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parameter thresholds", "topics": [ "exclude_nca_by_param" ] }, { "page": "filter_interval", "title": "Subset data to the rows used for calculations within an interval", "topics": [ "filter_interval" ] }, { "page": "filter.PKNCAresults", "title": "dplyr filtering for PKNCA", "concept": [ "dplyr verbs" ], "topics": [ "filter.PKNCAconc", "filter.PKNCAdose", "filter.PKNCAresults" ] }, { "page": "find.dose.regimen", "title": "Find the dosing regimen from the dose times of one subject", "concept": [ "Interval determination" ], "topics": [ "find.dose.regimen" ] }, { "page": "find.tau", "title": "Find the repeating interval within a vector of doses", "concept": [ "Interval determination" ], "topics": [ "find.tau" ] }, { "page": "findOperator", "title": "Find the first occurrence of an operator in a formula and return the left, right, or both sides of the operator.", "concept": [ "Formula parsing" ], "topics": [ "findOperator" ] }, { "page": "fit_half_life", "title": "Perform the half-life fit given the data. The function simply fits the data without any validation. No selection of points or any other components are done.", "topics": [ "fit_half_life" ] }, { "page": "fit_half_life_tobit", "title": "Perform a Tobit half-life fit given the data. The function fits the data using maximum likelihood without any point selection or validation.", "topics": [ "fit_half_life_tobit" ] }, { "page": "fit_half_life_tobit_LL", "title": "Negative log-likelihood for Tobit half-life regression", "topics": [ "fit_half_life_tobit_LL" ] }, { "page": "formula.PKNCAconc", "title": "Extract the formula from a PKNCAconc object.", "topics": [ "formula.PKNCAconc", "formula.PKNCAdose" ] }, { "page": "geomean", "title": "Compute the geometric mean, sd, and CV", "topics": [ "geocv", "geomean", "geosd" ] }, { "page": "get_halflife_curve", "title": "Interpolate and extrapolate concentrations along the half-life fit", "topics": [ "get_halflife_curve" ] }, { "page": "get_halflife_fit", "title": "Get the half-life fit line for each interval", "topics": [ "get_halflife_fit" ] }, { "page": "get_halflife_points", "title": "Determine which concentrations were used for half-life calculation", "topics": [ "get_halflife_points" ] }, { "page": "get_impute_column", "title": "Get the name of the intervals column that the imputation methods come from", "concept": [ "Imputation" ], "topics": [ "get_impute_column" ] }, { "page": "get_impute_method", "title": "Get the imputation methods for the intervals", "concept": [ "Imputation" ], "topics": [ "get_impute_method" ] }, { "page": "get.best.model", "title": "Extract the best model from a list of models using the AIC.", "topics": [ "get.best.model" ] }, { "page": "get.interval.cols", "title": "Get the columns that can be used in an interval specification", "concept": [ "Interval specifications" ], "topics": [ "get.interval.cols" ] }, { "page": "get.parameter.deps", "title": "Get all columns that depend on a parameter", "concept": [ "Interval specifications" ], "topics": [ "get.parameter.deps" ] }, { "page": "getAttributeColumn", "title": "Retrieve the value of an attribute column.", "topics": [ "getAttributeColumn" ] }, { "page": "getColumnValueOrNot", "title": "Get the value from a column in a data frame if the value is a column there, otherwise, the value should be a scalar or the length of the data.", "topics": [ "getColumnValueOrNot" ] }, { "page": "getDataName", "title": "Get the name of the element containing the data for the current object.", "concept": [ "PKNCA object extractors" ], "topics": [ "getDataName", "getDataName.default", "getDataName.PKNCAconc", "getDataName.PKNCAdose", "getDataName.PKNCAresults" ] }, { "page": "getDepVar", "title": "Get the dependent variable (left hand side of the formula) from a PKNCA object.", "concept": [ "PKNCA object extractors" ], "topics": [ "getDepVar" ] }, { "page": "getGroups.PKNCAconc", "title": "Get the groups (right hand side after the '|' from a PKNCA object).", "topics": [ "getGroups.PKNCAconc", "getGroups.PKNCAdata", "getGroups.PKNCAdose", "getGroups.PKNCAresults" ] }, { "page": "getIndepVar", "title": "Get the independent variable (right hand side of the formula) from a PKNCA object.", "concept": [ "PKNCA object extractors" ], "topics": [ "getIndepVar" ] }, { "page": "group_by.PKNCAresults", "title": "dplyr grouping for PKNCA", "concept": [ "dplyr verbs" ], "topics": [ "group_by.PKNCAconc", "group_by.PKNCAdose", "group_by.PKNCAresults", "ungroup.PKNCAconc", "ungroup.PKNCAdose", "ungroup.PKNCAresults" ] }, { "page": "group_vars.PKNCAconc", "title": "Get grouping variables for a PKNCA object", "topics": [ "group_vars.PKNCAconc", "group_vars.PKNCAdata", "group_vars.PKNCAdose", "group_vars.PKNCAresults" ] }, { "page": "inner_join.PKNCAresults", "title": "dplyr joins for PKNCA", "concept": [ "dplyr verbs" ], "topics": [ "full_join.PKNCAconc", "full_join.PKNCAdose", "full_join.PKNCAresults", "inner_join.PKNCAconc", "inner_join.PKNCAdose", "inner_join.PKNCAresults", "left_join.PKNCAconc", "left_join.PKNCAdose", "left_join.PKNCAresults", "right_join.PKNCAconc", "right_join.PKNCAdose", "right_join.PKNCAresults" ] }, { "page": "interp_extrap_conc_method", "title": "Interpolate or extrapolate concentrations using the provided method", "topics": [ "extrapolate_conc_lambdaz", "interpolate_conc_linear", "interpolate_conc_log", "interp_extrap_conc_method" ] }, { "page": "interp.extrap.conc", "title": "Interpolate concentrations between measurements or extrapolate concentrations after the last measurement.", "concept": [ "Concentration interpolation and extrapolation" ], "topics": [ "extrapolate.conc", "interp.extrap.conc", "interp.extrap.conc.dose", "interpolate.conc" ] }, { "page": "interval_add_impute", "title": "Add or remove an imputation method in the intervals of a PKNCAdata object", "concept": [ "Interval specifications" ], "topics": [ "interval_add_impute", "interval_remove_impute" ] }, { "page": "interval_add_param", "title": "Add or remove parameters in the intervals of a PKNCAdata object", "concept": [ "Interval specifications" ], "topics": [ "interval_add_param", "interval_remove_param" ] }, { "page": "interval_add_secondary", "title": "Link a secondary parameter to the interval it is calculated against", "concept": [ "Interval specifications" ], "topics": [ "interval_add_secondary" ] }, { "page": "is_sparse_pk", "title": "Is a PKNCA object used for sparse PK?", "topics": [ "is_sparse_pk", "is_sparse_pk.PKNCAconc", "is_sparse_pk.PKNCAdata", "is_sparse_pk.PKNCAresults" ] }, { "page": "model.frame.PKNCAconc", "title": "Extract the columns used in the formula (in order) from a PKNCAconc or PKNCAdose object.", "topics": [ "model.frame.PKNCAconc", "model.frame.PKNCAdose" ] }, { "page": "mutate.PKNCAresults", "title": "dplyr mutate-based modification for PKNCA", "concept": [ "dplyr verbs" ], "topics": [ "mutate.PKNCAconc", "mutate.PKNCAdose", "mutate.PKNCAresults" ] }, { "page": "normalize", "title": "Normalize parameters in a PKNCAresults object or data.frame", "topics": [ "normalize" ] }, { "page": "normalize_by_col", "title": "Normalize PKNCA results by a column of the concentration data", "topics": [ "normalize_by_col" ] }, { "page": "normalize_exclude", "title": "Normalize the exclude column by setting blanks to NA", "topics": [ "normalize_exclude" ] }, { "page": "parse_formula_to_cols", "title": "Convert a formula representation to the columns for input data", "concept": [ "Formula parsing" ], "topics": [ "parse_formula_to_cols" ] }, { "page": "pk_nca_result_to_df", "title": "Convert the grouping info and list of results for each group into a results data.frame", "topics": [ "pk_nca_result_to_df" ] }, { "page": "pk.business", "title": "Run any function with a maximum missing fraction of X and 0s possibly counting as missing. The maximum fraction missing comes from 'PKNCA.options(\"max.missing\")'.", "topics": [ "pk.business" ] }, { "page": "pk.calc.ae", "title": "Calculate amount excreted (typically in urine or feces)", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.ae" ] }, { "page": "pk.calc.aucabove", "title": "Calculate the AUC above a given concentration", "topics": [ "pk.calc.aucabove" ] }, { "page": "pk.calc.aucinf.obs_sparse", "title": "Sparse estimators for the AUC and AUMC to infinity", "concept": [ "Sparse Methods" ], "topics": [ "pk.calc.aucinf.obs_sparse", "pk.calc.aumcinf.obs_sparse" ] }, { "page": "pk.calc.aucivlast_sparse", "title": "Sparse AUC and AUMC for IV bolus dosing with C0 back-extrapolation", "concept": [ "Sparse Methods" ], "topics": [ "pk.calc.aucivall_sparse", "pk.calc.aucivinf.obs_sparse", "pk.calc.aucivlast_sparse", "pk.calc.aumcivall_sparse", "pk.calc.aumcivinf.obs_sparse", "pk.calc.aumcivlast_sparse" ] }, { "page": "pk.calc.auclast_sparse", "title": "Sparse estimators for the AUC and AUMC to the last measured concentration", "concept": [ "Sparse Methods" ], "topics": [ "pk.calc.aucall_sparse", "pk.calc.auclast_sparse", "pk.calc.aumcall_sparse", "pk.calc.aumclast_sparse" ] }, { "page": "pk.calc.aucpext", "title": "Calculate the AUC percent extrapolated", "concept": [ "Half-life and elimination" ], "topics": [ "pk.calc.aucpext" ] }, { "page": "pk.calc.auxc", "title": "Compute the Area Under the (Moment) Curve", "concept": [ "AUC calculations" ], "topics": [ "pk.calc.auc", "pk.calc.auc.all", "pk.calc.auc.inf", "pk.calc.auc.inf.obs", "pk.calc.auc.inf.pred", "pk.calc.auc.last", "pk.calc.aumc", "pk.calc.aumc.all", "pk.calc.aumc.inf", "pk.calc.aumc.inf.obs", "pk.calc.aumc.inf.pred", "pk.calc.aumc.last", "pk.calc.auxc" ] }, { "page": "pk.calc.auxcint", "title": "Calculate AUXC (AUC or AUMC) over an interval with interpolation/extrapolation", "concept": [ "AUC calculations", "AUMC calculations" ], "topics": [ "pk.calc.aucint", "pk.calc.aucint.all", "pk.calc.aucint.inf.obs", "pk.calc.aucint.inf.pred", "pk.calc.aucint.last", "pk.calc.aumcint", "pk.calc.aumcint.all", "pk.calc.aumcint.inf.obs", "pk.calc.aumcint.inf.pred", "pk.calc.aumcint.last", "pk.calc.auxcint" ] }, { "page": "pk.calc.auxciv", "title": "Calculate AUXC (AUC or AUMC) for IV dosing with C0 back-extrapolation", "concept": [ "AUC calculations", "AUMC calculations" ], "topics": [ "pk.calc.auciv", "pk.calc.auciv_pbext", "pk.calc.aumciv", "pk.calc.auxciv" ] }, { "page": "pk.calc.c0", "title": "Estimate the concentration at dosing time for an IV bolus dose.", "concept": [ "NCA parameters for concentrations during the intervals" ], "topics": [ "pk.calc.c0", "pk.calc.c0.method.c0", "pk.calc.c0.method.c1", "pk.calc.c0.method.cmin", "pk.calc.c0.method.logslope", "pk.calc.c0.method.set0" ] }, { "page": "pk.calc.cav", "title": "Calculate the average concentration during an interval.", "concept": [ "NCA parameters for concentrations during the intervals" ], "topics": [ "pk.calc.cav" ] }, { "page": "pk.calc.ceoi", "title": "Determine the concentration at the end of infusion", "concept": [ "NCA parameters for concentrations during the intervals" ], "topics": [ "pk.calc.ceoi" ] }, { "page": "pk.calc.cl", "title": "Calculate the (observed oral) clearance", "concept": [ "Clearance and volume parameters" ], "topics": [ "pk.calc.cl" ] }, { "page": "pk.calc.clast.obs", "title": "Determine the last observed concentration above the limit