Man pages for billdenney/pknca
Perform Pharmacokinetic Non-Compartmental Analysis
| add_impute_to_intervals | Add the imputation column to the intervals, if it is not... |
| add.interval.col | Add columns for calculations within PKNCA intervals |
| addProvenance | Add a hash and associated information to enable checking... |
| adj.r.squared | Calculate the adjusted r-squared value |
| any_sparse_dense_in_interval | Determine if there are any sparse or dense calculations... |
| as.data.frame.PKNCAresults | Extract the parameter results from a PKNCAresults and return... |
| as_PKNCAconc | Convert an object into a PKNCAconc object |
| assert_aucmethod | Assert that a value is a valid AUC method |
| assert_conc_time | Verify that concentration measurements are valid |
| assert_dosetau | Assert that a value is a dosing interval |
| assert_intervaltime_single | Assert that an interval is accurately defined as an interval,... |
| assert_lambdaz | Assert that a lambda.z value is valid |
| assert_number_between | Confirm that a value is greater than another value |
| assert_numeric_between | Confirm that a value is greater than another value |
| assert_PKNCAdata | Assert that an object is a PKNCAdata object |
| as_sparse_pk | Generate a sparse_pk object |
| auc_integrate | Support function for AUC integration |
| business.mean | Generate functions to do the named function (e.g. mean)... |
| check.conversion | Check that the conversion to a data type does not change the... |
| check.interval.deps | Take in a single row of an interval specification and return... |
| check.interval.specification | Check the formatting of a calculation interval specification... |
| checkProvenance | Check the hash of an object to confirm its provenance. |
| choose.auc.intervals | Choose intervals to compute AUCs from time and dosing... |
| choose_interval_method | Choose how to interpolate, extrapolate, or integrate data in... |
| clean.conc.blq | Handle BLQ values in the concentration measurements as... |
| clean.conc.na | Handle NA values in the concentration measurements as... |
| cov_holder | Calculate the covariance for two time points with sparse... |
| defunct | The following functions are defunct |
| exclude | Exclude data points or results from calculations or... |
| exclude_nca | Exclude NCA parameters based on examining the parameter set. |
| filter.PKNCAresults | dplyr filtering for PKNCA |
| findOperator | Find the first occurrence of an operator in a formula and... |
| find.tau | Find the repeating interval within a vector of doses |
| fit_half_life | Perform the half-life fit given the data. The function... |
| formula.PKNCAconc | Extract the formula from a PKNCAconc object. |
| geomean | Compute the geometric mean, sd, and CV |
| getAttributeColumn | Retrieve the value of an attribute column. |
| get.best.model | Extract the best model from a list of models using the AIC. |
| getColumnValueOrNot | Get the value from a column in a data frame if the value is a... |
| getDataName | Get the name of the element containing the data for the... |
| getDepVar | Get the dependent variable (left hand side of the formula)... |
| get.first.model | Get the first model from a list of models |
| getGroups.PKNCAconc | Get the groups (right hand side after the '|' from a PKNCA... |
| get_impute_method | Get the impute function from either the intervals column or... |
| getIndepVar | Get the independent variable (right hand side of the formula)... |
| 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 |
| group_by.PKNCAresults | dplyr grouping for PKNCA |
| group_vars.PKNCAconc | Get grouping variables for a PKNCA object |
| inner_join.PKNCAresults | dplyr joins for PKNCA |
| interp.extrap.conc | Interpolate concentrations between measurements or... |
| interp_extrap_conc_method | Interpolate or extrapolate concentrations using the provided... |
| is_sparse_pk | Is a PKNCA object used for sparse PK? |
| model.frame.PKNCAconc | Extract the columns used in the formula (in order) from a... |
| mutate.PKNCAresults | dplyr mutate-based modification for PKNCA |
| normalize_exclude | Normalize the exclude column by setting blanks to NA |
| parse_formula_to_cols | Convert a formula representation to the columns for input... |
| pk.business | Run any function with a maximum missing fraction of X and 0s... |
| pk.calc.ae | Calculate amount excreted (typically in urine or feces) |
