PKNCA: Perform Pharmacokinetic Non-Compartmental Analysis

Compute standard Non-Compartmental Analysis (NCA) parameters and summarize them. In addition to this core work, it also provides standardized plotting routines, basic assessments for biocomparison or drug interaction, and model-based estimation routines for calculating doses to reach specific values of AUC or Cmax.

AuthorBill Denney [aut, cre], Clare Buckeridge [aut], Sridhar Duvvuri [ctb]
Date of publication2016-08-15 16:28:48
MaintainerBill Denney <wdenney@humanpredictions.com>
LicenseAGPL-3
Version0.7.1
https://github.com/billdenney/pknca

View on CRAN

Man pages

add.interval.col: Add columns for calculations within PKNCA intervals

adj.r.squared: Calculate the adjusted r-squared value

AIC.list: Assess the AIC for all models in a list of models

as.data.frame.PKNCAresults: Extract the parameter results from a PKNCAresults and return...

business.mean: Generate functions to do the named function (e.g. mean)...

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...

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...

choose.auc.intervals: Choose intervals to compute AUCs from time and dosing...

clean.conc.blq: Handle BLQ values in the concentration measurements as...

clean.conc.na: Handle NA values in the concentration measurements as...

count.non.missing: Count the number of values that are not NA

findOperator: Find the first occurrence of an operator in a formula and...

find.tau: Find the repeating interval within a vector of doses

formula.parseFormula: Convert the parsed formula back into the original

formula.PKNCAconc: Extract the formula from a PKNCAconc object.

geomean: Compute the geometric mean, sd, and CV

get.best.model: Extract the best model from a list of models using AIC.list.

getData.PKNCAconc: Extract all the original data from a PKNCAconc or PKNCAdose...

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...

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

interp.extrap.conc: Interpolate concentrations between measurements or...

merge.splitByData: Merge lists of data to make a list of lists.

model.frame.PKNCAconc: Extract the columns used in the formula (in order) from a...

parseFormula: Parse a formula into its component parts.

pk.business: Run any function with a maximum missing fraction of X and 0s...

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.cl: Calculate the (observed oral) clearance

pk.calc.clast.obs: Determine the last observed concentration above the limit of...

pk.calc.cmax: Determine maximum observed PK concentration

pk.calc.ctrough: Determine the trough (predose) concentration

pk.calc.f: Calculate the absolute (or relative) bioavailability

pk.calc.half.life: Compute the half-life and associated parameters

pk.calc.kel: Calculate the elimination rate (Kel)

pk.calc.mrt: Calcuate the mean residence time (MRT)

pk.calc.ptr: Determine the peak-to-trough ratio

pk.calc.thalf.eff: Calculate the effective half-life

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.vd: Calculate the volume of distribution (Vd) or observed volume...

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

pk.nca.interval: Compute all PK parameters for a single concentration-time...

PKNCA.options: Set default options for PKNCA functions

PKNCAresults: Generate a PKNCAresults object

PKNCA.set.summary: Define how NCA parameters are summarized.

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...

plot.PKNCAconc: Plot a PKNCAconc object

print.PKNCAconc: Print and/or summarize a PKNCAconc or PKNCAdose object.

print.PKNCAdata: Print a PKNCAdata object

roundingSummarize: During the summarization of PKNCAresults, do the rounding of...

roundString: Round a value to a defined number of digits printing out...

sapplyBy: Similar to lapplyBy but returning a data frame

signifString: Round a value to a defined number of significant digits...

sort.interval.cols: Sort the interval columns by dependencies.

summary.PKNCAdata: Summarize a PKNCAdata object showing important details about...

summary.PKNCAresults: Summarize PKNCA results

superposition: Compute noncompartmental superposition for repeated dosing

tss.monoexponential.generate.formula: A helper function to generate the formula and starting values...