of quantification (LOQ).", "concept": [ "NCA parameters for concentrations during the intervals" ], "topics": [ "pk.calc.clast.obs" ] }, { "page": "pk.calc.clr", "title": "Calculate renal clearance", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.clr" ] }, { "page": "pk.calc.cmax", "title": "Determine maximum observed PK concentration", "concept": [ "NCA parameters for concentrations during the intervals" ], "topics": [ "pk.calc.cmax", "pk.calc.cmin" ] }, { "page": "pk.calc.count_conc", "title": "Count the number of concentration measurements in an interval", "concept": [ "NCA parameters for concentrations during the intervals" ], "topics": [ "pk.calc.count_conc", "pk.calc.count_conc_measured" ] }, { "page": "pk.calc.ctrough", "title": "Determine the trough (end of interval) concentration", "concept": [ "NCA parameters for concentrations during the intervals" ], "topics": [ "pk.calc.cstart", "pk.calc.ctrough" ] }, { "page": "pk.calc.deg.fluc", "title": "Determine the degree of fluctuation", "concept": [ "Multiple-dose PK parameters" ], "topics": [ "pk.calc.deg.fluc", "pk.calc.swing" ] }, { "page": "pk.calc.dn", "title": "Determine dose normalized NCA parameter", "topics": [ "pk.calc.dn" ] }, { "page": "pk.calc.erint", "title": "Calculate the excretion rate over the interval", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.erint" ] }, { "page": "pk.calc.erlst", "title": "Calculate the last measurable excretion rate", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.erlst" ] }, { "page": "pk.calc.ermax", "title": "Calculate the maximum excretion rate", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.ermax" ] }, { "page": "pk.calc.ertlst", "title": "Calculate the midpoint collection time of the last measurable excretion rate", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.ertlst" ] }, { "page": "pk.calc.ertmax", "title": "Calculate the midpoint collection time of the maximum excretion rate", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.ertmax" ] }, { "page": "pk.calc.f", "title": "Calculate the absolute (or relative) bioavailability", "topics": [ "pk.calc.f" ] }, { "page": "pk.calc.fe", "title": "Calculate fraction excreted (typically in urine or feces)", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.fe" ] }, { "page": "pk.calc.half.life", "title": "Compute the half-life and associated parameters", "concept": [ "Half-life and elimination", "NCA parameter calculations" ], "topics": [ "pk.calc.half.life" ] }, { "page": "pk.calc.kel", "title": "Calculate the elimination rate (Kel)", "concept": [ "Clearance and volume parameters" ], "topics": [ "pk.calc.kel" ] }, { "page": "pk.calc.mrt", "title": "Calculate the mean residence time (MRT) for single-dose data or linear multiple-dose data.", "concept": [ "Mean residence time" ], "topics": [ "pk.calc.mrt", "pk.calc.mrt.iv", "pk.calc.mrt.md", "pk.calc.mrt.md.iv" ] }, { "page": "pk.calc.ptr", "title": "Determine the peak-to-trough ratio", "concept": [ "Multiple-dose PK parameters" ], "topics": [ "pk.calc.ptr" ] }, { "page": "pk.calc.ratio", "title": "Calculate the ratio of a parameter between two intervals", "topics": [ "pk.calc.ratio" ] }, { "page": "pk.calc.sparse_auc", "title": "Calculate AUC and related parameters using sparse NCA methods", "concept": [ "Sparse Methods" ], "topics": [ "pk.calc.sparse_auc", "pk.calc.sparse_auclast" ] }, { "page": "pk.calc.sparse_aumc", "title": "Calculate AUMC and related parameters using sparse NCA methods", "concept": [ "Sparse Methods" ], "topics": [ "pk.calc.sparse_aumc", "pk.calc.sparse_aumclast" ] }, { "page": "pk.calc.thalf.eff", "title": "Calculate the effective half-life", "concept": [ "Half-life and elimination" ], "topics": [ "pk.calc.thalf.eff" ] }, { "page": "pk.calc.time_above", "title": "Determine time at or above a set value", "topics": [ "pk.calc.time_above" ] }, { "page": "pk.calc.tlag", "title": "Determine the observed lag time (time before the first concentration above the limit of quantification or above the first concentration in the interval)", "concept": [ "NCA time parameters" ], "topics": [ "pk.calc.tlag" ] }, { "page": "pk.calc.tlast", "title": "Determine time of last observed concentration above the limit of quantification.", "concept": [ "NCA time parameters" ], "topics": [ "pk.calc.tfirst", "pk.calc.tlast" ] }, { "page": "pk.calc.tmax", "title": "Determine time of maximum observed PK concentration", "concept": [ "NCA time parameters" ], "topics": [ "pk.calc.tmax" ] }, { "page": "pk.calc.tmin", "title": "Determine time of minimum observed PK concentration", "concept": [ "NCA time parameters" ], "topics": [ "pk.calc.tmin" ] }, { "page": "pk.calc.totdose", "title": "Extract the dose used for calculations", "topics": [ "pk.calc.totdose" ] }, { "page": "pk.calc.volpk", "title": "Calculate the total urine volume", "concept": [ "Urine/Excretion parameters" ], "topics": [ "pk.calc.volpk" ] }, { "page": "pk.calc.vz", "title": "Calculate the terminal volume of distribution (Vz)", "concept": [ "Clearance and volume parameters" ], "topics": [ "pk.calc.vss", "pk.calc.vz" ] }, { "page": "pk.nca", "title": "Compute NCA parameters for each interval for each subject.", "topics": [ "pk.nca" ] }, { "page": "pk.nca.interval", "title": "Compute all PK parameters for a single concentration-time data set", "topics": [ "pk.nca.interval" ] }, { "page": "pk.nca.intervals", "title": "Compute NCA for multiple intervals", "topics": [ "pk.nca.intervals" ] }, { "page": "pk.tss", "title": "Compute the time to steady-state (tss)", "concept": [ "Time to steady-state calculations" ], "topics": [ "pk.tss" ] }, { "page": "pk.tss.data.prep", "title": "Clean