{ "_id": "6a115ce3acfb0bcc41cec72b", "Type": "Package", "Package": "invivoPKfit", "Title": "Fits Toxicokinetic Models to In Vivo PK Data Sets", "Version": "2.0.2", "Date": "2025-8-26", "Authors@R": "c(person(\"John\", \"Wambaugh\", email = \"wambaugh.john@epa.gov\", \nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-4024-534X\")),\nperson(\"Caroline\", \"Ring\", email = \"Ring.Caroline@epa.gov\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-0463-1251\")),\nperson(\"Gilberto\", \"Padilla Mercado\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-5423-1646\")),\nperson(\"Chris\", \"Cook\", role = c(\"aut\"))\n)", "Author": "John Wambaugh [aut, cre] (ORCID:\n), Caroline Ring [aut]\n(ORCID: ), Gilberto\nPadilla Mercado [aut] (ORCID:\n), Chris Cook [aut]", "Maintainer": "John Wambaugh ", "Description": "Takes in vivo toxicokinetic concentration-time data and\nfits parameters of 1-compartment and 2-compartment models for\neach chemical. These methods are described in detail in\n\"Informatics for Toxicokinetics\" (2025).", "License": "GPL-3", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "TRUE", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-23 07:46:07 UTC", "User": "root" }, "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://jfwambaugh.r-universe.dev", "Date/Publication": "2025-08-26 14:10:02 UTC", "RemoteUrl": "https://github.com/cran/invivoPKfit", "RemoteRef": "HEAD", "RemoteSha": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "MD5sum": "79a7083386c4e0670280766cc58720bd", "_user": "jfwambaugh", "_type": "src", "_file": "invivoPKfit_2.0.2.tar.gz", "_fileid": "25798e6be7e40fd0879c5922839e7750682a1e3ce046af498ced927b2a9d0a6c", "_filesize": 2439974, "_sha256": "25798e6be7e40fd0879c5922839e7750682a1e3ce046af498ced927b2a9d0a6c", "_created": "2026-05-23T07:46:07.000Z", "_published": "2026-05-23T07:53:07.222Z", "_distro": "noble", "_jobs": [ { "job": 77507207341, "time": 361, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7175435103" }, { "job": 77507207335, "time": 364, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7175435438" }, { "job": 77507207324, "time": 273, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7175423558" }, { "job": 77507207334, "time": 285, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7175422522" }, { "job": 77507013848, "time": 232, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7175399448" }, { "job": 77507207328, "time": 143, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7175412835" }, { "job": 77507207356, "time": 353, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7175434404" }, { "job": 77507207358, "time": 309, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7175429952" }, { "job": 77507207371, "time": 300, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7175428875" } ], "_buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/invivoPKfit", "_commit": { "id": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "author": "John Wambaugh ", "committer": "cran-robot ", "message": "version 2.0.2\n", "time": 1756217402 }, "_maintainer": { "name": "John Wambaugh", "email": "wambaugh.john@epa.gov", "login": "jfwambaugh", "orcid": "0000-0002-4024-534X", "description": "I am working to develop and evaluate high throughput methods for exposure assessment, toxicokinetics, and toxicity testing.", "uuid": 29150644 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cli", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "httk", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "mirai", "role": "Imports" }, { "package": "numDeriv", "role": "Imports" }, { "package": "optimx", "role": "Imports" }, { "package": "PK", "role": "Imports" }, { "package": "pracma", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "cowplot", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "stringr", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "glue", "role": "Suggests" }, { "package": "tidyverse", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-35", "n": 1 } ], "_tags": [ { "name": "2.0.2", "date": "2025-08-26" } ], "_stars": 0, "_contributors": [ { "user": "jfwambaugh", "count": 3, "uuid": 29150644 } ], "_userbio": { "uuid": 29150644, "type": "user", "name": "John Wambaugh", "description": "I am working to develop and evaluate high throughput methods for exposure assessment, toxicokinetics, and toxicity testing." }, "_downloads": { "count": 188, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/invivoPKfit" }, "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/invivoPKfit.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "jfwambaugh", "_cranurl": false, "_releases": [ { "version": "2.0.0", "date": "2025-01-09" }, { "version": "2.0.1", "date": "2025-03-24" }, { "version": "2.0.2", "date": "2025-08-26" } ], "_exports": [ "AAFE", "add_pk", "adjust_model_name", "AFE", "auc_1comp", "auc_2comp", "auc_flat", "auc_httk_gas_pbtk", "auto_units", "calc_nca", "check_required_status", "coef_sd", "compare_models", "convert_summary_to_log10", "convert_time", "cp_1comp", "cp_2comp", "cp_2comp_dt", "cp_flat", "cp_httk_gas_pbtk", "data_summary", "dlnorm_summary", "dnorm_summary", "do_data_info", "do_fit", "do_prefit", "do_preprocess", "eval_tkstats", "facet_data", "fit_sigma.pk", "fold_error", "get_data", "get_data_group", "get_data_info", "get_data_original", "get_data_sigma_group", "get_data_summary", "get_error_group", "get_fit", "get_hessian", "get_mapping", "get_nca", "get_nca_group", "get_params_httk_gas_pbtk", "get_prefit", "get_scale_conc", "get_scale_time", "get_settings_optimx", "get_settings_preprocess", "get_stat_model", "get_status", "get_tkstats", "get_winning_model", "is.pk", "is.pk_faceted", "is.pk_scales", "is.pkproto", "log_likelihood", "mapping", "nca", "pk", "pk_add", "pk_model", "pk_subtract", "recalculate_httk_pbtk_params", "rmse", "rsq", "scale_conc", "set_params_optimize", "set_params_starts", "settings_preprocess", "stat_error_model", "stat_loq_group", "stat_nca_group", "stat_sd_group", "subtract_pk", "tkstats_1comp", "tkstats_2comp", "tkstats_flat", "tkstats_httk_gas_pbtk", "toggle_clearance_mode", "transformed_params_2comp", "twofold_test" ], "_datasets": [ { "name": "cvt", "title": "CvTdb data", "object": "cvt", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "conc_time_id", "fk_series_id", "time_original", "time_hr", "conc_original", "conc_sd_original", "conc", "conc_sd", "fk_analyzed_chemical_id", "analyzed_chem_dtxsid", "analyzed_chem_name_original", "analyzed_chem_casrn", "analyzed_chem_name", "analyzed_chem_name_secondary_original", "time_units_original", "conc_units_original", "conc_units_normalized", "loq", "loq_units", "n_subjects_in_series", "radiolabeled", "fk_study_id", "fk_dosed_chemical_id", "dosed_chem_dtxsid", "dosed_chem_name_original", "dosed_chem_casrn", "dosed_chem_name", "dosed_chem_name_secondary_original", "dose_volume", "dose_volume_units", "dose_vehicle", "dose_duration", "dose_duration_units", "dose_frequency_original", "dose_frequency_normalized", "fasting_period", "dose_level_normalized", "dose_level_original", "dose_level_units_original", "dose_level_units_normalized", "conc_medium_original", "conc_medium_normalized", "administration_route_original", "administration_route_normalized", "fk_subject_id", "weight_kg", "species", "sex", "age", "age_units", "age_category", "fk_extraction_document_id", "pmid", "year", "other_study_identifier", "url", "doi", "extracted", "curation_set_tag", "n_subjects_normalized" ], "rows": 22182, "table": true, "tojson": true }, { "name": "cvt_2.0.0", "title": "CvTdb data for invivoPKfit 2.0.0 release (old)", "object": "cvt_2.0.0", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "conc_time_id", "time_original", "time_hr", "conc_original", "conc_sd_original", "conc", "conc_sd", "fk_series_id", "analyte_name_original", "analyte_dtxsid", "analyte_casrn", "fk_analyzed_chemical_id", "fk_test_chemical_id", "test_substance_dtxsid", "analyte_name_secondary_original", "conc_medium_normalized", "conc_medium_original", "time_units_original", "conc_units_original", "conc_units_normalized", "conc_unit_norm_factor", "loq", "loq_units", "n_subjects_in_series", "radiolabeled", "fk_study_id", "administration_route_normalized", "fk_dosed_chemical_id", "dose_volume", "dose_volume_units", "dose_vehicle", "dose_duration", "dose_duration_units", "dose_frequency", "fasting_period", "dose_level_normalized", "dose_level_original", "dose_level_units_original", "fk_subject_id", "weight_kg", "species", "sex", "age", "age_units", "age_category", "fk_extraction_document_id", "pmid", "year", "other_study_identifier", "url", "doi", "extracted", "curation_set_tag", "n_subjects_normalized", "invivPK_dose_level_units", "invivPK_conc_units", "invivPK_conc", "invivPK_dose_level", "invivPK_loq", "invivPK_loq_units", "ivivPK_loq_units", "invivPK_conc_sd" ], "rows": 7918, "table": true, "tojson": true }, { "name": "cvt_date", "title": "CvTdb download date", "object": "cvt_date", "class": [ "Date" ], "fields": [], "table": false, "tojson": true }, { "name": "cvtdb_original", "title": "SQL query result (current)", "object": "cvtdb_original", "class": [ "data.frame" ], "fields": [ "conc_time_id", "fk_series_id", "time_original", "time_hr", "conc_original", "conc_sd_original", "conc", "conc_sd", "fk_analyzed_chemical_id", "analyzed_chem_dtxsid", "analyzed_chem_name_original", "analyzed_chem_casrn", "analyzed_chem_name", "analyzed_chem_name_secondary_original", "time_units_original", "conc_units_original", "conc_units_normalized", "loq", "loq_units", "n_subjects_in_series", "radiolabeled", "fk_study_id", "fk_dosed_chemical_id", "dosed_chem_dtxsid", "dosed_chem_name_original", "dosed_chem_casrn", "dosed_chem_name", "dosed_chem_name_secondary_original", "dose_volume", "dose_volume_units", "dose_vehicle", "dose_duration", "dose_duration_units", "dose_frequency_original", "dose_frequency_normalized", "fasting_period", "dose_level_normalized", "dose_level_original", "dose_level_units_original", "dose_level_units_normalized", "conc_medium_original", "conc_medium_normalized", "administration_route_original", "administration_route_normalized", "fk_subject_id", "weight_kg", "species", "sex", "age", "age_units", "age_category", "fk_extraction_document_id", "pmid", "year", "other_study_identifier", "url", "doi", "extracted", "curation_set_tag" ], "rows": 35669, "table": true, "tojson": true }, { "name": "model_1comp", "title": "1-compartment model", "object": "model_1comp", "class": [ "list", "pk_model" ], "fields": [], "table": false, "tojson": true }, { "name": "model_2comp", "title": "2-compartment model", "object": "model_2comp", "class": [ "list", "pk_model" ], "fields": [], "table": false, "tojson": true }, { "name": "model_flat", "title": "Flat model", "object": "model_flat", "class": [ "list", "pk_model" ], "fields": [], "table": false, "tojson": true }, { "name": "model_httk_gas_pbtk", "title": "Gas pbtk 'httk' model", "object": "model_httk_gas_pbtk", "class": [ "list", "pk_model" ], "fields": [], "table": false, "tojson": false }, { "name": "pkdataset_nheerlcleaned", "title": "Toxicokinetic data from the \"Concentration vs. Time Database\"", "object": "pkdataset_nheerlcleaned", "class": [ "data.table", "data.frame" ], "fields": [ "Compound", "CAS", "Reference", "Species", "Species.Weight", "Species.Weight.Units", "Dose", "Dose.Units.and.Type", "Time", "Time.Units", "Media", "Media.Units", "Value", "Units", "Route", "Source", "LOQ", "Subject", "info" ], "rows": 2454, "table": true, "tojson": true }, { "name": "status_data_info", "title": "Status ID for data summary info", "object": "status_data_info", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "status_fit", "title": "Status ID for fitting", "object": "status_fit", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "status_init", "title": "Status ID for