml"
      ]
    },
    {
      "page": "names-mrgmod-method",
      "title": "Get all names from a model object",
      "topics": [
        "names,mrgmod-method"
      ]
    },
    {
      "page": "nmext",
      "title": "Import model estimates from a NONMEM ext file",
      "topics": [
        "nmext"
      ]
    },
    {
      "page": "nmxml",
      "title": "Import model estimates from a NONMEM xml file",
      "topics": [
        "NMXML",
        "nmxml"
      ]
    },
    {
      "page": "numerics_only",
      "title": "Prepare data.frame for input to mrgsim()",
      "topics": [
        "numerics_only"
      ]
    },
    {
      "page": "obsaug",
      "title": "Augment observations in the simulated output",
      "topics": [
        "obsaug"
      ]
    },
    {
      "page": "obsonly",
      "title": "Collect only observation records in the simulated output",
      "topics": [
        "obsonly"
      ]
    },
    {
      "page": "omega",
      "title": "Manipulate OMEGA matrices",
      "topics": [
        "omat",
        "omat,list-method",
        "omat,matrix-method",
        "omat,missing-method",
        "omat,mrgmod-method",
        "omat,mrgsims-method",
        "omat,NULL-method",
        "omat,omegalist-method",
        "OMEGA",
        "omega"
      ]
    },
    {
      "page": "outvars",
      "title": "Show names of current output variables",
      "topics": [
        "outvars"
      ]
    },
    {
      "page": "param",
      "title": "Create and work with parameter objects",
      "topics": [
        "allparam",
        "param",
        "param,ANY-method",
        "param,list-method",
        "param,missing-method",
        "param,mrgmod-method",
        "param,mrgsims-method"
      ]
    },
    {
      "page": "param_tags",
      "title": "Return parameter tags",
      "topics": [
        "param_tags"
      ]
    },
    {
      "page": "PKMODEL",
      "title": "Parse PKMODEL BLOCK data",
      "topics": [
        "PKMODEL"
      ]
    },
    {
      "page": "plot_mrgsims",
      "title": "Generate a quick plot of simulated data",
      "topics": [
        "plot",
        "plot,mrgsims,character-method",
        "plot,mrgsims,formula-method",
        "plot,mrgsims,missing-method",
        "plot_mrgsims"
      ]
    },
    {
      "page": "plot_sims",
      "title": "Plot data as an mrgsims object",
      "topics": [
        "plot_sims"
      ]
    },
    {
      "page": "qsim",
      "title": "Basic, simple simulation from model object",
      "topics": [
        "qsim"
      ]
    },
    {
      "page": "read_nmext",
      "title": "Extract estimates from NONMEM ext file",
      "topics": [
        "read_nmext"
      ]
    },
    {
      "page": "realize_addl",
      "title": "Make addl doses explicit in an event object or data set",
      "topics": [
        "realize_addl",
        "realize_addl.data.frame",
        "realize_addl.ev"
      ]
    },
    {
      "page": "Req",
      "title": "Request simulated output",
      "topics": [
        "Req",
        "req",
        "req.mrgmod"
      ]
    },
    {
      "page": "reserved",
      "title": "Reserved words",
      "topics": [
        "reserved"
      ]
    },
    {
      "page": "reset_tol",
      "title": "Reset all model tolerances",
      "topics": [
        "reset_atol",
        "reset_rtol",
        "reset_tol"
      ]
    },
    {
      "page": "revar",
      "title": "Get model random effect variances and covariances",
      "topics": [
        "revar",
        "revar,mrgmod-method"
      ]
    },
    {
      "page": "see",
      "title": "Print model code to the console",
      "topics": [
        "see",
        "see,mrgmod-method"
      ]
    },
    {
      "page": "sigma",
      "title": "Manipulate SIGMA matrices",
      "topics": [
        "SIGMA",
        "sigma",
        "smat",
        "smat,list-method",
        "smat,matrix-method",
        "smat,missing-method",
        "smat,mrgmod-method",
        "smat,mrgsims-method",
        "smat,NULL-method",
        "smat,sigmalist-method"
      ]
    },
    {
      "page": "simargs",
      "title": "Access or clear arguments for calls to mrgsim()",
      "topics": [
        "simargs"
      ]
    },
    {
      "page": "soloc",
      "title": "Return the location of the model shared object",
      "topics": [
        "soloc"
      ]
    },
    {
      "page": "solversettings",
      "title": "Optional inputs for lsoda",
      "topics": [
        "solversettings"
      ]
    },
    {
      "page": "summary.mrgmod",
      "title": "Print summary of a mrgmod object",
      "topics": [
        "summary.mrgmod"
      ]
    },
    {
      "page": "tscale",
      "title": "Re-scale time in the simulated output",
      "topics": [
        "tscale"
      ]
    },
    {
      "page": "update",
      "title": "Update the model object",
      "topics": [
        "update",
        "update,mrgmod-method",
        "update,omegalist-method",
        "update,parameter_list-method",
        "update,sigmalist-method"
      ]
    },
    {
      "page": "use_custom_tol",
      "title": "Set up a model object to use either scalar or custom tolerances",
      "topics": [
        "use_custom_tol",
        "use_scalar_tol"
      ]
    },
    {
      "page": "valid_data_set",
      "title": "Validate and prepare data sets for simulation",
      "topics": [
        "valid_data_set",
        "valid_data_set.matrix"
      ]
    },
    {
      "page": "valid_idata_set",
      "title": "Validate and prepare idata data sets for simulation",
      "topics": [
        "valid_idata_set"
      ]
    },
    {
      "page": "within",
      "title": "Update parameters, initials, and settings within a model object",
      "topics": [
        "within",
        "within,mrgmod-method",
        "within.mrgmod"
      ]
    },
    {
      "page": "zero_re",
      "title": "Zero out random effects in a model object",
      "topics": [
        "zero_re",
        "zero_re,mrgmod-method"
      ]
    }
  ],
  "_readme": "https://github.com/metrumresearchgroup/mrgsolve/raw/HEAD/README.md",
  "_rundeps": [
    "BH",
    "cli",
    "dplyr",
    "generics",
    "glue",
    "lifecycle",
    "magrittr",
    "pillar",
    "pkgconfig",
    "R6",
    "Rcpp",
    "RcppArmadillo",
    "rlang",
    "tibble",
    "tidyselect",
    "utf8",
    "vctrs",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
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