up the time to steady-state parameters and return a data frame for use by the tss calculators.", "topics": [ "pk.tss.data.prep" ] }, { "page": "pk.tss.monoexponential", "title": "Compute the time to steady state using nonlinear, mixed-effects modeling of trough concentrations.", "concept": [ "Time to steady-state calculations" ], "topics": [ "pk.tss.monoexponential" ] }, { "page": "pk.tss.monoexponential.individual", "title": "A helper function to estimate individual and single outputs for monoexponential time to steady-state.", "topics": [ "pk.tss.monoexponential.individual" ] }, { "page": "pk.tss.monoexponential.population", "title": "A helper function to estimate population and popind outputs for monoexponential time to steady-state.", "topics": [ "pk.tss.monoexponential.population" ] }, { "page": "pk.tss.stepwise.linear", "title": "Compute the time to steady state using stepwise test of linear trend", "concept": [ "Time to steady-state calculations" ], "topics": [ "pk.tss.stepwise.linear" ] }, { "page": "PKNCA", "title": "Compute noncompartmental pharmacokinetics", "topics": [ "PKNCA-package", "PKNCA" ] }, { "page": "pknca_cdisc_codes", "title": "Every registered CDISC PPTESTCD/PPTEST code, with CT membership", "concept": [ "Interval specifications" ], "topics": [ "pknca_cdisc_codes" ] }, { "page": "pknca_check_parameter_classification", "title": "Report parameters that PKNCA cannot classify for automatic selection", "concept": [ "Interval specifications" ], "topics": [ "pknca_check_parameter_classification" ] }, { "page": "pknca_concept", "title": "The concept a parameter calculation function computes", "topics": [ "pknca_concept", "pknca_concept<-" ] }, { "page": "pknca_concepts", "title": "Concepts, tiers, and contexts used to classify NCA parameters", "concept": [ "Interval specifications" ], "topics": [ "pknca_concepts", "pknca_dosing", "pknca_routes", "pknca_sample_types", "pknca_tiers" ] }, { "page": "pknca_difftime_to_unit", "title": "Convert a difftime to a number in a time unit", "topics": [ "pknca_difftime_to_unit" ] }, { "page": "pknca_exclude_rules", "title": "List the automatic NCA result exclusion rules", "concept": [ "Result exclusions" ], "topics": [ "pknca_exclude_rules" ] }, { "page": "pknca_find_units_param", "title": "Find NCA parameters with a given unit type", "topics": [ "pknca_find_units_param" ] }, { "page": "PKNCA_impute_fun_list", "title": "Separate out a vector of PKNCA imputation methods into a list of functions", "concept": [ "Imputation" ], "topics": [ "PKNCA_impute_fun_list" ] }, { "page": "PKNCA_impute_method", "title": "Methods for imputation of data with PKNCA", "concept": [ "Imputation" ], "topics": [ "PKNCA_impute_method", "PKNCA_impute_method_end_conc_drop", "PKNCA_impute_method_start_cmin", "PKNCA_impute_method_start_conc0", "PKNCA_impute_method_start_predose", "PKNCA_impute_method_start_predose_conc0" ] }, { "page": "pknca_impute_methods", "title": "List the imputation methods", "concept": [ "Imputation" ], "topics": [ "pknca_impute_methods" ] }, { "page": "pknca_interval_table", "title": "Build an interval specification from a description of the analysis", "concept": [ "Interval specifications" ], "topics": [ "pknca_interval_table" ] }, { "page": "pknca_match_route", "title": "Match spellings of a route of administration to the route PKNCA uses", "concept": [ "Interval specifications" ], "topics": [ "pknca_match_route" ] }, { "page": "pknca_missing_samples", "title": "Find the samples missing from each subject's nominal sampling schedule", "concept": [ "Result exclusions" ], "topics": [ "pknca_missing_samples" ] }, { "page": "PKNCA_options_defaults", "title": "Get the default values of PKNCA options without changing them", "concept": [ "PKNCA calculation and summary settings" ], "topics": [ "PKNCA_options_defaults" ] }, { "page": "pknca_parameter_table", "title": "How each NCA parameter is classified for interval selection", "concept": [ "Interval specifications" ], "topics": [ "pknca_parameter_table" ] }, { "page": "pknca_presets", "title": "Named argument sets for building an interval specification", "concept": [ "Interval specifications" ], "topics": [ "pknca_presets" ] }, { "page": "pknca_ref", "title": "Mark a formalsmap entry as coming from the reference interval", "concept": [ "Interval specifications" ], "topics": [ "is_pknca_ref", "pknca_ref" ] }, { "page": "pknca_unit_conversion", "title": "Perform unit conversion (if possible) on PKNCA results", "topics": [ "pknca_unit_conversion" ] }, { "page": "pknca_unit_reconcile_factor", "title": "Find the conversion factor between two units, when there is one", "topics": [ "pknca_unit_reconcile_factor" ] }, { "page": "pknca_units_add_paren", "title": "Add parentheses to a unit value, if needed", "topics": [ "pknca_units_add_paren" ] }, { "page": "pknca_units_conversion_factor", "title": "Find the factor converting a value from one unit to another", "topics": [ "pknca_units_conversion_factor" ] }, { "page": "pknca_units_table", "title": "Create a unit assignment and conversion table", "topics": [ "pknca_units_table", "pknca_units_table.default", "pknca_units_table.PKNCAdata" ] }, { "page": "PKNCA.choose.option", "title": "Choose either the value from an option list or the current set value for an option.", "concept": [ "PKNCA calculation and summary settings" ], "topics": [ "PKNCA.choose.option" ] }, { "page": "PKNCA.options", "title": "Set default options for PKNCA functions", "concept": [ "PKNCA calculation and summary settings" ], "topics": [ "PKNCA.options" ] }, { "page": "PKNCA.options.describe", "title": "Describe a PKNCA.options option