{ "_id": "6a104bc1acfb0bcc41ca0049", "Package": "httkexamples", "Version": "0.0.1", "Date": "2025-12-03", "Title": "High-Throughput Toxicokinetics Examples", "Description": "High throughput toxicokinetics (\"HTTK\") is the combination\nof 1) chemical-specific in vitro measurements or in silico\npredictions and 2) generic mathematical models, to predict\nabsorption, distribution, metabolism, and excretion by the\nbody. HTTK methods have been described by Pearce et al. (2017)\n() and Breen et al. (2021)\n(). Here we provide examples\n(vignettes) applying HTTK to solve various problems in\nbioinformatics, toxicology, and exposure science. In accordance\nwith Davidson-Fritz et al. (2025)\n(), whenever a new HTTK model\nis developed, the code to generate the figures evaluating that\nmodel is added as a new vignettte.", "Authors@R": "c(\nperson(\"John\", \"Wambaugh\", email = \"john.wambaugh@UL.org\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4024-534X\")),\nperson(\"Robert\", \"Pearce\", role = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-3168-4049\")),\nperson(\"Caroline\", \"Ring\", email = \"Ring.Caroline@epa.gov\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-0463-1251\")),\nperson(\"Greg\", \"Honda\", email = \"honda.gregory@epa.gov\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0001-7713-9850\")),\nperson(\"Matt\", \"Linakis\", email = \"MLINAKIS@ramboll.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0003-0526-2395\")),\nperson(\"Dustin\", \"Kapraun\", email = \"kapraun.dustin@epa.gov\",\nrole = c(\"aut\"), comment = c(ORCID= \"0000-0001-5570-6383\")),\nperson(\"Kimberly\", \"Truong\", email = \"truong.kimberly@epa.gov\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0003-1716-1006\")),\nperson(\"Meredith\", \"Scherer\", email=\"Scherer.Meredith@epa.gov\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-9785-7363\")),\nperson(\"Annabel\", \"Meade\", email = \"aemeade7@gmail.com\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-5452-8797\")),\nperson(\"Celia\", \"Schacht\", email=\"Schacht.Celia@epa.gov\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0002-8131-513X\")),\nperson(\"Elaina\", \"Kenyon\",\nrole = c(\"ctb\"), comment = c(ORCID = \"0000-0001-8781-2391\"))\n)", "RdMacros": "Rdpack", "License": "MIT + file LICENSE", "LazyData": "true", "LazyDataCompression": "xz", "Encoding": "UTF-8", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "URL": "https://chemicalinsights.ul.org/", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-10 07:51:26 UTC", "User": "root" }, "Author": "John Wambaugh [aut, cre] (ORCID:\n), Robert Pearce [aut]\n(ORCID: ), Caroline Ring\n[aut] (ORCID: ), Greg\nHonda [aut] (ORCID: ),\nMatt Linakis [aut] (ORCID:\n), Dustin Kapraun [aut]\n(ORCID: ), Kimberly\nTruong [aut] (ORCID: ),\nMeredith Scherer [aut] (ORCID:\n), Annabel Meade [aut]\n(ORCID: ), Celia Schacht\n[aut] (ORCID: ), Elaina\nKenyon [ctb] (ORCID: )", "Maintainer": "John Wambaugh ", "Config/pak/sysreqs": "cmake make libuv1-dev", "Repository": "https://wambaughul.r-universe.dev", "Date/Publication": "2025-12-10 21:39:07 UTC", "RemoteUrl": "https://github.com/cran/httkexamples", "RemoteRef": "HEAD", "RemoteSha": "f98d97a130b1c257e689749454589ee7fea43860", "MD5sum": "994ab6a9b3df03c8a030132d1dbdad9f", "_user": "wambaughul", "_type": "src", "_file": "httkexamples_0.0.1.tar.gz", "_fileid": "6a924a1f08659a495c56fa44fc9e4d0bf6dd527df9935fb37884a94ff300b2f7", "_filesize": 2861290, "_sha256": "6a924a1f08659a495c56fa44fc9e4d0bf6dd527df9935fb37884a94ff300b2f7", "_created": "2026-05-10T07:51:26.000Z", "_published": "2026-05-22T12:27:45.893Z", "_distro": 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(2024) (doi:10.1016/j.envint.2024.109047 ) determined the half-lives of 15 per- and polyfluoroalkyl substances in a single male volunteer.", "object": "PFAS2025", "class": [ "data.frame" ], "fields": [ "compound", "DTXSID", "PREFERRED_NAME", "CASRN", "Cluri.mlpmin", "Cltot.mlpmin", "fup", "Clfilt.mlpmin", "Clfec.mlpmin", "C0.PE.ugpL", "C0.95.ugpL", "Kel.pd", "Halflife.PE.d", "Halflife.95.d", "Vd.PE.mlpkg", "Vd.95.mlpkg" ], "rows": 15, "table": true, "tojson": true }, { "name": "armitage_input", "title": "Parameters for in vitro distribution analysis in Honda et al. (2019) Honda et al. (2019) (doi:10.1371/journal.pone.0217564 ) used the Armitage et al. (2014) (doi:10.1021/es501955g ) mass-balance model to predict the impact of in vitro partitioning on free chemical concentrations.", "object": "armitage_input", "class": [ "data.table", "data.frame" ], "fields": [ "compound_name", "casrn", "MW", "MP", "gkow", "gkaw", "gswat" ], "rows": 1194, "table": true, "tojson": true }, { "name": "aylward2014", "title": "Aylward et al. 2014", "object": "Kapraun2022Vignette", "class": [ "data.frame" ], "fields": [ "Specific.Chemical", "DTXSID", "PREFERRED_NAME", "MOLECULAR_FORMULA", "AVERAGE_MASS", "Study.Short.Citation", "Chemical.Category", "details.on.matrix.comparison...e.g...cord.blood.lipid..maternal.serum.lipid..or.cord.blood.wet.weight..maternal.whole.blood.wet.weight", "maternal.samples..number.of.detects", "maternal.samples..total.N", "infant.samples..number.of.detects", "infant.samples..total.N", "Paired.sample.results.reported..", "Study.size", "infant.central.tendency.concentration..only.for.non.paired.studies.", "maternal.central.tendency.concentration..only.for.non.paired.studies.", "units.for.sampling..only.for.non.paired.studies.", "Lipid.adjusted.", "infant.maternal.conc...Central.tendency..calculate.j.k..or.report.paired.result.", "Lower.bound", "Upper.bound", "Central.tendency.type..mean..geomean..median..other.", "LB.type..min..5th..ile..etc..", "UB.type..max..95th..ile..etc..", "Notes", "Population.notes" ], "rows": 491, "table": true, "tojson": true }, { "name": "concentration_data_Linakis2020", "title": "Concentration data involved in Linakis 2020 vignette analysis.", "object": "Linakis2020", "class": [ "data.frame" ], "fields": [ "X.1", "X", "PREFERRED_NAME", "DTXSID", "CASRN", "AVERAGE_MASS", "DOSE", "DOSE_U", "EXP_LENGTH", "TIME", "TIME_U", "CONC_SPECIES", "SAMPLING_MATRIX", "SOURCE_CVT", "ORIG_CONC_U", "CONCENTRATION" ], "rows": 2142, "table": true, "tojson": true }, { "name": "dermal.nonvolatilechems", "title": "Non-volatile chemicals with ToxCast data Meade et al. (submitted) performed in vitro-in vivo extrapolation for dermal exposures assuming 8 hours of exposure via hands submerged in a liquid with 1 ppm of chemical. These were the chemicals analyzed.", "object": "CvTdermal", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "dermal.toxcast", "title": "Chemicals with ToxCast data for Meade et al. (submitted) chemicals Meade et al. (submitted) performed in vitro-in vivo extrapolation for dermal exposures assuming 8 hours of exposure via hands submerged in a liquid with 1 ppm of chemical. These are the ToxCast in vitro screening data for those chemicals.", "object": "CvTdermal", "class": [ "data.frame" ], "fields": [ "Chemical", "DTXSID", "Total.Assays", "Unique.Assays", "Total.Hits", "Unique.Hits", "Low.AC50", "Low.AC10", "Low.ACC", "Q10.AC50", "Q10.AC10", "Q10.ACC", "Med.AC50", "Med.AC10", "Med.ACC", "Q90.AC50", "Q90.AC10", "Q90.ACC" ], "rows": 6506, "table": true, "tojson": true }, { "name": "dermalCvT2025", "title": "Toxicokinetic concentration vs. time (CvT) data for Meade et al. (submitted) chemicals Meade et al. (submitted) evaluated a generic PBTK model for dermal exposure using in vivo CvT data curated from the literature. These data will eventually be incorporated in the the CvTdb (Sayre et al., 2020, doi:10.1038/s41597-020-0455-1 ).", "object": "CvTdermal", "class": [ "data.frame" ], "fields": [ "id", "fk_series_id", "time_original", "conc_original", "conc_sd_original", "conc_lower_bound_original", "conc_upper_bound_original", "no_conc_val_type", "time_hr", "conc", "conc_sd", "conc_lower_bound", "conc_upper_bound", "analyte_name_original", "fk_analyzed_chemical_id", "figure_name", "figure_series_identifier", "time_units_original", "conc_units_original", "conc_units_normalized", "log_concentration_values", "loq", "loq_units", "analytical_method_detail", "n_subjects_in_series", "fk_subject_id", "conc_medium_original", "conc_medium_normalized", "fk_study_id", "radiolabeled", "analyte_dtxsid", "analyte_casrn", "test_substance_dtxsid", "test_substance_casrn", "fk_test_chemical_id", "analyte_name_secondary_original", "analyte_casrn_original", "figure_type", "x_min", "x_max", "y_min", "y_max", "lod", "lod_units", "log_conc_units", "fk_conc_medium_id", "cumulative_amount", "fk_reference_document_id", "fk_extraction_document_id", "fk_dosed_chemical_id", "test_substance_name_original", "dose_level_normalized", "dose_level_original", "dose_level_original_units", "administration_route_original", "administration_route_normalized", "dose_duration", "dose_frequency", "dose_vehicle", "dose_volume", "fasting_period", "test_substance_name_secondary_original", "test_substance_casrn_original", "dose_duration_units", "dermal_dose_vehicle_pH", "dermal_applied_area", "aerosol_particle_diameter_mean", "aerosol_particle_diameter_gsd", "aerosol_particle_density", "aerosol_particle_density_units", "aerosol_particle_diameter_units", "dermal_applied_area_units", "fk_administration_route", "species", "sex", "age", "age_category", "notes", "subtype", "height", "weight", "weight_kg", "weight_estimated", "age_units", "height_units", "weight_units", "height_cm", "extraction_document_pmid" ], "rows": 1928, "table": true, "tojson": true }, { "name": "Dimitrijevic.IVD", "title": "Dimitrijevic et al. (2022)In Vitro Cellular and Nominal Concentration", "object": "Scherer2025Vignette", "class": [ "data.table", "data.frame" ], "fields": [ "Name", "casrn", "Type", "Arnot_pka", "Arnot_pkb", "log KOW,N", "log KAW,N", "Reported_Ccell_µM", "Predicted_Ccell_µM", "FoA", "FBSf", "v_working", "cell_yield", "sarea", "nomconc", "well_number", "v_total", "Notes" ], "rows": 12, "table": true, "tojson": true }, { "name": "fetalpcs", "title": "Fetal Partition Coefficients", "object": "Kapraun2022Vignette", "class": [ "data.frame" ], "fields": [ "Compound", "DTXSID", "Tissue", "PC", "Fup", "Rb2p", "HTTK.pred.t2up", "HTTK.pred.nocal.t2up", "HTTK.pred", "HTTK.pred.nocal", "Weijs2013" ], "rows": 87, "table": true, "tojson": true }, { "name": "Frank2018invivo", "title": "Literature In Vivo Data on Doses Causing Neurological Effects", "object": "Frank2018", "class": [ "data.frame" ], "fields": [ "Substance_CASRN", "Chemical", "DSSTox_Substance_Id", "Species", "Exposure", "Dose.Route", "Endpoint", "Reference", "Dose", "Dose.Units", "Route", "Days", "Critical.concentration", "Lower.95..CI", "Higher.95..CI", "Compound.abbrev" ], "rows": 14, "table": true, "tojson": true }, { "name": "howgate", "title": "Howgate et al. (2006)", "object": "vignettes", "class": [ "data.table", "data.frame" ], "fields": [ "Compound", "Short.name", "Route", "Number.studies", "Total.subjects", "Female.subjects", "Age.min", "Age.max", "Median.Clearance..1.h.", "X90..CI.min", "X90..CI.max" ], "rows": 24, "table": true, "tojson": true }, { "name": "huh2011", "title": "Huh et al. 2011 Huh et al. (2011) (doi:10.3109/00498254.2011.598582 ) provided interspecies allometric scaling parameters for whole body clearance for a a variety of pharmaceuticals.", "object": "PFAS2025", "class": [ "data.frame" ], "fields": [ "...1", "Compounds", "MW", "Observed CL (Mean (CV%), ml/min/kg) in human", "Character", "Elimination", "Fu%", "a", "b", "Reference", "DTXSID", "PREFERRED_NAME", "CASRN" ], "rows": 83, "table": true, "tojson": true }, { "name": "johnson", "title": "Johnson et al. (2006)", "object": "vignettes", "class": [ "data.table", "data.frame" ], "fields": [ "Compound", "Route", "Total.subjects", "Age.min", "Age.max", "BW.mean", "BW.sd", "Clearance.mean", "Clearance.sd", "Clearance.units", "Race" ], "rows": 60, "table": true, "tojson": true }, { "name": "meade2025", "title": "Simulation outputs from Meade et