Perform Pharmacokinetic Non-Compartmental Analysis
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Documentation for package ‘PKNCA’ version 0.10.1
Help Pages
A B C E F G I L M N P R S T U V
-- A --
| add.interval.col | Add columns for calculations within PKNCA intervals |
| addProvenance | Add a hash and associated information to enable checking object provenance. |
| adj.r.squared | Calculate the adjusted r-squared value |
| AIC.list | Assess the AIC for all models in a list of models |
| any_sparse_dense_in_interval | Determine if there are any sparse or dense calculations requested within an interval |
| as.data.frame.PKNCAresults | Extract the parameter results from a PKNCAresults and return them as a data frame. |
| as_sparse_pk | Generate a sparse_pk object |
-- B --
| business.cv | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.geocv | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.geomean | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.max | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.mean | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.median | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.min | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.range | Generate functions to do the named function (e.g. mean) applying the business rules. |
| business.sd | Generate functions to do the named function (e.g. mean) applying the business rules. |
-- C --
| check.conc.time | Verify that the concentration and time are valid |
| check.conversion | Check that the conversion to a data type does not change the number of NA values |
| check.interval.deps | Take in a single row of an interval specification and return that row updated with any additional calculations that must be done to fulfill all dependencies. |
| check.interval.specification | Check the formatting of a calculation interval specification data frame. |
| checkProvenance | Check the hash of an object to confirm its provenance. |
| choose.auc.intervals | Choose intervals to compute AUCs from time and dosing information |
| choose_interp_extrap_method | Choose a method for calculation in the interval between concentrations |
| clean.conc.blq | Handle BLQ values in the concentration measurements as requested by the user. |
| clean.conc.na | Handle NA values in the concentration measurements as requested by the user. |
| cov_holder | Calculate the covariance for two time points with sparse sampling |
-- E --
| exclude | Exclude data points or results from calculations or summarization. |
| exclude.default | Exclude data points or results from calculations or summarization. |
| exclude_nca | Exclude NCA parameters based on examining the parameter set. |
| exclude_nca_max.aucinf.pext | Exclude NCA parameters based on examining the parameter set. |
| exclude_nca_min.hl.r.squared | Exclude NCA parameters based on examining the parameter set. |
| exclude_nca_span.ratio | Exclude NCA parameters based on examining the parameter set. |
| extrapolate.conc | Interpolate concentrations between measurements or extrapolate concentrations after the last measurement. |
| extrapolate_conc_lambdaz | Interpolate or extrapolate concentrations using the provided method |
-- F --
| filter.PKNCAconc | dplyr filtering for PKNCA |
| filter.PKNCAdose | dplyr filtering for PKNCA |
| filter.PKNCAresults | dplyr filtering for PKNCA |
| find.tau | Find the repeating interval within a vector of doses |
| findOperator | Find the first occurrence of an operator in a formula and return the left, right, or both sides of the operator. |
| fit_half_life | 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. |
| formula.PKNCAconc | Extract the formula from a PKNCAconc object. |
| formula.PKNCAdose | Extract the formula from a PKNCAconc object. |
| full_join.PKNCAconc | dplyr joins for PKNCA |
| full_join.PKNCAdose | dplyr joins for PKNCA |
| full_join.PKNCAresults | dplyr joins for PKNCA |
-- G --
| geocv | Compute the geometric mean, sd, and CV |
| geomean | Compute the geometric mean, sd, and CV |
| geosd | Compute the geometric mean, sd, and CV |
| get.best.model | Extract the best model from a list of models using AIC.list. |
| get.first.model | Get the first model from a list of models |
| get.interval.cols | Get the columns that can be used in an interval specification |
| get.parameter.deps | Get all columns that depend on a parameter |
| getAttributeColumn | Retrieve the value of an attribute column. |
| getColumnValueOrNot | 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. |
| getDataName | Get the name of the element containing the data for the current object. |
