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  "Title": "Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations",
  "Version": "1.5.0",
  "Date": "2025-07-08",
  "Authors@R": "c(\nperson(\"Ron\", \"Keizer\", email = \"ron@insight-rx.com\", role = c(\"aut\", \"cre\")),\nperson(\"Jasmine\", \"Hughes\", email = \"jasmine@insight-rx.com\", role = \"aut\"),\nperson(\"Dominic\", \"Tong\", email = \"dominic@insight-rx.com\", role = \"aut\"),\nperson(\"Kara\", \"Woo\", email = \"kara@insight-rx.com\", role = c(\"aut\")),\nperson(\"Jordan\", \"Brooks\", email = \"jordan.brooks@insight-rx.com\", role = \"aut\"),\nperson(\"InsightRX\", role = c(\"cph\", \"fnd\")))",
  "Description": "Simulate dose regimens for pharmacokinetic-pharmacodynamic\n(PK-PD) models described by differential equation (DE) systems.\nSimulation using ADVAN-style analytical equations is also\nsupported (Abuhelwa et al. (2015)\n<doi:10.1016/j.vascn.2015.03.004>).",
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  "Date/Publication": "2026-06-25 13:48:34 UTC",
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  "Author": "Ron Keizer [aut, cre],\nJasmine Hughes [aut],\nDominic Tong [aut],\nKara Woo [aut],\nJordan Brooks [aut],\nInsightRX [cph, fnd]",
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    "add_ruv_to_quantile",
    "adherence_binomial",
    "adherence_markov",
    "advan",
    "advan_create_data",
    "advan_parse_output",
    "advan_process_infusion_doses",
    "apply_duration_scale",
    "available_default_literature_models",
    "calc_auc_analytic",
    "calc_ss_analytic",
    "calculate_parameters",
    "compile_sim_cpp",
    "covariate_last_obs_only",
    "covariates_table_to_list",
    "cv_to_omega",
    "detect_ode_syntax",
    "f_cov",
    "get_model_auc_compartment",
    "get_model_covariates",
    "get_model_fixed_parameters",
    "get_model_iov",
    "get_model_linearity",
    "get_model_parameters",
    "get_model_structure",
    "get_ode_model_size",
    "get_parameters_from_code",
    "get_var_y",
    "ifelse0",
    "install_default_literature_model",
    "is_positive_definite",
    "join_cov_and_par",
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    "model_library",
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    "new_covariate_model",
    "new_ode_model",
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    "nm_to_regimen",
    "pkpdsim_to_nlmixr",
    "pop_regimen",
    "print_list",
    "read_model_json",
    "regimen_to_nm",
    "reparametrize",
    "search_replace_in_file",
    "shift_regimen",
    "sim",
    "sim_core",
    "sim_ode",
    "sim_ode_shiny",
    "table_to_list",
    "test_model",
    "test_pointer",
    "translate_ode",
    "triangle_to_full"
  ],
  "_datasets": [
    {
      "name": "pkdata",
      "title": "PK dataset",
      "object": "pkdata",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "TIME",
        "DV",
        "AMT",
        "CMT",
        "MDV",
        "EVID",
        "WT",
        "CRCL",
        "AGE",
        "SEX",
        "CENT"
      ],
      "rows": 624,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
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      "page": "add_quotes",
      "title": "Put vector values in quotes",
      "topics": [
        "add_quotes"
      ]
    },
    {
      "page": "add_ruv",
      "title": "Add residual variability to the dependent variable",
      "topics": [
        "add_ruv"
      ]
    },
    {
      "page": "add_ruv_to_quantile",
      "title": "Calculate the increase in a specific quantile for a distribution on y when residual variability is added",
      "topics": [
        "add_ruv_to_quantile"
      ]
    },
    {
      "page": "adherence_binomial",
      "title": "Binomial adherence",
      "topics": [
        "adherence_binomial"
      ]
    },
    {
      "page": "adherence_markov",
      "title": "Markov adherence model",
      "topics": [
        "adherence_markov"
      ]
    },
    {
      "page": "advan",
      "title": "ADVAN-style functions to calculate linear PK systems",
      "topics": [
        "advan"
      ]
    },
    {
      "page": "advan_create_data",
      "title": "Create ADVAN-style dataset",
      "topics": [
        "advan_create_data"
      ]
    },
    {
      "page": "advan_parse_output",
      "title": "Internal function to parse the raw output from ADVAN-style functions",
      "topics": [
        "advan_parse_output"
      ]
    },
    {
      "page": "advan_process_infusion_doses",
      "title": "Add column RATEALL to ADVAN-style dataset to handle infusions",
      "topics": [
        "advan_process_infusion_doses"
      ]
    },
    {
      "page": "apply_duration_scale",
      "title": "Apply infusion duration scale to a regimen",
      "topics": [
        "apply_duration_scale"
      ]
    },
    {
      "page": "available_default_literature_models",
      "title": "See models from the literature available for installation",
      "topics": [