initialization", "object": "status_init", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "status_prefit", "title": "Status ID for pre-fitting", "object": "status_prefit", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "status_preprocess", "title": "Status ID for preprocessing", "object": "status_preprocess", "class": [ "integer" ], "fields": [], "table": false, "tojson": true }, { "name": "time_conversions", "title": "Time conversion table", "object": "time_conversions", "class": [ "data.frame" ], "fields": [ "TimeFrom", "TimeTo", "conversion" ], "rows": 121, "table": true, "tojson": true }, { "name": "time_units", "title": "Allowable time units", "object": "time_units", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "dot-pk", "title": "Subtract a pkproto object from a pk object", "topics": [ "-.pk" ] }, { "page": "plus-.pk", "title": "Add a `pkproto` object to a `pk` object", "topics": [ "+.pk" ] }, { "page": "AAFE", "title": "AAFE()", "topics": [ "AAFE" ] }, { "page": "AAFE.default", "title": "Default method for AAFE()", "topics": [ "AAFE.default" ] }, { "page": "AAFE.pk", "title": "Calculate absolute average fold error (AAFE)", "concept": [ "fit evaluation metrics", "methods for fitted pk objects" ], "topics": [ "AAFE.pk" ] }, { "page": "add_pk", "title": "Add various `pkproto` objects to a `pk` object", "topics": [ "add_pk" ] }, { "page": "adjust_model_name", "title": "Sets the `name` element for models to the `pk_model` object name in the environment", "concept": [ "pk_model modifiers" ], "topics": [ "adjust_model_name" ] }, { "page": "AFE", "title": "AFE()", "topics": [ "AFE" ] }, { "page": "AFE.default", "title": "Default method for AFE()", "topics": [ "AFE.default" ] }, { "page": "AFE.pk", "title": "Calculate average fold error", "concept": [ "fit evaluation metrics", "methods for fitted pk objects" ], "topics": [ "AFE.pk" ] }, { "page": "AIC.pk", "title": "Akaike information criterion", "concept": [ "fit evaluation metrics", "log likelihood functions", "methods for fitted pk objects" ], "topics": [ "AIC.pk" ] }, { "page": "auc_1comp", "title": "Analytic AUC for 1-compartment model", "concept": [ "1-compartment model functions", "built-in model functions", "model AUC functions" ], "topics": [ "auc_1comp" ] }, { "page": "auc_2comp", "title": "Analytical AUC for the 2-compartment model", "concept": [ "2-compartment model functions", "built-in model functions", "model AUC functions" ], "topics": [ "auc_2comp" ] }, { "page": "auc_flat", "title": "AUC for flat model", "concept": [ "built-in model functions", "flat model functions", "model AUC functions" ], "topics": [ "auc_flat" ] }, { "page": "auc_httk_gas_pbtk", "title": "Calculates AUC for `httk`'s `gas_pbtk` PBPK model", "concept": [ "built-in model functions", "httk model functions", "model auc functions" ], "topics": [ "auc_httk_gas_pbtk" ] }, { "page": "auto_units", "title": "Automatically select new time units", "topics": [ "auto_units" ] }, { "page": "BIC.pk", "title": "Bayesian information criterion", "concept": [ "fit evaluation metrics", "log likelihood functions", "methods for fitted pk objects" ], "topics": [ "BIC.pk" ] }, { "page": "calc_hessian", "title": "Calculate Hessian", "topics": [ "calc_hessian" ] }, { "page": "calc_nca", "title": "Non-compartmental analysis", "topics": [ "calc_nca" ] }, { "page": "calc_rmse", "title": "Calculate RMSE (root mean squared error)", "topics": [ "calc_rmse" ] }, { "page": "calc_rsq", "title": "Calculate r-squared for observed vs. predicted values", "topics": [ "calc_rsq" ] }, { "page": "calc_sds_alerts", "title": "Calculate parameter SDs", "topics": [ "calc_sds_alerts" ] }, { "page": "check_group_hierarchy", "title": "Checking data, error, and summary group hierarchical structure", "topics": [ "check_group_hierarchy" ] }, { "page": "check_method", "title": "Check methods", "topics": [ "check_method" ] }, { "page": "check_model", "title": "Check models", "topics": [ "check_model" ] }, { "page": "check_newdata", "title": "Check new data", "topics": [ "check_newdata" ] }, { "page": "check_params_1comp", "title": "Check 1-compartment model parameters", "topics": [ "check_params_1comp" ] }, { "page": "check_params_2comp", "title": "Check 2-compartment model parameters", "topics": [ "check_params_2comp" ] }, { "page": "check_params_flat", "title": "Check flat model parameters", "topics": [ "check_params_flat" ] }, { "page": "check_required_status", "title": "Check required status", "topics": [ "check_required_status" ] }, { "page": "check_required_status.default", "title": "Default method for checking required status", "topics": [ "check_required_status.default" ] }, { "page": "check_required_status.pk", "title": "Check required status", "topics": [ "check_required_status.pk" ] }, { "page": "coef_sd", "title": "Coefficient standard deviations", "topics": [ "coef_sd" ] }, { "page": "coef_sd.default", "title": "Coefficient standard deviation default", "topics": [ "coef_sd.default" ] }, { "page": "coef_sd.pk", "title": "Get coefficient standard deviations", "concept": [ "methods for fitted pk objects" ], "topics": [ "coef_sd.pk" ] }, { "page": "coef.pk", "title": "Get coefficients", "concept": [ "methods for fitted pk objects" ], "topics": [ "coef.pk" ] }, { "page": "combined_sd", "title": "Combined standard deviation", "topics": [ "combined_sd" ] }, { "page": "compare_models", "title": "Model comparison", "topics": [ "compare_models" ] }, { "page": "compare_models.default", "title": "Default method for compare_models()", "topics": [ "compare_models.default" ] }, { "page": "compare_models.pk", "title": "Model comparison for [pk()] objects", "topics": [ "compare_models.pk" ] }, { "page": "conc_scale_use", "title": "Get concentration scalings", "topics": [ "conc_scale_use" ] }, { "page": "convert_summary_to_log10", "title": "Convert sample mean and SD to log10-scale", "topics": [ "convert_summary_to_log10" ] }, { "page": "convert_time", "title": "Helper function to convert time units", "topics": [ "convert_time" ] }, { "page": "cp_1comp", "title": "Analytical 1-compartment model", "concept": [ "1-compartment model functions", "built-in model functions", "model concentration functions" ], "topics": [ "cp_1comp" ] }, { "page": "cp_2comp", "title": "Analytical 2-compartment model", "concept": [ "2-compartment model functions", "built-in model functions", "model concentration functions" ], "topics": [ "cp_2comp" ] }, { "page": "cp_2comp_dt", "title": "Time derivative of analytical 2-compartment model", "concept": [ "2-compartment model functions", "built-in model functions" ], "topics": [ "cp_2comp_dt" ] }, { "page": "cp_flat", "title": "Flat model", "concept": [ "built-in model functions", "flat model functions", "model concentration functions" ], "topics": [ "cp_flat" ] }, { "page": "cp_httk_gas_pbtk", "title": "Calculates plasma concentration for `httk`'s `gas_pbtk` model", "concept": [ "built-in model functions", "httk model functions", "model concentration functions" ], "topics": [ "cp_httk_gas_pbtk" ] }, { "page": "cvt", "title": "CvTdb data", "topics": [ "cvt" ] }, { "page": "cvt_2.0.0", "title": "CvTdb data for invivoPKfit 2.0.0 release (old)", "topics": [ "cvt_2.0.0" ] }, { "page": "cvt_date", "title": "CvTdb download date", "topics": [ "cvt_date" ] }, { "page": "cvtdb_original", "title": "SQL query result (current)", "topics": [ "cvtdb_original" ] }, { "page": "data_summary", "title": "data_summary()", "topics": [ "data_summary" ] }, { "page": "data_summary.default", "title": "Default method for data_summary()", "topics": [ "data_summary.default" ] }, { "page": "data_summary.pk", "title": "Data summary for a `pk` object", "topics": [ "data_summary.pk" ] }, { "page": "dlnorm_summary", "title": "Log-normal distribution density function for summary data", "topics": [ "dlnorm_summary" ] }, { "page": "dnorm_summary", "title": "Normal distribution density function for summary data", "topics": [ "dnorm_summary" ] }, { "page": "do_data_info", "title": "do_data_info generic", "topics": [ "do_data_info" ] }, { "page": "do_data_info.default", "title": "do_data_info default method", "topics": [ "do_data_info.default" ] }, { "page": "do_data_info.pk", "title": "calculate summary data info", "topics": [ "do_data_info.pk" ] }, { "page": "do_fit", "title": "Fitting", "topics": [ "do_fit" ] }, { "page": "do_fit.default", "title": "do_fit default method", "topics": [ "do_fit.default" ] }, { "page": "do_fit.pk", "title": "Do fitting", "topics": [ "do_fit.pk" ] }, { "page": "do_prefit", "title": "Prefitting", "topics": [ "do_prefit" ] }, { "page": "do_prefit.default", "title": "do_prefit default method", "topics": [ "do_prefit.default" ] }, { "page": "do_prefit.pk", "title": "Do pre-fitting", "topics": [ "do_prefit.pk" ] }, { "page": "do_preprocess", "title": "Preprocess data generic", "topics": [ "do_preprocess" ] }, { "page": "do_preprocess.default", "title": "do_preprocess default method", "topics": [ "do_preprocess.default" ] }, { "page": "do_preprocess.pk", "title": "Do pre-processing", "topics": [ "do_preprocess.pk" ] }, { "page": "eval_tkstats", "title": "eval_tkstats()", "topics": [ "eval_tkstats" ] }, { "page": "eval_tkstats.default", "title": "Default method for eval_tkstats()", "topics": [ "eval_tkstats.default" ] }, { "page": "eval_tkstats.pk", "title": "Evaluate TK statistics", "concept": [ "methods for fitted pk objects" ], "topics": [ "eval_tkstats.pk" ] }, { "page": "facet_data", "title": "Facet a PK fit", "topics": [ "facet_data" ] }, { "page": "fill_params_1comp", "title": "Fill parameters for 1-compartment model", "topics": [ "fill_params_1comp" ] }, { "page": "fill_params_2comp", "title": "Fill parameters for 2-compartment model", "topics": [ "fill_params_2comp" ] }, { "page": "fill_params_flat", "title": "Fill parameters for flat model", "topics": [ "fill_params_flat" ] }, { "page": "fit_group", "title": "Fit a single group of data", "topics": [ "fit_group" ] }, { "page": "fit_sigma.pk", "title": "Hyperparameter fitting", "topics": [ "fit_sigma.pk" ] }, { "page": "fold_error", "title": "Fold error", "topics": [ "fold_error" ] }, { "page": "fold_error.default", "title": "fold_error default method", "topics": [ "fold_error.default" ] }, { "page": "fold_error.pk", "title": "Fold errors", "topics": [ "fold_error.pk" ] }, { "page": "get_data", "title": "get_data()", "topics": [ "get_data" ] }, { "page": "get_data_group", "title": "get_data_group()", "topics": [ "get_data_group" ] }, { "page": "get_data_group.default", "title": "Default method for get_data_group()", "topics": [ "get_data_group.default" ] }, { "page": "get_data_group.pk", "title": "Get data grouping", "topics": [ "get_data_group.pk" ] }, { "page": "get_data_info", "title": "get_data_info()", "topics": [ "get_data_info" ] }, { "page": "get_data_info.default", "title": "Default method for get_data_info()", "topics": [ "get_data_info.default" ] }, { "page": "get_data_info.pk", "title": "Get data_info", "topics": [ "get_data_info.pk" ] }, { "page": "get_data_original", "title": "get_data_original()", "topics": [ "get_data_original" ] }, { "page": "get_data_original.default", "title": "Default method for get_data_original()", "topics": [ "get_data_original.default" ] }, { "page": "get_data_original.pk", "title": "Get data_original", "topics": [ "get_data_original.pk" ] }, { "page": "get_data_sigma_group", "title": "get_data_sigma_group()", "topics": [ "get_data_sigma_group" ] }, { "page": "get_data_sigma_group.default", "title": "Default method for get_data_sigma_group()", "topics": [ "get_data_sigma_group.default" ] }, { "page": "get_data_sigma_group.pk", "title": "Get data_sigma_group", "topics": [ "get_data_sigma_group.pk" ] }, { "page": "get_data_summary", "title": "get_data_summary()", "topics": [ "get_data_summary" ] }, { "page": "get_data_summary.default", "title": "Default method for get_data_summary()", "topics": [ "get_data_summary.default" ] }, { "page": "get_data.default", "title": "Default