al. (submitted) Meade et al. (submitted) performed generic PBTK simulations for dermal exposure under a variety of assumptions. Although the code to recreate these simulations is provided, it is time-intensive. The 2025 outputs from the simulations are stored in this list of data.frames.", "object": "CvTdermal", "class": [ "data.frame" ], "fields": [ "PREFERRED_NAME", "DTXSID", "Water.Solubility.mg.L", "Vapor.Pressure.mmHg", "Boiling.Point.C", "logP", "MW", "Volatility" ], "rows": 14, "table": true, "tojson": true }, { "name": "metabolism_data_Linakis2020", "title": "Metabolism data involved in Linakis et al. 2020 (doi:10.1038/s41370-020-0238-y ) vignette analysis.", "object": "Linakis2020", "class": [ "data.frame" ], "fields": [ "X", "PREFERRED_NAME", "DTXSID", "CASRN", "AVERAGE_MASS", "QSAR_READY_SMILES", "HENRYS_LAW_ATM.M3.MOLE_OPERA_PRED", "OCTANOL_AIR_PARTITION_COEFF_LOGKOA_OPERA_PRED", "OCTANOL_WATER_PARTITION_LOGP_OPERA_PRED", "VAPOR_PRESSURE_MMHG_OPERA_PRED", "WATER_SOLUBILITY_MOL.L_OPERA_PRED", "EXPOS_AVAIL", "OSHA_PEL", "CAL_OSHA_PEL", "NIOSH_REL", "ACGIH_2015_TLV", "max.value", "VMAX", "VMAX_U", "KM", "KM_U", "SOURCE_MET", "SPECIES", "CALC_FUP", "EXP_FUP", "HENRYS_LAW_DIMENSIONLESS", "LOG_HENRYS_LAW_DIMENSIONLESS", "CALC_PBA", "EXP_PBA", "CALC_CLINT", "EXP_CLINT", "WTKG", "GLKG", "CHEM_CLASS" ], "rows": 83, "table": true, "tojson": true }, { "name": "Obach2008", "title": "Published Pharmacokinetic Parameters from Obach et al. 2008", "object": "vignettes", "class": [ "data.frame" ], "fields": [ "Name", "CAS", "VDss (L/kg)", "CL (mL/min/kg)", "fu", "MRT (h)", "t1/2 (h)" ], "rows": 670, "table": true, "tojson": true }, { "name": "onlyp", "title": "NHANES Exposure Data", "object": "vignettes", "class": [ "data.table", "data.frame" ], "fields": [ "exposure.median", "exposure.median.95CI.lower", "exposure.median.95CI.upper", "chemcas", "ExpoCast.group" ], "rows": 1060, "table": true, "tojson": true }, { "name": "pc.data", "title": "Partition Coefficient Data", "object": "vignettes", "class": [ "data.frame" ], "fields": [ "CAS", "Drug", "Tissue", "Species", "fu", "A.B.N", "LogP", "Exp_PC" ], "rows": 1221, "table": true, "tojson": true }, { "name": "pharma", "title": "DRUGS|NORMAN: Pharmaceutical List with EU, Swiss, US Consumption Data", "object": "wambaugh2019", "class": [ "matrix", "array" ], "fields": {}, "rows": 14, "table": true, "tojson": true }, { "name": "pksim.pcs", "title": "Partition Coefficients from PK-Sim", "object": "Kapraun2022Vignette", "class": [ "data.frame" ], "fields": [ "Drug", "DTXSID", "Tissue", "PKSim.pred", "Blood-to-plasma concentration ratio", "Tissue-to-blood partition coefficient", "Method", "HTTK.pred" ], "rows": 72, "table": true, "tojson": true }, { "name": "pregnonpregaucs", "title": "AUCs for Pregnant and Non-Pregnant Women", "object": "Kapraun2022Vignette", "class": [ "data.frame" ], "fields": [ "Drug", "DTXSID", "PREFERRED_NAME", "CASRN", "AVERAGE_MASS", "Dose", "Dose Units", "Dosing frequency", "Dose.Route", "Gestational.Age.Weeks", "NonPreg.Duration.Days", "Preg.Duration.Days", "Parameter", "Units", "Observed.Non.Pregnant", "Predicted Non-Pregnant", "Ratio Non-Pregnant", "Observed.Pregnant", "Predicted Pregnant", "Ratio Pregnant", "Mass Conversion", "Converted Units", "Observed.Non.Pregnant2", "Predicted Non-Pregnant3", "Ratio Non-Pregnant4", "Observed.Pregnant5", "Predicted Pregnant6", "Ratio Pregnant7", "Source observed data non-pregnant", "Source observed data pregnant", "Predicted.Non.Pregnant.httk", "Predicted.Pregnant.httk", "Ratio.obs", "Ratio.httk" ], "rows": 12, "table": true, "tojson": true }, { "name": "Scherer2025.IVD", "title": "Literature Measurements of In Vitro Cellular and Nominal Concentration", "object": "Scherer2025Vignette", "class": [ "data.table", "data.frame" ], "fields": [ "well_number", "well_desc", "sysID", "diam", "area_bottom", "v_total", "PaperTitle", "Citation", "ChemicalName", "CellType", "Species", "ExposureDuration_hrs", "SerumType", "NominalDose_uM", "ExperimentalDose_uM", "CellConcentration_uM", "MediaConcentration_uM", "FigureNumber", "Notes", "radius", "height", "sarea", "Vcell_uL", "casrn", "nomconc", "FBSf", "v_working", "cell_yield" ], "rows": 153, "table": true, "tojson": true }, { "name": "supptab1_Linakis2020", "title": "Supplementary output from Linakis 2020 vignette analysis.", "object": "Linakis2020", "class": [ "data.frame" ], "fields": [ "Chemical", "DTXSID", "CASRN", "CAMEO.Chemical.Class", "Molecular.Weight..g.mol.", "Log.P", "Solubility..mol.L.", "Blood.Air.Partition.Coefficient", "Available.Species.Data", "Vmax..pmol.min.10.6.cells.", "KM..uM.", "Metabolism.Data.Source", "Concentration.Time.Data.Source" ], "rows": 50, "table": true, "tojson": true }, { "name": "supptab2_Linakis2020", "title": "More supplementary output from Linakis 2020 vignette analysis.", "object": "Linakis2020", "class": [ "data.frame" ], "fields": [ "Chemical.Dropped", "Regression.Slope", "Regression.R.2", "Regression.RMSE", "Orthogonal.RMSE", "Percent.Data.Censored", "Cmax.Regression.Slope", "Cmax.Regression.R.2", "Cmax.Orthogonal.RMSE", "AUC.Regression.Slope", "AUC.Regression.R.2", "AUC.Orthogonal.RMSE" 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(2018) screened the blood of 75 pregnant women for the presence of environmental organic acids (EOAs) and identified mass spectral features corresponding to 453 chemical formulae of which 48 could be mapped to likely structures. Of the 48 with tentative structures the identity of six were confirmed with available chemical standards.", "object": "Kapraun2022Vignette", "class": [ "matrix", "array" ], "fields": {}, "rows": 20, "table": true, "tojson": true }, { "name": "Wetmore2012", "title": "Published toxicokinetic predictions based on in vitro data from Wetmore et al. 2012.", "object": "vignettes", "class": [ "data.frame" ], "fields": [ "Chemical", "CAS", "Literature.Css", "Lit.Css.Low", "Lit.Css.High", "Notes", "Fub..Clint", "Notes.1", "Fub..Clint..Caco.2", "Notes.2", "Fub..Clint2", "Notes.3", "Fub..Clint..Caco.23", "Notes.4", "X" ], "rows": 13, "table": true, "tojson": true } ], "_help": [ { "page": "abraham2024", "title": "Abraham et al. 2024 Abraham et al. (2024) (doi:10.1016/j.envint.2024.109047 ) determined the half-lives of 15 per- and polyfluoroalkyl substances in a single male volunteer.", "topics": [ "Abraham2024", "abraham2024" ] }, { "page": "armitage_input", "title": "Parameters for in vitro distribution analysis in Honda et al. (2019) Honda et al. (2019) (doi:10.1371/journal.pone.0217564 ) used the Armitage et al. (2014) (doi:10.1021/es501955g ) mass-balance model to predict the impact of in vitro partitioning on free chemical concentrations.", "topics": [ "Armitage_input", "armitage_input" ] }, { "page": "aylward2014", "title": "Aylward et al. 2014", "topics": [ "Aylward2014", "aylward2014" ] }, { "page": "concentration_data_Linakis2020", "title": "Concentration data involved in Linakis 2020 vignette analysis.", "topics": [ "concentration_data_Linakis2020" ] }, { "page": "dermal.nonvolatilechems", "title": "Non-volatile chemicals with ToxCast data Meade et al. (submitted) performed in vitro-in vivo extrapolation for dermal exposures assuming 8 hours of exposure via hands submerged in a liquid with 1 ppm of chemical. These were the chemicals analyzed.", "topics": [ "dermal.nonvolatilechems" ] }, { "page": "dermal.toxcast", "title": "Chemicals with ToxCast data for Meade et al. (submitted) chemicals Meade et al. (submitted) performed in vitro-in vivo extrapolation for dermal exposures assuming 8 hours of exposure via hands submerged in a liquid with 1 ppm of chemical. These are the ToxCast in vitro screening data for those chemicals.", "topics": [ "dermal.toxcast" ] }, { "page": "dermalCvT2025", "title": "Toxicokinetic concentration vs. time (CvT) data for Meade et al. (submitted) chemicals Meade et al. (submitted) evaluated a generic PBTK model for dermal exposure using in vivo CvT data curated from the literature. These