by name.", "topics": [ "PKNCA.options.describe" ] }, { "page": "PKNCA.set.summary", "title": "Define how NCA parameters are summarized.", "concept": [ "PKNCA calculation and summary settings" ], "topics": [ "PKNCA.set.summary" ] }, { "page": "PKNCAconc", "title": "Create a PKNCAconc object", "concept": [ "PKNCA objects" ], "topics": [ "PKNCAconc", "PKNCAconc.data.frame", "PKNCAconc.default", "PKNCAconc.tbl_df" ] }, { "page": "PKNCAdata", "title": "Create a PKNCAdata object.", "concept": [ "PKNCA objects" ], "topics": [ "PKNCAdata", "PKNCAdata.default", "PKNCAdata.PKNCAconc", "PKNCAdata.PKNCAdose" ] }, { "page": "PKNCAdose", "title": "Create a PKNCAdose object", "concept": [ "PKNCA objects" ], "topics": [ "PKNCAdose", "PKNCAdose.data.frame", "PKNCAdose.default", "PKNCAdose.tbl_df" ] }, { "page": "PKNCAresults", "title": "Generate a PKNCAresults object", "concept": [ "PKNCA objects" ], "topics": [ "PKNCAresults" ] }, { "page": "print.PKNCAconc", "title": "Print and/or summarize a PKNCAconc or PKNCAdose object.", "topics": [ "print.PKNCAconc", "print.PKNCAdose", "summary.PKNCAconc", "summary.PKNCAdose" ] }, { "page": "print.PKNCAdata", "title": "Print a PKNCAdata object", "topics": [ "print.PKNCAdata" ] }, { "page": "print.provenance", "title": "Print the summary of a provenance object", "topics": [ "print.provenance" ] }, { "page": "print.summary_PKNCAresults", "title": "Print the results summary", "topics": [ "print.summary_PKNCAresults" ] }, { "page": "resolve_dose_tau", "title": "Determine the dosing interval (tau) to use for a calculation interval", "concept": [ "Interval determination" ], "topics": [ "resolve_dose_tau" ] }, { "page": "roundingSummarize", "title": "During the summarization of PKNCAresults, do the rounding of values based on the instructions given.", "topics": [ "roundingSummarize" ] }, { "page": "roundString", "title": "Round a value to a defined number of digits printing out trailing zeros, if applicable.", "topics": [ "roundString" ] }, { "page": "select_minimal_grouping_cols", "title": "Find Minimal Grouping Columns for Strata Reconstruction", "topics": [ "select_minimal_grouping_cols" ] }, { "page": "set_intervals", "title": "Set Intervals", "topics": [ "set_intervals" ] }, { "page": "setAttributeColumn", "title": "Add an attribute to an object where the attribute is added as a name to the names of the object.", "topics": [ "setAttributeColumn" ] }, { "page": "setDuration", "title": "Set the duration of dosing or measurement", "topics": [ "setDuration", "setDuration.PKNCAconc", "setDuration.PKNCAdose" ] }, { "page": "setExcludeColumn", "title": "Set the exclude parameter on an object", "topics": [ "setExcludeColumn" ] }, { "page": "setRoute", "title": "Set the dosing route", "topics": [ "setRoute", "setRoute.PKNCAdose" ] }, { "page": "signifString", "title": "Round a value to a defined number of significant digits printing out trailing zeros, if applicable.", "topics": [ "signifString", "signifString.data.frame", "signifString.default" ] }, { "page": "sparse_auc_weight_linear", "title": "Calculate the weight for sparse AUC calculation with the linear-trapezoidal rule", "concept": [ "Sparse Methods" ], "topics": [ "sparse_auc_weight_linear" ] }, { "page": "sparse_bootstrap", "title": "Bootstrap resampling of sparse PK data", "concept": [ "Sparse Methods" ], "topics": [ "sparse_bootstrap" ] }, { "page": "sparse_mean", "title": "Calculate the mean concentration at all time points for use in sparse NCA calculations", "concept": [ "Sparse Methods" ], "topics": [ "sparse_mean" ] }, { "page": "sparse_pk_attribute", "title": "Set or get a sparse_pk object attribute", "topics": [ "sparse_pk_attribute" ] }, { "page": "sparse_to_dense_pk", "title": "Extract the mean concentration-time profile as a data.frame", "topics": [ "sparse_to_dense_pk" ] }, { "page": "summary.PKNCAdata", "title": "Summarize a PKNCAdata object showing important details about the concentration, dosing, and interval information.", "topics": [ "summary.PKNCAdata" ] }, { "page": "summary.PKNCAresults", "title": "Summarize PKNCA results", "topics": [ "summary.PKNCAresults" ] }, { "page": "summary.PKNCAresults_sparse_bootstrap", "title": "Summarize the results of a sparse bootstrap", "concept": [ "Sparse Methods" ], "topics": [ "summary.PKNCAresults_sparse_bootstrap" ] }, { "page": "superposition", "title": "Compute noncompartmental superposition for repeated dosing", "concept": [ "Superposition" ], "topics": [ "superposition", "superposition.numeric", "superposition.PKNCAconc" ] }, { "page": "time_calc", "title": "Times relative to an event (typically dosing)", "topics": [ "time_calc" ] }, { "page": "tss.monoexponential.generate.formula", "title": "A helper function to generate the formula and starting values for the parameters in monoexponential models.", "topics": [ "tss.monoexponential.generate.formula" ] }, { "page": "update.PKNCAresults", "title": "Update existing PKNCAresults with new data", "topics": [ "update.PKNCAresults" ] }, { "page": "var_sparse_auc", "title": "Calculate the variance for the AUC of sparsely sampled PK", "topics": [ "var_sparse_auc" ] } ], "_readme": "https://github.com/humanpred/pknca/raw/HEAD/README.md", "_rundeps": [ "backports", "checkmate", "cli", "cpp11", "digest", "dplyr", "generics", "glue", "lattice", "lifecycle", "lubridate", "magrittr", "nlme", "pillar", "pkgconfig", "purrr", "R6", "rlang", "stringi", "stringr", "tibble", "tidyr", "tidyselect", "timechange", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "v05-auc-calculation-with-PKNCA.Rmd", "filename": "v05-auc-calculation-with-PKNCA.html", "title": "AUC Calculation with