| getDataName.default | Get the name of the element containing the data for the current object. |
| getDataName.PKNCAconc | Get the name of the element containing the data for the current object. |
| getDataName.PKNCAdose | Get the name of the element containing the data for the current object. |
| getDataName.PKNCAresults | Get the name of the element containing the data for the current object. |
| getDepVar | Get the dependent variable (left hand side of the formula) from a PKNCA object. |
| getGroups.PKNCAconc | Get the groups (right hand side after the '|' from a PKNCA object). |
| getGroups.PKNCAdose | Get the groups (right hand side after the '|' from a PKNCA object). |
| getGroups.PKNCAresults | Get the groups (right hand side after the '|' from a PKNCA object). |
| getIndepVar | Get the independent variable (right hand side of the formula) from a PKNCA object. |
| group_by.PKNCAconc | dplyr grouping for PKNCA |
| group_by.PKNCAdose | dplyr grouping for PKNCA |
| group_by.PKNCAresults | dplyr grouping for PKNCA |
| group_vars.PKNCAconc | Get grouping variables for a PKNCA object |
| group_vars.PKNCAdose | Get grouping variables for a PKNCA object |
-- I --
| inner_join.PKNCAconc | dplyr joins for PKNCA |
| inner_join.PKNCAdose | dplyr joins for PKNCA |
| inner_join.PKNCAresults | dplyr joins for PKNCA |
| interp.extrap.conc | Interpolate concentrations between measurements or extrapolate concentrations after the last measurement. |
| interp.extrap.conc.dose | Interpolate concentrations between measurements or extrapolate concentrations after the last measurement. |
| interpolate.conc | Interpolate concentrations between measurements or extrapolate concentrations after the last measurement. |
| interpolate_conc_linear | Interpolate or extrapolate concentrations using the provided method |
| interpolate_conc_log | Interpolate or extrapolate concentrations using the provided method |
| interp_extrap_conc_method | Interpolate or extrapolate concentrations using the provided method |
| is_sparse_pk | Is a PKNCA object used for sparse PK? |
| is_sparse_pk.PKNCAconc | Is a PKNCA object used for sparse PK? |
| is_sparse_pk.PKNCAdata | Is a PKNCA object used for sparse PK? |
| is_sparse_pk.PKNCAresults | Is a PKNCA object used for sparse PK? |
-- L --
| left_join.PKNCAconc | dplyr joins for PKNCA |
| left_join.PKNCAdose | dplyr joins for PKNCA |
| left_join.PKNCAresults | dplyr joins for PKNCA |
-- M --
| model.frame.PKNCAconc | Extract the columns used in the formula (in order) from a PKNCAconc or PKNCAdose object. |
| model.frame.PKNCAdose | Extract the columns used in the formula (in order) from a PKNCAconc or PKNCAdose object. |
| mutate.PKNCAconc | dplyr mutate-based modification for PKNCA |
| mutate.PKNCAdose | dplyr mutate-based modification for PKNCA |
| mutate.PKNCAresults | dplyr mutate-based modification for PKNCA |
-- N --
| normalize_exclude | Normalize the exclude column by setting blanks to NA |
-- P --
| parse_formula_to_cols | Convert a formula representation to the columns for input data |
| pk.business | 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")'. |
| pk.calc.ae | Calculate amount excreted (typically in urine or feces) |
| pk.calc.auc | A compute the Area Under the (Moment) Curve |
| pk.calc.auc.all | A compute the Area Under the (Moment) Curve |
| pk.calc.auc.inf | A compute the Area Under the (Moment) Curve |
| pk.calc.auc.inf.obs | A compute the Area Under the (Moment) Curve |
| pk.calc.auc.inf.pred | A compute the Area Under the (Moment) Curve |
| pk.calc.auc.last | A compute the Area Under the (Moment) Curve |
| pk.calc.aucabove | Calculate the AUC above a given concentration |
| pk.calc.aucint | Calculate the AUC over an interval with interpolation and/or extrapolation of concentrations for the beginning and end of the interval. |
| pk.calc.aucint.all | Calculate the AUC over an interval with interpolation and/or extrapolation of concentrations for the beginning and end of the interval. |
| pk.calc.aucint.inf.obs | Calculate the AUC over an interval with interpolation and/or extrapolation of concentrations for the beginning and end of the interval. |
| pk.calc.aucint.inf.pred | Calculate the AUC over an interval with interpolation and/or extrapolation of concentrations for the beginning and end of the interval. |
| pk.calc.aucint.last | Calculate the AUC over an interval with interpolation and/or extrapolation of concentrations for the beginning and end of the interval. |
| pk.calc.auciv | Calculate AUC for intravenous dosing |
| pk.calc.auciv_pbext | Calculate AUC for intravenous dosing |