data will eventually be incorporated in the the CvTdb (Sayre et al., 2020, doi:10.1038/s41597-020-0455-1 ).", "topics": [ "dermalCvT2025" ] }, { "page": "Dimitrijevic.IVD", "title": "Dimitrijevic et al. (2022)In Vitro Cellular and Nominal Concentration", "topics": [ "Dimitrijevic.IVD" ] }, { "page": "fetalpcs", "title": "Fetal Partition Coefficients", "topics": [ "fetalPCs", "fetalpcs" ] }, { "page": "Frank2018invivo", "title": "Literature In Vivo Data on Doses Causing Neurological Effects", "topics": [ "Frank2018invivo" ] }, { "page": "howgate", "title": "Howgate et al. (2006)", "topics": [ "howgate" ] }, { "page": "huh2011", "title": "Huh et al. 2011 Huh et al. (2011) (doi:10.3109/00498254.2011.598582 ) provided interspecies allometric scaling parameters for whole body clearance for a a variety of pharmaceuticals.", "topics": [ "Huh2011", "huh2011" ] }, { "page": "johnson", "title": "Johnson et al. (2006)", "topics": [ "johnson" ] }, { "page": "meade2025", "title": "Simulation outputs from Meade et al. (submitted) Meade et al. (submitted) performed generic PBTK simulations for dermal exposure under a variety of assumptions. Although the code to recreate these simulations is provided, it is time-intensive. The 2025 outputs from the simulations are stored in this list of data.frames.", "topics": [ "Meade2025", "meade2025" ] }, { "page": "metabolism_data_Linakis2020", "title": "Metabolism data involved in Linakis et al. 2020 (doi:10.1038/s41370-020-0238-y ) vignette analysis.", "topics": [ "metabolism_data_Linakis2020" ] }, { "page": "Obach2008", "title": "Published Pharmacokinetic Parameters from Obach et al. 2008", "topics": [ "Obach2008" ] }, { "page": "onlyp", "title": "NHANES Exposure Data", "topics": [ "onlyp" ] }, { "page": "pc.data", "title": "Partition Coefficient Data", "topics": [ "pc.data" ] }, { "page": "pharma", "title": "DRUGS|NORMAN: Pharmaceutical List with EU, Swiss, US Consumption Data", "topics": [ "pharma" ] }, { "page": "pksim.pcs", "title": "Partition Coefficients from PK-Sim", "topics": [ "pksim.pcs" ] }, { "page": "pregnonpregaucs", "title": "AUCs for Pregnant and Non-Pregnant Women", "topics": [ "pregnonpregaucs" ] }, { "page": "Scherer2025.IVD", "title": "Literature Measurements of In Vitro Cellular and Nominal Concentration", "topics": [ "Scherer2025.IVD" ] }, { "page": "supptab1_Linakis2020", "title": "Supplementary output from Linakis 2020 vignette analysis.", "topics": [ "supptab1_Linakis2020" ] }, { "page": "supptab2_Linakis2020", "title": "More supplementary output from Linakis 2020 vignette analysis.", "topics": [ "supptab2_Linakis2020" ] }, { "page": "thyroid.ac50s", "title": "ToxCast thyroid-related bioactivity data", "topics": [ "thyroid.ac50s" ] }, { "page": "truong25.seem3", "title": "SEEM3 Example Data for Truong et al. 2025", "topics": [ "truong25.seem3" ] }, { "page": "wallis2023", "title": "Wallis et al. 2023 Wallis et al. (2023) (doi:10.1021/acs.est.2c08241 ) estimated the human toxicokinetic half-lives for a range of per- and poly-fluorinated alkyl substances (PFAS).", "topics": [ "Wallis2023", "wallis2023" ] }, { "page": "wambaugh2019", "title": "in vitro Toxicokinetic Data from Wambaugh et al. (2019)", "topics": [ "wambaugh2019" ] }, { "page": "wambaugh2019.nhanes", "title": "NHANES Chemical Intake Rates for chemicals in Wambaugh et al. (2019)", "topics": [ "wambaugh2019.nhanes" ] }, { "page": "wambaugh2019.raw", "title": "Raw Bayesian in vitro Toxicokinetic Data Analysis from Wambaugh et al. (2019)", "topics": [ "wambaugh2019.raw" ] }, { "page": "wambaugh2019.seem3", "title": "ExpoCast SEEM3 Consensus Exposure Model Predictions for Chemical Intake Rates", "topics": [ "wambaugh2019.seem3" ] }, { "page": "wambaugh2019.tox21", "title": "Tox21 2015 Active Hit Calls (EPA)", "topics": [ "wambaugh2019.tox21" ] }, { "page": "wang2018", "title": "Wang et al. 2018 Wang et al. (2018) screened the blood of 75 pregnant women for the presence of environmental organic acids (EOAs) and identified