PKNCA", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Preparation", "AUC to the Last Value Above the Limit of Quantification (AUC~last~)", "AUC~all~", "AUC to Infinity (AUC~$\\infty$~)", "Partial AUCs" ], "created": "2022-10-04 21:03:19", "modified": "2026-09-27 18:11:52", "commits": 5 }, { "source": "v23-auc-integration-methods.Rmd", "filename": "v23-auc-integration-methods.html", "title": "AUC integration methods", "engine": "knitr::rmarkdown", "headings": [ "Integration methods for Area Under the Concentration-Time curve (AUC)", "Definitions and abbreviations", "Description of methods of integrating between two concentrations before T~last~", "Linear up/logarithmic down (\"lin up/log down\") interpolation", "Linear trapezoidal (\"linear\") interpolation", "Linear to T~max~/logarithmic after T~max~ (\"lin-log\") interpolation", "Description of methods of integrating between two concentrations after T~last~", "\"AUClast\" extrapolation", "\"AUCall\" extrapolation", "\"AUCinf\" extrapolation", "Examples" ], "created": "2023-09-30 17:12:57", "modified": "2023-10-07 14:10:05", "commits": 3 }, { "source": "v50-bioequivalence.Rmd", "filename": "v50-bioequivalence.html", "title": "Bioequivalence Calculations", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "How the calculation works", "Optional packages", "Simulating a 2x2 crossover study", "Noncompartmental analysis", "Bioequivalence assessment", "Interpreting the results", "Reference scaling and regulatory frameworks", "A replicate-design study", "Comparing frameworks side by side", "Unequal variances, covariates, and descriptive comparisons", "Reporting checklist" ], "created": "2026-08-13 22:04:42", "modified": "2026-09-28 12:28:50", "commits": 2 }, { "source": "v02-example-theophylline.Rmd", "filename": "v02-example-theophylline.html", "title": "Computing NCA Parameters for Theophylline", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Load the data", "Merge the Concentration and Dose", "Compute the parameters", "Multiple Dose Example" ], "created": "2022-10-04 21:03:19", "modified": "2026-08-09 15:14:48", "commits": 4 }, { "source": "v08-data-imputation.Rmd", "filename": "v08-data-imputation.html", "title": "Data Imputation", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "How does imputation occur?", "How to select imputation methods to use", "Imputation for the full dataset", "Imputation by calculation interval", "Advanced: Writing your own imputation functions" ], "created": "2022-10-12 17:20:27", "modified": "2026-08-25 16:03:01", "commits": 6 }, { "source": "v31-FDA-introduction.Rmd", "filename": "v31-FDA-introduction.html", "title": "PKNCA – an R package for noncompartmental analysis of pharmacokinetic data", "author": "William Denney", "engine": "knitr::rmarkdown", "headings": [ "PKNCA – an R package for noncompartmental analysis of pharmacokinetic data", "Introduction to PKNCA", "Dataset Basics", "NCA Data are Not Tidy as a Single Dataset", "Dataset Basics: What columns are needed?", "Dataset Basics: Example interval data", "PKNCA Functions", "What functions are the most used?", "How do I do a simple calculation? all steps", "How do I do a simple calculation? Concentration data", "How do I do a simple calculation? Dose data", "How do I do a simple calculation? Calculate results", "How do I do a simple calculation? Get results", "How do I do a simple calculation? Get summary results", "How do I do a simple calculation? Get individual results", "PKNCA datasets", "How does PKNCA think about data?", "What is an \"interval\" and how is it different than a \"group\"?", "Reporting", "Best practices for Data -> PKNCA -> knitr/Quarto", "Graphics are intentionally not part of PKNCA, but there are some tricks that can help...", "Validation of PKNCA", "More information" ], "created": "2026-04-17 20:05:15", "modified": "2026-10-05 01:22:16", "commits": 4 }, { "source": "v06-half-life-calculation.Rmd", "filename": "v06-half-life-calculation.html", "title": "Half-Life Calculation", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Curve Stripping Method", "Select the Points", "Select the Best Fit", "Example", "Manual Point Selection", "Choosing a Point Selection Method", "Column Requirements", "Exclusion of Specific Points with Curve Stripping", "Specification of the Exact Points for Analysis" ], "created": "2022-10-04 21:03:19", "modified": "2026-10-06 20:25:51", "commits": 9 }, { "source": "v06-half-life-calculation-tobit.Rmd", "filename": "v06-half-life-calculation-tobit.html", "title": "Half-life calculation with Tobit regression", "engine": "knitr::rmarkdown", "headings": [ "Half-life calculation with Tobit regression", "Comparison to semi-log regression", "Automatic point selection", "Automatic point selection with semi-log regression", "Automatic point selection with Tobit regression", "Comparison of Tobit and semi-log regression", "Usage", "Basic usage: a single subject", "Example 1: All observations above the LLOQ", "Example 2: BLQ observations before T~last~", "Using the global option", "Full NCA workflow with PKNCAdata", "Controlling Tobit point selection" ], "created": "2024-03-12 16:16:37", "modified": "2026-09-01 00:31:49", "commits": 7 }, { "source": "v01-introduction-and-usage.Rmd", "filename": "v01-introduction-and-usage.html", "title": "Introduction to PKNCA and Usage Instructions", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Quick Start", "Data Handling", "Options: Make PKNCA Work Your Way", "Calculation Options: the PKNCA.options Function", "Summarization Options: the PKNCA.set.summary Function", "Grouping NCA Data", "Selecting Calculation Intervals", "Selection of