| pk.calc.aucpext | Calculate the AUC percent extrapolated |
| pk.calc.aumc | A compute the Area Under the (Moment) Curve |
| pk.calc.aumc.all | A compute the Area Under the (Moment) Curve |
| pk.calc.aumc.inf | A compute the Area Under the (Moment) Curve |
| pk.calc.aumc.inf.obs | A compute the Area Under the (Moment) Curve |
| pk.calc.aumc.inf.pred | A compute the Area Under the (Moment) Curve |
| pk.calc.aumc.last | A compute the Area Under the (Moment) Curve |
| pk.calc.auxc | A compute the Area Under the (Moment) Curve |
| pk.calc.c0 | Estimate the concentration at dosing time for an IV bolus dose. |
| pk.calc.c0.method.c0 | Estimate the concentration at dosing time for an IV bolus dose. |
| pk.calc.c0.method.c1 | Estimate the concentration at dosing time for an IV bolus dose. |
| pk.calc.c0.method.cmin | Estimate the concentration at dosing time for an IV bolus dose. |
| pk.calc.c0.method.logslope | Estimate the concentration at dosing time for an IV bolus dose. |
| pk.calc.c0.method.set0 | Estimate the concentration at dosing time for an IV bolus dose. |
| pk.calc.cav | Calculate the average concentration during an interval. |
| pk.calc.ceoi | Determine the concentration at the end of infusion |
| pk.calc.cl | Calculate the (observed oral) clearance |
| pk.calc.clast.obs | Determine the last observed concentration above the limit of quantification (LOQ). |
| pk.calc.clr | Calculate renal clearance |
| pk.calc.cmax | Determine maximum observed PK concentration |
| pk.calc.cmin | Determine maximum observed PK concentration |
| pk.calc.cstart | Determine the concentration at the beginning of the interval |
| pk.calc.ctrough | Determine the trough (end of interval) concentration |
| pk.calc.deg.fluc | Determine the degree of fluctuation |
| pk.calc.dn | Determine dose normalized NCA parameter |
| pk.calc.f | Calculate the absolute (or relative) bioavailability |
| pk.calc.fe | Calculate fraction excreted (typically in urine or feces) |
| pk.calc.half.life | Compute the half-life and associated parameters |
| pk.calc.kel | Calculate the elimination rate (Kel) |
| pk.calc.mrt | Calculate the mean residence time (MRT) for single-dose data or linear multiple-dose data. |
| pk.calc.mrt.iv | Calculate the mean residence time (MRT) for single-dose data or linear multiple-dose data. |
| pk.calc.mrt.md | Calculate the mean residence time (MRT) for multiple-dose data with nonlinear kinetics. |
| pk.calc.ptr | Determine the peak-to-trough ratio |
| pk.calc.sparse_auc | Calculate AUC and related parameters using sparse NCA methods |
| pk.calc.sparse_auclast | Calculate AUC and related parameters using sparse NCA methods |
| pk.calc.swing | Determine the PK swing |
| pk.calc.tfirst | Determine time of last observed concentration above the limit of quantification. |
| pk.calc.thalf.eff | Calculate the effective half-life |
| pk.calc.time_above | Determine time at or above a set value |
| pk.calc.tlag | Determine the observed lag time (time before the first concentration above the limit of quantification or above the first concentration in the interval) |
| pk.calc.tlast | Determine time of last observed concentration above the limit of quantification. |
| pk.calc.tmax | Determine time of maximum observed PK concentration |
| pk.calc.vd | Calculate the volume of distribution (Vd) or observed volume of distribution (Vd/F) |
| pk.calc.vss | Calculate the steady-state volume of distribution (Vss) |
| pk.calc.vz | Calculate the terminal volume of distribution (Vz) |
| pk.nca | Compute NCA parameters for each interval for each subject. |
| pk.nca.interval | Compute all PK parameters for a single concentration-time data set |
| pk.nca.intervals | Compute NCA for multiple intervals |
| pk.tss | Compute the time to steady-state (tss) |
| pk.tss.data.prep | Clean up the time to steady-state parameters and return a data frame for use by the tss calculators. |
| pk.tss.monoexponential | Compute the time to steady state using nonlinear, mixed-effects modeling of trough concentrations. |
| pk.tss.monoexponential.individual | A helper function to estimate individual and single outputs for monoexponential time to steady-state. |
| pk.tss.monoexponential.population | A helper function to estimate population and popind outputs for monoexponential time to steady-state. |
| pk.tss.stepwise.linear | Compute the time to steady state using stepwise test of linear trend |
| PKNCA | Compute noncompartmental pharmacokinetics |
| PKNCA.choose.option | Choose either the value from an option list or the current set value for an option. |
| PKNCA.options | Set default options for PKNCA functions |