| pk.calc.aucabove | Calculate the AUC above a given concentration |
| pk.calc.aucint | Calculate the AUC over an interval with interpolation and/or... |
| pk.calc.auciv | Calculate AUC for intravenous dosing |
| pk.calc.aucpext | Calculate the AUC percent extrapolated |
| pk.calc.auxc | A compute the Area Under the (Moment) Curve |
| pk.calc.c0 | Estimate the concentration at dosing time for an IV bolus... |
| 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... |
| pk.calc.clr | Calculate renal clearance |
| pk.calc.cmax | Determine maximum observed PK concentration |
| pk.calc.count_conc | Count the number of concentration measurements in an interval |
| 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... |
| pk.calc.mrt.md | Calculate the mean residence time (MRT) for multiple-dose... |
| pk.calc.ptr | Determine the peak-to-trough ratio |
| pk.calc.sparse_auc | Calculate AUC and related parameters using sparse NCA methods |
| pk.calc.swing | Determine the PK swing |
| 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... |
| pk.calc.tlast | Determine time of last observed concentration above the limit... |
| pk.calc.tmax | Determine time of maximum observed PK concentration |
| pk.calc.totdose | Extract the dose used for calculations |
| 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. |
| PKNCA | Compute noncompartmental pharmacokinetics |
| PKNCA.choose.option | Choose either the value from an option list or the current... |
| PKNCAconc | Create a PKNCAconc object |
| PKNCAdata | Create a PKNCAdata object. |
| PKNCAdose | Create a PKNCAdose 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... |
| PKNCA_impute_method | Methods for imputation of data with PKNCA |
| pk.nca.interval | Compute all PK parameters for a single concentration-time... |
| pk.nca.intervals | Compute NCA for multiple intervals |
| PKNCA.options | Set default options for PKNCA functions |
| PKNCA.options.describe | Describe a PKNCA.options option by name. |
| PKNCAresults | Generate a PKNCAresults object |
| pk_nca_result_to_df | Convert the grouping info and list of results for each group... |
| PKNCA.set.summary | Define how NCA parameters are summarized. |
| pknca_unit_conversion | Perform unit conversion (if possible) on PKNCA results |
| pknca_units_add_paren | Add parentheses to a unit value, if needed |
| pknca_units_table | Create a unit assignment and conversion table |
| pk.tss | Compute the time to steady-state (tss) |
| pk.tss.data.prep | Clean up the time to steady-state parameters and return a... |
| pk.tss.monoexponential | Compute the time to steady state using nonlinear,... |
| pk.tss.monoexponential.individual | A helper function to estimate individual and single outputs... |
| pk.tss.monoexponential.population | A helper function to estimate population and popind outputs... |
| pk.tss.stepwise.linear | Compute the time to steady state using stepwise test of... |
| print.PKNCAconc | Print and/or summarize a PKNCAconc or PKNCAdose object. |
| print.PKNCAdata | Print a PKNCAdata object |
| print.provenance | Print the summary of a provenance object |
| print.summary_PKNCAresults | Print the results summary |
| reexports | Objects exported from other packages |
| roundingSummarize | During the summarization of PKNCAresults, do the rounding of... |
| roundString | Round a value to a defined number of digits printing out... |
| setAttributeColumn | Add an attribute to an object where the attribute is added as... |
| setDuration | Set the duration of dosing or measurement |
| setExcludeColumn | Set the exclude parameter on an object |
| setRoute | Set the dosing route |
| signifString | Round a value to a defined number of significant digits... |
| sort.interval.cols | Sort the interval columns by dependencies. |
| sparse_auc_weight_linear | Calculate the weight for sparse AUC calculation with the... |
| sparse_mean | Calculate the mean concentration at all time points for use... |
| 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.PKNCAdata | Summarize a PKNCAdata object showing important details about... |
| summary.PKNCAresults | Summarize PKNCA results |
| superposition | Compute noncompartmental superposition for repeated dosing |
| time_calc | Times relative to an event (typically dosing) |
| tss.monoexponential.generate.formula | A helper function to generate the formula and starting values... |
| var_sparse_auc | Calculate the variance for the AUC of sparsely sampled PK |