Data Used for Calculation", "Automatic Interval Determination", "Manual Interval Specification", "Keeping a column from intervals", "Summarizing results", "Updating existing results" ], "created": "2022-10-04 21:03:19", "modified": "2026-08-20 23:14:28", "commits": 12 }, { "source": "v21-methods-for-dose-aware-interpolation-and-extrapolation.Rmd", "filename": "v21-methods-for-dose-aware-interpolation-and-extrapolation.html", "title": "Methods Used for Dose-Aware Concentration Interpolation/Extrapolation", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Methods", "Appendix: Complete Methods Table" ], "created": "2022-10-04 21:03:19", "modified": "2026-08-09 15:14:48", "commits": 2 }, { "source": "v22-time-to-steady-state.Rmd", "filename": "v22-time-to-steady-state.html", "title": "Noncompartmental evaluation of time to steady-state", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Example", "Data setup", "Estimate time to Steady State", "Monoexponential", "Stepwise Linear", "References" ], "created": "2022-10-05 01:29:27", "modified": "2026-08-09 15:14:48", "commits": 6 }, { "source": "v40-options-for-controlling-PKNCA.Rmd", "filename": "v40-options-for-controlling-PKNCA.html", "title": "Options for Controlling PKNCA", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Summary", "Options" ], "created": "2022-10-04 21:03:19", "modified": "2022-10-04 21:03:19", "commits": 1 }, { "source": "v30-training-session.Rmd", "filename": "v30-training-session.html", "title": "PKNCA Training Sessions", "author": "William Denney", "engine": "knitr::rmarkdown", "headings": [ "Introduction to PKNCA and Basics of Its Use", "Introduction to PKNCA", "Enjoy!", "Some NCA Definitions", "Dataset Basics", "NCA Data are Not Tidy as a Single Dataset", "Dataset Basics: Minimum data", "Dataset Basics: What columns are needed?", "Dataset Basics: Example data", "Dataset Basics: Example concentration data", "Dataset Basics: Example dosing data", "Dataset Basics: Example interval data", "Hands-on: First NCA calculation with PKNCA", "PKNCA Functions", "What functions are the most used?", "How do I do a simple calculation? all steps", "How do I do a simple calculation? Concentration data", "How do I do a simple calculation? Dose data", "How do I do a simple calculation? Calculate results", "How do I do a simple calculation? Get results", "How do I do a simple calculation? Get summary results", "How do I do a simple calculation? Get individual results", "PKNCA datasets", "How does PKNCA think about data?", "What is an \"interval\" and how is it different than a \"group\"?", "Common data management requirements before sending data to PKNCA", "Setup your concentration data", "Setup your dosing data (if you have it and even if you don't)", "Define your intervals", "Define your intervals: example", "Calculations above the hood", "Prepare your data for calculation", "Calculate without dosing data", "Calculate without dosing data, try 2", "Dosing data helps with interval setup", "AUC considerations with PKNCA (1/3)", "AUC considerations with PKNCA (2/3)", "AUC considerations with PKNCA (3/3)", "Hands-on workshop", "Steady-state intramuscular administration", "Day 2 Start", "Control your data", "Including and excluding data points", "Exclude data points overall", "Exclude data points overall", "Digression: How is λz automatically calculated?", "λz control (manual exclusions and inclusions of data points)", "Less-common calculations", "Urine calculations", "Urine calculations: understanding what is happening and potential hiccups", "Calculations below the hood", "PKNCA only calculates what is required, not every possible parameter (1 of 2)", "PKNCA only calculates what is required, not every possible parameter (2 of 2)", "How to select the correct parameters for calculations (aka, why are there r sum(grepl(x=names(PKNCA.options(\"single.dose.aucs\")), pattern=\"^auc\")) types of AUC in PKNCA?)", "When are intervals (partly) ignored?", "Control your results", "Excluding results (Not the best way)", "Excluding results (The best way, 1/2)", "Excluding results (The best way, 2/2)", "NCA-related calculations", "Superposition", "Time-to-Steady-state calculations", "Reporting", "Graphics are intentionally not part of PKNCA, but there are some tricks that can help...", "Best practices for Data -> PKNCA -> knitr", "Units (especially clearance)", "Data imputation", "IV bolus AUC (need to add C0)", "Combined, multi-subject data (e.g. sparse animal sampling)", "Limitations", "Secondary parameters (e.g. bioavailability and renal clearance)", "Validation of PKNCA", "Hands-on", "Single- and Multiple-dose, single analyte: Setup the underlying datasets", "Single- and Multiple-dose, single analyte: Setup the concentration and dose datasets", "Single- and Multiple-dose, single analyte: Perform basic analysis", "Single- and Multiple-dose, single analyte: Use intervals for fewer subjects", "Single- and Multiple-dose, single analyte: Use custom intervals per subjects", "Single- and Multiple-dose, parent and metabolite" ], "created": "2022-10-04 21:03:19", "modified": "2026-09-27 18:11:52", "commits": 11 }, { "source": "v60-PKNCA-validation.Rmd", "filename": "v60-PKNCA-validation.html", "title": "PKNCA Validation", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Summary of Testing", "Session Information" ], "created": "2022-10-04 21:03:19", "modified": "2026-08-09 15:14:48", "commits": 3 }, { "source": "v07-post-processing.Rmd", "filename": "v07-post-processing.html", "title": "Post-Processing", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Setup", "Modifying Results", "Exclusion of Select