mass spectral features corresponding to 453 chemical formulae of which 48 could be mapped to likely structures. Of the 48 with tentative structures the identity of six were confirmed with available chemical standards.", "topics": [ "Wang2018", "wang2018" ] }, { "page": "Wetmore2012", "title": "Published toxicokinetic predictions based on in vitro data from Wetmore et al. 2012.", "topics": [ "Wetmore2012" ] } ], "_readme": "https://github.com/cran/httkexamples/raw/HEAD/README.md", "_rundeps": [ "base64enc", "bslib", "cachem", "cli", "cpp11", "data.table", "DBI", "deSolve", "digest", "dplyr", "evaluate", "expm", "farver", "fastmap", "fontawesome", "fs", "generics", "ggplot2", "glue", "gtable", "highr", "htmltools", "httk", "isoband", "jquerylib", "jsonlite", "knitr", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "memoise", "mime", "minqa", "mitools", "msm", "mvtnorm", "numDeriv", "pillar", "pkgconfig", "purrr", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "Rdpack", "rlang", "rmarkdown", "S7", "sass", "scales", "survey", "survival", "tibble", "tidyselect", "tinytex", "truncnorm", "utf8", "vctrs", "viridisLite", "withr", "xfun", "yaml" ], "_vignettes": [ { "source": "Va_Pearce2017.Rmd", "filename": "Va_Pearce2017.html", "title": "Pearce et al. 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Wambaugh", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "HTTK Version", "Prepare for session", "Clear the memory", "eval = execute.vignette", "Load the relevant libraries", "Prepare custom functions", "Number of chemicals", "Aylward cord-blood data", "Load/format the data", "Convert the units:", "Compare HTTK predictions with maternal:fetal observations from Aylward 2014", "Aylward Ratio figures:", "Clean up repeated observations:", "Cord Blood Ratio Predictions without Fup Adjustement:", "Generate text for results section:", "Cord Blood Ratio Predictions with Fup Adjustement:", "Examine performance when excluding certain chemical classes:", "Evaluation of Area Under the Curve Predictions", "Predict AUC", "Generate AUC Predicted vs. Observed Figure", "Evaluation of Partition Coefficient Predictions", "Predict partition coefficients", "Create Observed vs. Predicted Plot", "First indicate compound:", "Then indicate tissues:", "Compare httk partition coefficients with PKsim:", "Chemical Prioritization on the Basis of Fetal Brain Concentration", "Make predictions for fetal:maternal plasma ratio using three daily doses from week 13 to full term", "Create final table holding all predictions for paper:", "Error in fetal:maternal ratio (inverse of maternal:fetal ratio):", "brain:plasma partitioning", "brain:plasma uncertainty partitioning", "Combine different ratio predicitons together for figure", "Make prioritization figure:", "Look at ionization state:", "Evaluate any value added by PBPK model over just using partition coefficients:", "Repeat analysis without fetal protein binding change:", "Protein Binding Figures", "Plot the fetal protein binding changes predicted:", "Maternal-Fetal Predictions across HTTK Chemical Library:", "Histogram of maternal-fetal ratio", "Statistics on maternal-fetal ratio for full HTTK library", "Examine Maternal-Fetal ratio Predictions without fetaul Fup correction:", "Supplemental Histogram of maternal-fetal ratio without Fup correction", "Statistics on maternal-fetal ratio for full HTTK library without Fup correction", "Code used to create data distributed with vignette" ], "created": "2025-12-10 21:39:07", "modified": "2025-12-10 21:39:07", "commits": 1 }, { "source": "Vj_Truong2025.Rmd", "filename": "Vj_Truong2025.html", "title": "Truong et al. (2025): Full Human Gestational IVIVE", "author": "Kimberly T.Truong, John F. Wambaugh, Dustin F. Kapraun, Sarah E. Davidson-Fritz, Stephanie Eytcheson, Richard Judson, Katie Paul-Friedman", "engine": "knitr::rmarkdown", "headings": [ "Overview", "HTTK Version", "eval = execute.vignette", "Data Import", "Load libraries", "IVIVE using 3-compartment steady