method for get_data()", "topics": [ "get_data.default" ] }, { "page": "get_data.pk", "title": "Get data", "topics": [ "get_data.pk" ] }, { "page": "get_elbow", "title": "Get an elbow point", "topics": [ "get_elbow" ] }, { "page": "get_error_group", "title": "get_error_group()", "topics": [ "get_error_group" ] }, { "page": "get_error_group.default", "title": "Default method for get_error_group()", "topics": [ "get_error_group.default" ] }, { "page": "get_error_group.pk", "title": "Get error group", "topics": [ "get_error_group.pk" ] }, { "page": "get_fit", "title": "get_fit()", "topics": [ "get_fit" ] }, { "page": "get_fit.default", "title": "Default method for get_fit()", "topics": [ "get_fit.default" ] }, { "page": "get_fit.pk", "title": "Get fits from a `pk` object", "concept": [ "methods for fitted pk objects" ], "topics": [ "get_fit.pk" ] }, { "page": "get_hessian", "title": "get_hessian()", "topics": [ "get_hessian" ] }, { "page": "get_hessian.default", "title": "Default method for get_hessian()", "topics": [ "get_hessian.default" ] }, { "page": "get_hessian.pk", "title": "Get Hessian matrixes", "concept": [ "methods for fitted pk objects" ], "topics": [ "get_hessian.pk" ] }, { "page": "get_mapping", "title": "get_mapping()", "topics": [ "get_mapping" ] }, { "page": "get_mapping.default", "title": "Default method for get_mapping()", "topics": [ "get_mapping.default" ] }, { "page": "get_mapping.pk", "title": "Get mapping", "topics": [ "get_mapping.pk" ] }, { "page": "get_nca", "title": "get_nca()", "topics": [ "get_nca" ] }, { "page": "get_nca_group", "title": "get_nca_group()", "topics": [ "get_nca_group" ] }, { "page": "get_nca_group.default", "title": "Default method for get_nca_group()", "topics": [ "get_nca_group.default" ] }, { "page": "get_nca_group.pk", "title": "Get nca_group", "topics": [ "get_nca_group.pk" ] }, { "page": "get_nca.default", "title": "Default method for get_nca()", "topics": [ "get_nca.default" ] }, { "page": "get_nca.pk", "title": "Get NCA", "topics": [ "get_nca.pk" ] }, { "page": "get_params_1comp", "title": "Get parameters for 1-compartment model", "concept": [ "1-compartment model functions", "built-in model functions", "get_params functions" ], "topics": [ "get_params_1comp" ] }, { "page": "get_params_2comp", "title": "Get parameters for 2-compartment model", "concept": [ "2-compartment model functions", "built-in model functions", "get_params functions" ], "topics": [ "get_params_2comp" ] }, { "page": "get_params_flat", "title": "Get parameters to be optimized for flat model", "concept": [ "built-in model functions", "flat model functions", "get_params functions" ], "topics": [ "get_params_flat" ] }, { "page": "get_params_httk_gas_pbtk", "title": "Get parameters to fit `httk`'s `gas_pbtk` PBPK model", "concept": [ "built-in model functions", "httk model functions", "model concentration functions" ], "topics": [ "get_params_httk_gas_pbtk" ] }, { "page": "get_peak", "title": "Find the peak of a data series", "topics": [ "get_peak" ] }, { "page": "get_prefit", "title": "get_prefit()", "topics": [ "get_prefit" ] }, { "page": "get_prefit.default", "title": "Default method for get_prefit()", "topics": [ "get_prefit.default" ] }, { "page": "get_prefit.pk", "title": "Get prefit", "topics": [ "get_prefit.pk" ] }, { "page": "get_scale_conc", "title": "get_scale_conc()", "topics": [ "get_scale_conc" ] }, { "page": "get_scale_conc.default", "title": "Default method for get_scale_conc()", "topics": [ "get_scale_conc.default" ] }, { "page": "get_scale_conc.pk", "title": "Get scale_conc", "topics": [ "get_scale_conc.pk" ] }, { "page": "get_scale_time", "title": "get_scale_time()", "topics": [ "get_scale_time" ] }, { "page": "get_scale_time.default", "title": "Default method for get_scale_time()", "topics": [ "get_scale_time.default" ] }, { "page": "get_scale_time.pk", "title": "Get scale_time", "topics": [ "get_scale_time.pk" ] }, { "page": "get_settings_optimx", "title": "get_settings_optimx()", "topics": [ "get_settings_optimx" ] }, { "page": "get_settings_optimx.default", "title": "Default method for get_settings_optimx()", "topics": [ "get_settings_optimx.default" ] }, { "page": "get_settings_optimx.pk", "title": "Get settings_optimx", "topics": [ "get_settings_optimx.pk" ] }, { "page": "get_settings_preprocess", "title": "get_settings_preprocess()", "topics": [ "get_settings_preprocess" ] }, { "page": "get_settings_preprocess.default", "title": "Default method for get_settings_preprocess()", "topics": [ "get_settings_preprocess.default" ] }, { "page": "get_settings_preprocess.pk", "title": "Get settings_preprocess", "topics": [ "get_settings_preprocess.pk" ] }, { "page": "get_starts_1comp", "title": "Get starting values for 1-compartment model", "concept": [ "1-compartment model functions", "built-in model functions", "get_starts functions" ], "topics": [ "get_starts_1comp" ] }, { "page": "get_starts_2comp", "title": "Get starting values for 2-compartment model", "concept": [ "2-compartment model functions", "built-in model functions", "get_starts functions" ], "topics": [ "get_starts_2comp" ] }, { "page": "get_starts_flat", "title": "Get starting values for flat model", "concept": [ "built-in model functions", "flat model functions", "get_starts functions" ], "topics": [ "get_starts_flat" ] }, { "page": "get_starts_httk_gas_pbtk", "title": "Get starting values for httk `gas_pbtk` model with specific clearance", "concept": [ "built-in model functions", "get_starts functions", "httk model functions" ], "topics": [ "get_starts_httk_gas_pbtk" ] }, { "page": "get_stat_model", "title": "get_stat_model()", "topics": [ "get_stat_model" ] }, { "page": "get_stat_model.default", "title": "Default method for get_stat_model()", "topics": [ "get_stat_model.default" ] }, { "page": "get_stat_model.pk", "title": "Get stat_model", "topics": [ "get_stat_model.pk" ] }, { "page": "get_status", "title": "Get status", "topics": [ "get_status" ] }, { "page": "get_status.default", "title": "Default method for getting status", "topics": [ "get_status.default" ] }, { "page": "get_status.pk", "title": "Check status of a `pk` object", "topics": [ "get_status.pk" ] }, { "page": "get_tkstats", "title": "Get TK stats", "topics": [ "get_tkstats" ] }, { "page": "get_tkstats.default", "title": "Default method for get_tkstats()", "topics": [ "get_tkstats.default" ] }, { "page": "get_tkstats.pk", "title": "Get TK stats", "concept": [ "methods for fitted pk objects" ], "topics": [ "get_tkstats.pk" ] }, { "page": "get_winning_model", "title": "get_winning_model()", "topics": [ "get_winning_model" ] }, { "page": "get_winning_model.default", "title": "Default method for get_winning_model()", "topics": [ "get_winning_model.default" ] }, { "page": "get_winning_model.pk", "title": "Get winning model", "topics": [ "get_winning_model.pk" ] }, { "page": "hess_sd1", "title": "Inverse diagonal, method 1", "topics": [ "hess_sd1" ] }, { "page": "hess_sd2", "title": "Inverse diagonal, method 2", "topics": [ "hess_sd2" ] }, { "page": "ignore_unused_imports", "title": "Ignore unused imports", "topics": [ "ignore_unused_imports" ] }, { "page": "is.pk", "title": "Check whether an object is of class `pk`", "topics": [ "is.pk" ] }, { "page": "is.pk_faceted", "title": "Check whether an object is of class `pk_faceted`", "topics": [ "is.pk_faceted" ] }, { "page": "is.pk_model", "title": "Checks whether object is of class `pk_model`", "topics": [ "is.pk_model" ] }, { "page": "is.pk_scales", "title": "Is an object class `pk_scales`?", "topics": [ "is.pk_scales" ] }, { "page": "is.pkproto", "title": "Is an object pkproto?", "topics": [ "is.pkproto" ] }, { "page": "log_likelihood", "title": "Log-likelihood", "topics": [ "log_likelihood" ] }, { "page": "logLik.pk", "title": "Log-likelihood", "concept": [ "fit evaluation metrics", "log likelihood functions", "methods for fitted pk objects" ], "topics": [ "logLik.pk" ] }, { "page": "mapping", "title": "New mapping", "topics": [ "mapping" ] }, { "page": "midpt_log10", "title": "Log10-scaled midpoint", "topics": [ "midpt_log10" ] }, { "page": "model_1comp", "title": "1-compartment model", "topics": [ "model_1comp" ] }, { "page": "model_2comp", "title": "2-compartment model", "topics": [ "model_2comp" ] }, { "page": "model_flat", "title": "Flat model", "topics": [ "model_flat" ] }, { "page": "model_httk_gas_pbtk", "title": "Gas pbtk `httk` model", "topics": [ "model_httk_gas_pbtk" ] }, { "page": "nca", "title": "nca()", "topics": [ "nca" ] }, { "page": "nca.default", "title": "Default method for nca()", "topics": [ "nca.default" ] }, { "page": "nca.pk", "title": "NCA for a `pk` object", "topics": [ "nca.pk" ] }, { "page": "pk", "title": "Create a new `pk` object", "topics": [ "pk" ] }, { "page": "pk_add", "title": "Add a `pkproto` object to a `pk` object", "topics": [ "pk_add" ] }, { "page": "pk_add.default", "title": "Add pkproto object default method", "topics": [ "pk_add.default" ] }, { "page": "pk_add.pk_facet_data", "title": "Add facet_data()", "topics": [ "pk_add.pk_facet_data" ] }, { "page": "pk_add.pk_loq_group", "title": "Add loq_group", "topics": [ "pk_add.pk_loq_group" ] }, { "page": "pk_add.pk_nca_group", "title": "Add a `pk_nca_group` object.", "topics": [ "pk_add.pk_nca_group" ] }, { "page": "pk_add.pk_scales", "title": "Add a `pk_scales` object to a `pk` object.", "topics": [ "pk_add.pk_scales" ] }, { "page": "pk_add.pk_sd_group", "title": "Add sd_group", "topics": [ "pk_add.pk_sd_group" ] }, { "page": "pk_add.pk_settings_optimx", "title": "Add a `pk_settings_optimx` object.", "topics": [ "pk_add.pk_settings_optimx" ] }, { "page": "pk_add.pk_settings_preprocess", "title": "Add a `pk_settings_preprocess` object.", "topics": [ "pk_add.pk_settings_preprocess" ] }, { "page": "pk_add.pk_stat_error_model", "title": "Add a `pk_stat_error_model` object.", "topics": [ "pk_add.pk_stat_error_model" ] }, { "page": "pk_add.pk_stat_model", "title": "Add a `pk_stat_model` object.", "topics": [ "pk_add.pk_stat_model" ] }, { "page": "pk_add.uneval", "title": "Add an `uneval` object", "topics": [ "pk_add.uneval" ] }, { "page": "pk_model", "title": "Create a new `pk_model` object", "topics": [ "pk_model" ] }, { "page": "pk_subtract", "title": "Subtract a `pkproto` object from a `pk` object", "topics": [ "pk_subtract" ] }, { "page": "pk_subtract.default", "title": "Subtract pkproto object default method", "topics": [ "pk_subtract.default" ] }, { "page": "pk_subtract.pk_stat_model", "title": "Subtract a `pk_stat_model` object.", "topics": [ "pk_subtract.pk_stat_model" ] }, { "page": "pkdataset_nheerlcleaned", "title": "Toxicokinetic data from the \"Concentration vs. Time Database\"", "topics": [ "pkdataset_nheerlcleaned" ] }, { "page": "plot.pk", "title": "Plot a [pk()] object.", "topics": [ "plot.pk" ] }, { "page": "post_name_value", "title": "Creates a [cli::cli_fmt()] output for the pattern \"name(x), length = \"", "topics": [ "post_name_value" ] }, { "page": "predict.pk", "title": "Get predictions", "concept": [ "methods for fitted pk objects" ], "topics": [ "predict.pk" ] }, { "page": "print.pk", "title": "Print a user-friendly version of a `pk` object", "topics": [ "print.pk" ] }, { "page": "pseudo_cvt", "title": "Creating a simple test CvT dataset", "topics": [ "pseudo_cvt" ] }, { "page": "recalculate_httk_pbtk_params", "title": "Recalculating parameters for `httk`'s pbtk or gas_pbtk model", "topics": [ "recalculate_httk_pbtk_params" ] }, { "page": "rename2_cvt", "title": "Convert invivoPKfit output table names to the CvTdb names", "topics": [ "rename2_cvt" ] }, { "page": "residuals.pk", "title": "Get residuals", "concept": [ "methods for fitted pk objects" ], "topics": [ "residuals.pk" ] }, { "page": "rmse", "title": "Root mean squared error (RMSE)", "topics": [ "rmse" ] }, { "page": "rmse.default", "title": "Root mean squared error (RMSE) default method", "topics": [ "rmse.default" ] }, { "page": "rmse.pk", "title": "Root mean squared error", "concept": [ "fit evaluation metrics", "methods for fitted pk objects" ], "topics": [ "rmse.pk" ] }, { "page": "rowwise_calc_percentages", "title": "Helper function for calculating percentages of count data, by row", "topics": [ "rowwise_calc_percentages" ] }, { "page": "rsq", "title": "rsq()", "topics": [ "rsq" ] }, { "page": "rsq.default", "title": "Default method for rsq()", "topics": [ "rsq.default" ] }, { "page": "rsq.pk", "title": "Calculate R-squared for observed vs. predicted values", "concept": [ "fit evaluation metrics", "methods for fitted pk objects" ], "topics": [ "rsq.pk" ] }, { "page": "scale_conc", "title": "Scale concentrations", "topics": [ "scale_conc" ] }, { "page": "scale_time", "title": "Scale times", "topics": [ "scale_time" ] }, { "page": "set_params_optimize", "title": "Set model parameters to optimize", "concept": [ "pk_model modifiers" ], "topics": [ "set_params_optimize" ] }, { "page": "set_params_starts", "title": "Set model parameter starts", "concept": [ "pk_model modifiers" ], "topics": [ "set_params_starts" ] }, { "page": "settings_optimx", "title": "`optimx` optimizer settings", "topics": [ "settings_optimx" ] }, { "page": "settings_preprocess", "title": "Data preprocessing settings", "topics": [ "settings_preprocess" ] }, { "page": "stat_error_model", "title": "Error model", "topics": [ "stat_error_model" ] }, { "page": "stat_loq_group", "title": "LOQ Group", "topics": [ "stat_loq_group" ] }, { "page": "stat_model", "title": "Add PK model(s) to be fitted", "topics": [ "stat_model" ] }, { "page": "stat_nca_group", "title": "NCA group", "topics": [ "stat_nca_group" ] }, { "page": "stat_sd_group", "title": "SD Group", "topics": [ "stat_sd_group" ] }, { "page": "status_data_info", "title": "Status ID for data summary info", "topics": [ "status_data_info" ] }, { "page": "status_fit", "title": "Status ID for fitting", "topics": [ "status_fit" ] }, { "page": "status_init", "title": "Status ID for initialization", "topics": [ "status_init" ] }, { "page": "status_prefit", "title": "Status ID for pre-fitting", "topics": [ "status_prefit" ] }, { "page": "status_preprocess", "title": "Status ID for preprocessing", "topics": [ "status_preprocess" ] }, { "page": "subtract_pk", "title": "Subtract various `pkproto` objects from a `pk` object", "topics": [ "subtract_pk" ] }, { "page": "summary.pk", "title": "Print summary of a `pk` object", "topics": [ "summary.pk" ] }, { "page": "time_conversions", "title": "Time conversion table", "topics": [ "time_conversions" ] }, { "page": "time_units", "title": "Allowable time units", "topics": [ "time_units" ] }, { "page": "tkstats_1comp", "title": "Toxicokinetic statistics for 1-compartment model", "topics": [ "tkstats_1comp" ] }, { "page": "tkstats_2comp", "title": "Toxicokinetic statistics for 1-compartment model", "concept": [ "2-compartment model functions", "built-in model functions" ], "topics": [ "tkstats_2comp" ] }, { "page": "tkstats_flat", "title": "TK stats for flat model", "topics": [ "tkstats_flat" ] }, { "page": "tkstats_httk_gas_pbtk", "title": "TK stats for gas_pbtk model fit with inivivoPKfit", "topics": [ "tkstats_httk_gas_pbtk" ] }, { "page": "toggle_clearance_mode", "title": "Switch between model parameters to optimize", "concept": [ "pk_model modifiers" ], "topics": [ "toggle_clearance_mode" ] }, { "page": "transformed_params_2comp", "title": "Transformed parameters for 2-compartment model", "concept": [ "2-compartment model functions", "built-in model functions" ], "topics": [ "transformed_params_2comp" ] }, { "page": "twofold_test", "title": "twofold_test()", "topics": [ "twofold_test" ] }, { "page": "twofold_test.default", "title": "Default method for twofold_test()", "topics": [ "twofold_test.default" ] }, { "page": "twofold_test.pk", "title": "Evaluate whether data and predictions are within two-fold of mean or concentration, respectively", "topics": [ "twofold_test.pk" ] } ], "_pkglogo": "https://github.com/cran/invivoPKfit/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/cran/invivoPKfit/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "data.table", "DBI", "deSolve", "dplyr", "expm", "farver", "generics", "ggplot2", "glue", "gtable", "httk", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "minqa", "mirai", "mitools", "msm", "mvtnorm", "nanonext", "nloptr", "numDeriv", "optimx", "pillar", "PK", "pkgconfig", "pracma", "purrr", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "Rdpack", "rlang", "S7", "scales", "stringi", "stringr", "survey", "survival", "tibble", "tidyr", "tidyselect", "truncnorm", "utf8", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "manuscript2024_final.Rmd", "filename": "manuscript2024_final.html", "title": "Manuscript Figures and Tables (2024, submitted)", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Setup", "Pulling data from CvTdb", "Minimal PK object", "Running all possible fitting options", "Characterizing the data", "Number of data groups with both blood and plasma data available", "Number of data groups where time scaling could occur", "How many experiments (Chemical, Species, Reference, Route, Media) were flagged for potential dose dependence?", "Evaluating time and concentration ranges", "Evaluating data variability", "Figure 3", "Supplemental Figure 3: Histogram of data variability by time", "Evaluating fitting options", "Winning model tally", "RMSLE for Cmax and AUC (with some tallys for extreme values)", "AUC_inf and Cmax comparison", "Goodness of fit metrics", "Get all predictions", "Factor of two model error", "Evaluate the various GOF metrics", "Rank fitting options", "Supplemental Table 2: Save evaluation results", "Plots for evaluation of fitting options", "Goodness-of-fit metrics Rsq and RMSLE across fitting options", "Cmax RMSLE vs. AUC RMSLE across fitting options", "Analysis Plots and Tables for Best Set of Fitting