Results", "Exclusion Functions", "Missing Samples and $T_{max}$ Coverage", "Excluding Specific Results", "Multiple Exclusions", "Normalizing Results", "Example: Normalize by a column in the concentration data", "Doing custom normalizations", "Extracting Results", "Summary Results", "Listing of Results", "Concentrations Used for Half-Life Estimation", "The Half-Life Fit", "Concentrations Along the Half-Life Fit" ], "created": "2022-10-04 21:03:19", "modified": "2026-10-07 17:02:32", "commits": 7 }, { "source": "v09-secondary-parameters.Rmd", "filename": "v09-secondary-parameters.html", "title": "Secondary Parameters (Renal Clearance, Bioavailability, and Ratios)", "engine": "knitr::rmarkdown", "headings": [ "What a secondary parameter is", "Linking two intervals by hand", "Renal clearance, start to finish", "The reference interval gains what the link needs", "Letting PKNCA find the reference interval", "When more than one profile could be the reference", "Steering the choice with group_ref", "Writing the linkage into the intervals", "Bioavailability", "Exclusions cross the link", "Units that differ between the two profiles", "A ratio standardizes to a fraction", "A quotient that is not a fraction", "Reporting", "Limitations", "See also" ], "created": "2026-08-31 15:44:57", "modified": "2026-08-31 15:44:57", "commits": 1 }, { "source": "v03-selection-of-calculation-intervals.Rmd", "filename": "v03-selection-of-calculation-intervals.html", "title": "Selection of Calculation Intervals", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Group Matching", "Selecting the Subjects for an Interval", "Intervals", "Automatic Selection of Intervals", "Finding the Dosing Interval", "To Infinity", "Multiple Intervals", "Overlapping Intervals and Different Calculations by Interval", "Intervals with Duration", "Multiple-Dose MRT and Vss", "Intravenous Infusions", "Parameters Available for Calculation in an Interval" ], "created": "2022-10-04 21:03:19", "modified": "2026-10-07 20:46:52", "commits": 13 }, { "source": "v24-sparse-auc-to-infinity.Rmd", "filename": "v24-sparse-auc-to-infinity.html", "title": "Sparse AUC to Infinity and the Uncertainty of lambda.z", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Summary and recommendations", "Introduction", "The sparse AUC to the last measurement", "Extrapolation to infinity (Yuan 1993)", "IV bolus: the back-extrapolated C0", "The uncertainty of lambda.z (delta method)", "Degrees of freedom", "An alternative: lambda.z from the individual samples", "Simulation-estimation study", "Design", "Results: coverage of the AUC to infinity", "Results: coverage of the AUMC to infinity", "Results: the bootstrap", "Results: the bootstrap with more animals at each time", "Results: the Tobit half-life with BLQ samples", "Results: accuracy of the point estimates", "Findings", "Arithmetic or geometric mean profiles", "Calculating it with PKNCA", "Discussion", "References" ], "created": "2026-10-07 16:34:50", "modified": "2026-10-09 13:34:00", "commits": 3 }, { "source": "v04-sparse.Rmd", "filename": "v04-sparse.html", "title": "Sparse NCA Calculations", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Sparse NCA Calculations", "Sparse NCA Setup", "Data Setup Note", "How Subjects Are Grouped for Sparse Calculations", "Calculate!", "Results", "Sparse AUC, AUMC, and Derived Parameters", "Bootstrap", "Deprecated Parameter Names", "Notes on Sparse Calculation Behavior", "Degrees of freedom with multiple samples per subject", "More than half of the measurements below the limit of quantification", "Only the linear trapezoidal method is supported" ], "created": "2022-10-04 21:03:19", "modified": "2026-10-09 13:34:00", "commits": 8 }, { "source": "v20-superposition.Rmd", "filename": "v20-superposition.html", "title": "Superposition of Pharmacokinetic Data", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Load the data", "Compute the Superposition from Single-Dose Data to Steady-State", "Nonstandard Superposition Computations", "Compute the Superposition from Single-Dose Data to a Specific Dose", "Compute the Superposition from Single-Dose Data with >1 Dose Per Interval", "Simulate a Different Dose Amount", "Show the Curve to Steady-State", "Time Point Selection and Addition", "Interpolation and Extrapolation Methods" ], "created": "2022-10-04 21:03:19", "modified": "2026-08-09 15:14:48", "commits": 2 }, { "source": "v07-unit-conversion.Rmd", "filename": "v07-unit-conversion.html", "title": "Unit Assignment and Conversion with PKNCA", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Examples of each way to add units", "Steps to add units to an NCA analysis from the data", "Steps to manually add units to an NCA analysis", "Prepare a Unit Assignment and Conversion Table", "What happens when units are missing for some parameters?", "How do I add different unit conversions for different analytes?", "Date and time (POSIXct) input" ], "created": "2022-10-04 21:03:19", "modified": "2026-10-01 02:50:06", "commits": 7 }, { "source": "v80-writing-parameter-functions.Rmd", "filename": "v80-writing-parameter-functions.html", "title": "Writing PKNCA Parameter Functions", "author": "Bill Denney", "engine": "knitr::rmarkdown", "headings": [ "Writing PKNCA Parameter Functions", "Writing the Parameter Function", "Requirements", "Best Practices", "Tell PKNCA about the Parameter", "Passing a Constant with formalsmap", "Parameters That Need Another Interval", "Tell PKNCA How to Summarize the Parameter", "Putting It Together" ], "created": "2022-10-04 21:03:19", "modified": "2026-10-07 19:40:53", "commits": 6 } 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