        "available_default_literature_models"
      ]
    },
    {
      "page": "calc_auc_analytic",
      "title": "Convenience function to calculate the AUC based on PK model parameters at any given moment, for linear iv models.",
      "topics": [
        "calc_auc_analytic"
      ]
    },
    {
      "page": "calc_dydP",
      "title": "Calculate derivative",
      "topics": [
        "calc_dydP"
      ]
    },
    {
      "page": "calc_ss_analytic",
      "title": "Returns the state of a linear PK system at steady state (trough) using analytics equations (so for linear PK systems only).",
      "topics": [
        "calc_ss_analytic"
      ]
    },
    {
      "page": "calculate_parameters",
      "title": "Calculate model-specific variables using a dummy call to sim_ode()",
      "topics": [
        "calculate_parameters"
      ]
    },
    {
      "page": "check_obs_input",
      "title": "Checks obs input for valid combinations of cmt, var, scale",
      "topics": [
        "check_obs_input"
      ]
    },
    {
      "page": "compile_sim_cpp",
      "title": "Compile ODE model to c++ function",
      "topics": [
        "compile_sim_cpp"
      ]
    },
    {
      "page": "covariate_last_obs_only",
      "title": "Use only last observed covariate values",
      "topics": [
        "covariate_last_obs_only"
      ]
    },
    {
      "page": "covariates_table_to_list",
      "title": "Convert covariate table specified as data.frame",
      "topics": [
        "covariates_table_to_list"
      ]
    },
    {
      "page": "cv_to_omega",
      "title": "Create lower-diagonal omega matrix from CV for parameter estimates",
      "topics": [
        "cv_to_omega"
      ]
    },
    {
      "page": "detect_ode_syntax",
      "title": "Auto-detect the syntax for the ODE code",
      "topics": [
        "detect_ode_syntax"
      ]
    },
    {
      "page": "f_cov",
      "title": "covariate function builder",
      "topics": [
        "f_cov"
      ]
    },
    {
      "page": "get_fixed_parameters",
      "title": "Get fixed parameters from model definition.",
      "topics": [
        "get_fixed_parameters"
      ]
    },
    {
      "page": "get_model_info",
      "title": "Functions for getting information about a model",
      "topics": [
        "get_model_auc_compartment",
        "get_model_covariates",
        "get_model_fixed_parameters",
        "get_model_info",
        "get_model_iov",
        "get_model_linearity",
        "get_model_parameters",
        "get_model_structure"
      ]
    },
    {
      "page": "get_ode_model_size",
      "title": "Get the number of states in the ODE from the code code C++ code for model",
      "topics": [
        "get_ode_model_size"
      ]
    },
    {
      "page": "get_parameters_from_code",
      "title": "Get model parameters from code",
      "topics": [
        "get_parameters_from_code"
      ]
    },
    {
      "page": "get_var_y",
      "title": "Get expected variance/sd/ci of dependent variable based on PKPDsim model, parameters, and regimen",
      "topics": [
        "get_var_y"
      ]
    },
    {
      "page": "ifelse0",
      "title": "ifelse function but then based on whether value is NULL or not",
      "topics": [
        "ifelse0"
      ]
    },
    {
      "page": "install_default_literature_model",
      "title": "Install default literature model",
      "topics": [
        "install_default_literature_model"
      ]
    },
    {
      "page": "is_bolus_or_oral",
      "title": "Is regimen type oral or bolus? (i.e., treat t_inf as zero)",
      "topics": [
        "is_bolus_or_oral"
      ]
    },
    {
      "page": "is_positive_definite",
      "title": "Is matrix positive definite",
      "topics": [
        "is_positive_definite"
      ]
    },
    {
      "page": "join_cov_and_par",
      "title": "Combines covariates and parameters into a single list, useful for reparametrization of the model.",
      "topics": [
        "join_cov_and_par"
      ]
    },
    {
      "page": "join_regimen",
      "title": "Join two dosing regimens",
      "topics": [
        "join_regimen"
      ]
    },
    {
      "page": "lower_triangle_mat_size",
      "title": "Size of the lower triangle of the matrix",
      "topics": [
        "lower_triangle_mat_size"
      ]
    },
    {
      "page": "merge_regimen",
      "title": "Merge two regimens together.",
      "topics": [
        "merge_regimen"
      ]
    },
    {
      "page": "model_from_api",
      "title": "Load model definition from API, and compile to R library",
      "topics": [
        "model_from_api"
      ]
    },
    {
      "page": "model_library",
      "title": "Model library",
      "topics": [
        "model_library"
      ]
    },
    {
      "page": "mvrnorm2",
      "title": "More powerful multivariate normal sampling function",
      "topics": [
        "mvrnorm2"
      ]
    },
    {
      "page": "na_locf",
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