Options", "Supp Figure 7: invivoPKfit model performance", "Figure 4 and Supplemental Figures 4 & 5: Model performance vs Data Variability", "Figure 5: Multiple goodness-of-fit metrics validate model performance", "Figure 7: Examples fits for chemicals with R-squared and within 2-fold", "Supp. Fig 8: plots of the five data groups that were best fit by the null model", "Figure 6: Comparing derived TK stats with human TK stats from Lombardo et al.", "Supp. Fig. 9: Fgutabs comparison with literature values compiled by Musther et al. (2014)", "Supp. Fig. 10: Parallelization decreases runtime of invivoPKfit", "Summary fit data for all fitting options, all models, all data groups", "Individual study level analysis", "All plots for best set of fitting options", "Print sessionInfo()" ], "created": "2025-01-09 14:30:02", "modified": "2025-08-26 14:10:02", "commits": 3 }, { "source": "main_vignette.Rmd", "filename": "main_vignette.html", "title": "User Guide", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "The model fitting workflow", "Select data to be fit", "Initialize a pk object", "Step 1: Pre-processing data", "Step 2: Data information", "Step 3: Pre-fitting", "Step 4: Model fitting", "Fast-forward to model fitting", "Post-fitting: Getting information about the fitted models", "Coefficients, residuals, and predictions", "Plots", "Model evaluation metrics", "Data", "Toxicokinetic statistics", "Winning model", "Anatomy of a pk object", "Original data", "Variable mapping", "Expressions in the aes() mapping specification", "Current status", "Data grouping", "Settings for data pre-processing", "routes_keep", "media_keep", "ratio_conc_dose", "impute_loq, loq_group and calc_loq_factor", "impute_sd, sd_group", "Data information settings", "Optimizer settings", "Data transformations (scalings)", "Concentration transformations (scalings)", "dose_norm", "log10_trans", "my_pk$scales$time", "Models to be fitted", "Error model to apply during fitting", "\"Hierarchical\" error model", "\"Pooled\" analysis", "\"Separate\" analysis", "Providing new instructions for a pk object", "Checking the current instructions for a pk object", "Check original data", "Check mapping", "Check status", "Check data grouping", "Check settings_preprocess", "Check nca_group", "Check settings_optimx", "Check scale_conc", "Check scale_time", "Check stat_model", "Check stat_error_model", "Replacing instructions with new ones", "What happens to a pk object as you go through the steps of model fitting workflow", "Initialization", "Pre-processing data", "Data summary info", "Pre-fitting", "Fitting", "Keeping track of workflow status as you change instructions", "A few worked examples", "Compare fits made using different error models", "How to add a new PK model to invivopkfit", "Model function requirements", "conc_fun requirements", "auc_fun requirements", "params_fun requirements", "tkstats_fun requirements", "Simplified model modification interface", "Caveats" ], "created": "2025-01-09 14:30:02", "modified": "2025-08-26 14:10:02", "commits": 2 }, { "source": "mainfit.Rmd", "filename": "mainfit.html", "title": "Wambaugh et al. (2018): Estimating TK Parameters from In Vivo Data", "author": "John Wambaugh and Caroline Ring", "engine": "knitr::rmarkdown", "headings": [ "Initialized the Random Number Generator:", "Do the noncompartment model fit", "Do the 2-compartment model fit", "Plot the 2-compartment concentration vs. time", "Do the 1-compartment model fit", "Plot one compartment concentration vs. time", "Output the dataset analyzed:" ], "created": "2025-01-09 14:30:02", "modified": "2025-01-09 14:30:02", "commits": 1 } ], "_score": 3.1760912590556813, "_indexed": true, "_nocasepkg": "invivopkfit", "_universes": [ "jfwambaugh" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.2", "date": "2026-05-23T07:49:01.000Z", "distro": "noble", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "f813290e3cf7f41d69fb0add7495c440a1a7d3580187bfd3058b057dd1fcf47f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" }, { "r": "4.6.0", "os": "linux", "version": "2.0.2", "date": "2026-05-23T07:49:03.000Z", "distro": "noble", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "c963f643a36642c0065111c0faa269a3280eff6ada43283877dae988d0e7039e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" }, { "r": "4.5.3", "os": "mac", "version": "2.0.2", "date": "2026-05-23T07:48:26.000Z", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "a04dd731cb653e34eca3581b2138b8ccd63494cd6d060b28167b255788300ff3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" }, { "r": "4.6.0", "os": "mac", "version": "2.0.2", "date": "2026-05-23T07:48:21.000Z", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "df6031bda4db80638856cd8dfa6411dc4ebeb959a2e357003ecbcfe919de527e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" }, { "r": "4.6.0", "os": "wasm", "version": "2.0.2", "date": "2026-05-23T07:49:05.000Z", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "0ebfa92ced854a20e0ea425a93ff1a15e4f35c776309046271899b6c3a718eff", "status": "success", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" }, { "r": "4.7.0", "os": "win", "version": "2.0.2", "date": "2026-05-23T07:48:09.000Z", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "b08c1249c5387c5071f13d66392969d9771f4e96e6c3239a28d96bbea5551707", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" }, { "r": "4.5.3", "os": "win", "version": "2.0.2", "date": "2026-05-23T07:47:44.000Z", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "f6ae3d79d36158842c791f3ce5225779196e6bce1f9c0df5467e3cacc2bba06f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" }, { "r": "4.6.0", "os": "win", "version": "2.0.2", "date": "2026-05-23T07:47:59.000Z", "commit": "5d0fcf6da6be865b17fa947191e0da1142f43cd4", "fileid": "3ac6ac1a53303f1711ff18d4f0a985a43094d94e5f619687335ed71cada3b804", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/jfwambaugh/actions/runs/26327226241" } ] }