Files in this package

PKNCA
PKNCA/inst
PKNCA/inst/doc
PKNCA/inst/doc/Superposition.Rmd
PKNCA/inst/doc/Superposition.html
PKNCA/inst/doc/Superposition.R
PKNCA/inst/doc/Introduction-and-Usage.Rmd
PKNCA/inst/doc/Introduction-and-Usage.html
PKNCA/inst/doc/Introduction-and-Usage.R
PKNCA/inst/doc/Example-theophylline.R
PKNCA/inst/doc/Example-theophylline.Rmd
PKNCA/inst/doc/Example-theophylline.html
PKNCA/tests
PKNCA/tests/testthat.R
PKNCA/tests/testthat
PKNCA/tests/testthat/test-interpolate.conc.R
PKNCA/tests/testthat/test-data.classes.R
PKNCA/tests/testthat/test-check.intervals.R
PKNCA/tests/testthat/test-pk.calc.simple.R
PKNCA/tests/testthat/test-cleaners.R
PKNCA/tests/testthat/test-merge.splitByData.R
PKNCA/tests/testthat/test-time.to.steady.state.R
PKNCA/tests/testthat/test-general.functions.R
PKNCA/tests/testthat/test-pk.business.rules.R
PKNCA/tests/testthat/test-pk.calc.all.R
PKNCA/tests/testthat/test-auc.R
PKNCA/tests/testthat/test-superpostion.R
PKNCA/tests/testthat/test-PKNCA.options.R
PKNCA/tests/testthat/test-AIC.list.R
PKNCA/tests/testthat/test-parseFormula.R
PKNCA/tests/testthat/test-choose-intervals.R
PKNCA/tests/testthat/test-pk.calc.c0.R
PKNCA/tests/testthat/test-half.life.R
PKNCA/tests/testthat/generate.data.R
PKNCA/NAMESPACE
PKNCA/NEWS.md
PKNCA/R
PKNCA/R/parseFormula.R PKNCA/R/merge.splitByData.R PKNCA/R/data.classes.plotting.R PKNCA/R/superposition.R PKNCA/R/AIC.list.R PKNCA/R/tss.stepwise.linear.R PKNCA/R/001-add.interval.col.R PKNCA/R/tss.monoexponential.R PKNCA/R/pk.calc.c0.R PKNCA/R/pk.calc.all.R PKNCA/R/tss.R PKNCA/R/002-pk.business.rules.R PKNCA/R/data.classes.R PKNCA/R/check.intervals.R PKNCA/R/cleaners.R PKNCA/R/PKNCA.R PKNCA/R/half.life.R PKNCA/R/PKNCA.options.R PKNCA/R/choose.intervals.R PKNCA/R/general.functions.R PKNCA/R/pk.calc.simple.R PKNCA/R/auc.R PKNCA/R/interpolate.conc.R
PKNCA/vignettes
PKNCA/vignettes/Superposition.Rmd
PKNCA/vignettes/Introduction-and-Usage.Rmd
PKNCA/vignettes/PKNCA-ISoP_Study_Group-2016-05-25.pptx
PKNCA/vignettes/Example-theophylline.Rmd
PKNCA/vignettes/2015_ACoP_PKNCA_poster.pdf
PKNCA/vignettes/PKNCA-ISoP_New_England-2016-03-31.pptx
PKNCA/README.md
PKNCA/MD5
PKNCA/build
PKNCA/build/vignette.rds
PKNCA/DESCRIPTION
PKNCA/man
PKNCA/man/pk.calc.mrt.Rd PKNCA/man/pk.calc.half.life.Rd PKNCA/man/check.conc.time.Rd PKNCA/man/pk.calc.kel.Rd PKNCA/man/parseFormula.Rd PKNCA/man/as.data.frame.PKNCAresults.Rd PKNCA/man/sapplyBy.Rd PKNCA/man/geomean.Rd PKNCA/man/pk.calc.auxc.Rd PKNCA/man/pk.tss.data.prep.Rd PKNCA/man/pk.calc.tmax.Rd PKNCA/man/pk.nca.Rd PKNCA/man/plot.PKNCAconc.Rd PKNCA/man/business.mean.Rd PKNCA/man/PKNCAdose.Rd PKNCA/man/pk.tss.monoexponential.population.Rd PKNCA/man/print.PKNCAdata.Rd PKNCA/man/pk.calc.c0.Rd PKNCA/man/summary.PKNCAresults.Rd PKNCA/man/pk.calc.ctrough.Rd PKNCA/man/PKNCAconc.Rd PKNCA/man/pk.calc.clast.obs.Rd PKNCA/man/getDepVar.Rd PKNCA/man/choose.auc.intervals.Rd PKNCA/man/find.tau.Rd PKNCA/man/AIC.list.Rd PKNCA/man/pk.calc.vss.Rd PKNCA/man/merge.splitByData.Rd PKNCA/man/check.conversion.Rd PKNCA/man/signifString.Rd PKNCA/man/pk.tss.monoexponential.Rd PKNCA/man/superposition.Rd PKNCA/man/PKNCAdata.Rd PKNCA/man/sort.interval.cols.Rd PKNCA/man/pk.tss.stepwise.linear.Rd PKNCA/man/roundingSummarize.Rd PKNCA/man/get.first.model.Rd PKNCA/man/clean.conc.na.Rd PKNCA/man/getIndepVar.Rd PKNCA/man/roundString.Rd PKNCA/man/pk.tss.monoexponential.individual.Rd PKNCA/man/pk.calc.tlast.Rd PKNCA/man/pk.calc.cl.Rd PKNCA/man/adj.r.squared.Rd PKNCA/man/findOperator.Rd PKNCA/man/getGroups.PKNCAconc.Rd PKNCA/man/formula.PKNCAconc.Rd PKNCA/man/count.non.missing.Rd PKNCA/man/interp.extrap.conc.Rd PKNCA/man/pk.calc.vd.Rd PKNCA/man/PKNCA.Rd PKNCA/man/pk.calc.f.Rd PKNCA/man/formula.parseFormula.Rd PKNCA/man/pk.calc.thalf.eff.Rd PKNCA/man/get.interval.cols.Rd PKNCA/man/pk.calc.aucpext.Rd PKNCA/man/summary.PKNCAdata.Rd PKNCA/man/PKNCA.options.Rd PKNCA/man/pk.calc.tlag.Rd PKNCA/man/add.interval.col.Rd PKNCA/man/tss.monoexponential.generate.formula.Rd PKNCA/man/pk.calc.vz.Rd PKNCA/man/get.best.model.Rd PKNCA/man/model.frame.PKNCAconc.Rd PKNCA/man/pk.business.Rd PKNCA/man/PKNCAresults.Rd PKNCA/man/pk.tss.Rd PKNCA/man/check.interval.specification.Rd PKNCA/man/pk.calc.cav.Rd PKNCA/man/PKNCA.choose.option.Rd PKNCA/man/check.interval.deps.Rd PKNCA/man/pk.calc.cmax.Rd PKNCA/man/clean.conc.blq.Rd PKNCA/man/getData.PKNCAconc.Rd PKNCA/man/pk.calc.ptr.Rd PKNCA/man/print.PKNCAconc.Rd PKNCA/man/PKNCA.set.summary.Rd PKNCA/man/pk.nca.interval.Rd

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