| PKNCA.options.describe | Describe a PKNCA.options option by name. |
| PKNCA.set.summary | Define how NCA parameters are summarized. |
| PKNCAconc | Create a PKNCAconc object |
| PKNCAconc.data.frame | Create a PKNCAconc object |
| PKNCAconc.default | Create a PKNCAconc object |
| PKNCAconc.tbl_df | Create a PKNCAconc object |
| PKNCAdata | Create a PKNCAdata object. |
| PKNCAdata.default | Create a PKNCAdata object. |
| PKNCAdata.PKNCAconc | Create a PKNCAdata object. |
| PKNCAdata.PKNCAdose | Create a PKNCAdata object. |
| PKNCAdose | Create a PKNCAdose object |
| PKNCAdose.data.frame | Create a PKNCAdose object |
| PKNCAdose.default | Create a PKNCAdose object |
| PKNCAdose.tbl_df | Create a PKNCAdose object |
| PKNCAresults | Generate a PKNCAresults object |
| pknca_find_units_param | Find NCA parameters with a given unit type |
| PKNCA_impute_fun_list | Separate out a vector of PKNCA imputation methods into a list of functions |
| PKNCA_impute_method | Methods for imputation of data with PKNCA |
| PKNCA_impute_method_start_cmin | Methods for imputation of data with PKNCA |
| PKNCA_impute_method_start_conc0 | Methods for imputation of data with PKNCA |
| PKNCA_impute_method_start_predose | Methods for imputation of data with PKNCA |
| pknca_units_add_paren | Add parentheses to a unit value, if needed |
| pknca_units_table | Create a unit assignment and conversion table |
| pknca_unit_conversion | Perform unit conversion (if possible) on PKNCA results |
| pk_nca_result_to_df | Convert the grouping info and list of results for each group into a results data.frame |
| print.PKNCAconc | Print and/or summarize a PKNCAconc or PKNCAdose object. |
| print.PKNCAdata | Print a PKNCAdata object |
| print.PKNCAdose | Print and/or summarize a PKNCAconc or PKNCAdose object. |
| print.provenance | Print the summary of a provenance object |
| print.summary_PKNCAresults | Print the results summary |
-- R --
| right_join.PKNCAconc | dplyr joins for PKNCA |
| right_join.PKNCAdose | dplyr joins for PKNCA |
| right_join.PKNCAresults | dplyr joins for PKNCA |
| roundingSummarize | During the summarization of PKNCAresults, do the rounding of values based on the instructions given. |
| roundString | Round a value to a defined number of digits printing out trailing zeros, if applicable. |
-- S --
| setAttributeColumn | Add an attribute to an object where the attribute is added as a name to the names of the object. |
| setDuration | Set the duration of dosing or measurement |
| setDuration.PKNCAdose | Set the duration of dosing or measurement |
| setExcludeColumn | Set the exclude parameter on an object |
| setRoute | Set the dosing route |
| setRoute.PKNCAdose | Set the dosing route |
| signifString | Round a value to a defined number of significant digits printing out trailing zeros, if applicable. |
| signifString.data.frame | Round a value to a defined number of significant digits printing out trailing zeros, if applicable. |
| signifString.default | Round a value to a defined number of significant digits printing out trailing zeros, if applicable. |
| sort.interval.cols | Sort the interval columns by dependencies. |
| sparse_auc_weight_linear | Calculate the weight for sparse AUC calculation with the linear-trapezoidal rule |
| sparse_mean | Calculate the mean concentration at all time points for use in sparse NCA calculations |
| sparse_pk_attribute | Set or get a sparse_pk object attribute |
| sparse_to_dense_pk | Extract the mean concentration-time profile as a data.frame |
| summary.PKNCAconc | Print and/or summarize a PKNCAconc or PKNCAdose object. |
| summary.PKNCAdata | Summarize a PKNCAdata object showing important details about the concentration, dosing, and interval information. |
| summary.PKNCAdose | Print and/or summarize a PKNCAconc or PKNCAdose object. |
| summary.PKNCAresults | Summarize PKNCA results |
| superposition | Compute noncompartmental superposition for repeated dosing |
| superposition.numeric | Compute noncompartmental superposition for repeated dosing |
| superposition.PKNCAconc | Compute noncompartmental superposition for repeated dosing |
-- T --
| time_calc | Times relative to an event (typically dosing) |
| tss.monoexponential.generate.formula | A helper function to generate the formula and starting values for the parameters in monoexponential models. |
-- U --
| ungroup.PKNCAconc | dplyr grouping for PKNCA |
| ungroup.PKNCAdose | dplyr grouping for PKNCA |
| ungroup.PKNCAresults | dplyr grouping for PKNCA |
-- V --
| var_sparse_auc | Calculate the variance for the AUC of sparsely sampled PK |