state model", "Examine Chemicals", "In silico predictions of TK parameters", "Examine missing chemicals", "Predicting AEDs based on Css50 (in plasma)", "Load ExpoCast predictions (SEEM3)", "IVIVE using the Full Human Gestational Model", "Compute half-lives", "Simulate full-term human pregnancy model", "Calculate AEDs by Target and Tissue", "Figure 9: Priority Chemicals based on maternal-fetal BERs", "Comparing IVIVE models based on BER prioritization", "Table 8", "Figure 10: Understanding and Interpreting Maternal-Fetal BERs", "Code used to create data distributed with vignette" ], "created": "2025-12-10 21:39:07", "modified": "2025-12-10 21:39:07", "commits": 1 }, { "source": "Vk_WambaughSubmitted.Rmd", "filename": "Vk_WambaughSubmitted.html", "title": "Wambaugh (Submitted): HTTK for PFAS", "author": "John F. Wambaugh", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "HTTK Version", "Prepare for session", "Session Preparation", "Clear the memory", "eval = execute.vignette", "Load the relevant libraries", "Function to calculate root mean squared log10 error", "Analysis of Crizer et al. (2023) $Cl_{int}$ data", "Methods", "Evaluate Ratio Blood:Plasma Predictions", "Evaluate Membrane Affinity Predictions", "New In Vitro TK Parameters", "Examine Kbloodair", "HTTK Interspecies Clearance Differences", "Remove Rat-specific HTTK data:", "Add bioavailability predictions", "Compare default httk against in vivo clearance data:", "Add in Dawson 2023 predictions for later", "Calculate human:species clearance ratios", "Add non-PFAS clearances from literature", "Evaluating Machine Learning Model for PFAS TK", "New HTTK Model for PFAS", "Text for manuscript", "Other Analyses" ], "created": "2025-12-10 21:39:07", "modified": "2025-12-10 21:39:07", "commits": 1 }, { "source": "Vl_MeadeSubmitted.Rmd", "filename": "Vl_MeadeSubmitted.html", "title": "Meade (submitted): High Throughput Dermal Exposure Model", "author": "Annabel Meade, Celia Schacht, Alex George", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "HTTK Version", "Table of Contents (added by AG 01/02/2024)", "Prepare for session", "eval = FALSE", "Set working directory and install packages", "Result 1: Model Verification using In Vivo Data", "Step One: Load Data", "Display which chemicals are being looked at", "Step Two: Clean and Format Data", "Step Three: Simulate Data", "Simulation Set-Up", "Simulations: Nested For Loops", "Step Four: Calculate Root Mean Squared Log10 Errors (RMSLE)", "Step Five: Plot Simulations", "Results 2: IVIVE", "Step Two: Load Chemical Data", "Step Three: Clean Data (Only Non-Volatiles and a few of the Semi-Volatiles from the validation study)", "Step Four: Compute Q10.AC50 (and other parameters of interest)", "Step Five: Conduct In Vitro to In Vivo Extrapolation", "Save data", "Step Six: Plot Results" ], "created": "2025-12-10 21:39:07", "modified": "2025-12-10 21:39:07", "commits": 1 }, { "source": "Vm_SchererSubmitted.Rmd", "filename": "Vm_SchererSubmitted.html", "title": "Characterizing Accuracy of Model Predictions for Chemical Concentration in High Throughput Screening Assays", "author": "Meredith Scherer, Madison Feshuk, James M. Armitage, Jon A. Arnot, David Crizer, Michael Devito, Stephen S. Ferguson, Kimberly Freeman, Gregory S. Honda, Josh Harrill, Alessandro Sangion, Caroline Tebes-Stevens, Katie Paul Friedman, John F. Wambaugh", "engine": "knitr::rmarkdown", "headings": [ "Abstract", "HTTK Version", "Prepare for session", "Clear the memory", "eval = execute.vignette", "Load the relevant libraries", "Data Collection", "Load and format the data", "Run the in vitro distribution models", "Manipulate data and prep for plotting", "Main Paper Plots:", "Figure 1:", "Figure 2:", "Figure 3:", "Figure 4:", "Figure 5:", "Main Paper Calculations:", "Over/underestimation", "Effect of water solubility value for Cyclosporin A", "Effect of experimentally measured nominal dose", "Table S1.", "Table S2. 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