PKNCA: Perform Pharmacokinetic Non-Compartmental Analysis
Version 0.8.1

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.

Browse man pages Browse package API and functions Browse package files

AuthorBill Denney [aut, cre], Clare Buckeridge [aut], Sridhar Duvvuri [ctb]
Date of publication2017-02-27 08:15:20
MaintainerBill Denney <wdenney@humanpredictions.com>
LicenseAGPL-3
Version0.8.1
URL https://github.com/billdenney/pknca
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PKNCA")

Man pages

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
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...
checkProvenance: Check the hash of an object to confirm its provenance.
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...
exclude: Exclude data points or results from calculations or...
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.
getColumnValueOrNot: Get the value from a column in a data frame if the value is a...
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
get.parameter.deps: Get all columns that depend on a parameter
interp.extrap.conc: Interpolate concentrations between measurements or...
merge.splitlist: Merge two or more lists with a data.frame 'groupid' attribute...
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.deg.fluc: Determine the degree of fluctuation
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.swing: Determine the PK swing
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
PKNCA.options.describe: Describe a PKNCA.options option by name.
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
print.provenance: Print the summary of a provenance object
roundingSummarize: During the summarization of PKNCAresults, do the rounding of...
roundString: Round a value to a defined number of digits printing out...
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.
split.PKNCAconc: Divide into groups
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...

Functions

AIC.list Man page Source code
PKNCA Man page
PKNCA-package Man page
PKNCA.choose.option Man page Source code
PKNCA.options Man page Source code
PKNCA.options.describe Man page Source code
PKNCA.set.summary Man page Source code
PKNCAconc Man page Source code
PKNCAconc.data.frame Man page Source code
PKNCAconc.default Man page Source code
PKNCAconc.tbl_df Man page Source code
PKNCAdata Man page Source code
PKNCAdata.PKNCAconc Man page Source code
PKNCAdata.PKNCAdose Man page Source code
PKNCAdata.default Man page Source code
PKNCAdose Man page Source code
PKNCAdose.data.frame Man page Source code
PKNCAdose.default Man page Source code
PKNCAdose.tbl_df Man page Source code
PKNCAresults Man page Source code
add.interval.col Man page Source code
addProvenance Man page Source code
adj.r.squared Man page Source code
as.data.frame.PKNCAresults Man page Source code
business.cv Man page
business.geocv Man page
business.geomean Man page
business.max Man page
business.mean Man page
business.median Man page
business.min Man page
business.range Man page
business.sd Man page
check.conc.time Man page Source code
check.conversion Man page Source code
check.interval.deps Man page Source code
check.interval.specification Man page Source code
checkProvenance Man page Source code
choose.auc.intervals Man page Source code
clean.conc.blq Man page Source code
clean.conc.na Man page Source code
exclude Man page Source code
exclude.PKNCAconc Man page Source code
exclude.PKNCAdose Man page Source code
exclude.PKNCAresults Man page Source code
exclude.helper Source code
extrapolate.conc Man page Source code
find.tau Man page Source code
findOperator Man page Source code
formula.PKNCAconc Man page Source code
formula.PKNCAdose Man page Source code
formula.parseFormula Man page Source code
fun.auc.inf Source code
fun.auc.linear Source code
fun.auc.log Source code
geocv Man page Source code
geomean Man page Source code
geosd Man page Source code
geosd, Man page
get.best.model Man page Source code
get.first.model Man page Source code
get.interval.cols Man page Source code
get.parameter.deps Man page Source code
getColumnValueOrNot Man page Source code
getData.PKNCAconc Man page Source code
getData.PKNCAdose Man page Source code
getDepVar Man page Source code
getDepVar.PKNCAconc Source code
getDepVar.PKNCAdose Source code
getGroups.PKNCAconc Man page Source code
getGroups.PKNCAdose Man page Source code
getGroups.PKNCAresults Man page Source code
getIndepVar Man page Source code
getIndepVar.PKNCAconc Source code
getIndepVar.PKNCAdose Source code
interp.extrap.conc Man page Source code
interp.extrap.conc.dose Man page Source code
interpolate.conc Man page Source code
make.label Source code
merge.splitlist Man page Source code
model.frame.PKNCAconc Man page Source code
model.frame.PKNCAdose Man page Source code
parseFormula Man page Source code
pk.business Man page Source code
pk.calc.auc Man page Source code
pk.calc.auc.all Man page Source code
pk.calc.auc.inf Man page Source code
pk.calc.auc.inf.obs Man page Source code
pk.calc.auc.inf.pred Man page Source code
pk.calc.auc.last Man page Source code
pk.calc.aucpext Man page Source code
pk.calc.aucpext.obs Man page Source code
pk.calc.aucpext.pred Man page Source code
pk.calc.aumc Man page Source code
pk.calc.aumc.all Man page Source code
pk.calc.aumc.inf Man page Source code
pk.calc.aumc.inf.obs Man page Source code
pk.calc.aumc.inf.pred Man page Source code
pk.calc.aumc.last Man page Source code
pk.calc.auxc Man page Source code
pk.calc.c0 Man page Source code
pk.calc.c0.method.c0 Man page Source code
pk.calc.c0.method.c1 Man page Source code
pk.calc.c0.method.cmin Man page Source code
pk.calc.c0.method.logslope Man page Source code
pk.calc.c0.method.set0 Man page Source code
pk.calc.cav Man page Source code
pk.calc.cl Man page Source code
pk.calc.cl.all Man page Source code
pk.calc.cl.last Man page Source code
pk.calc.cl.obs Man page Source code
pk.calc.cl.pred Man page Source code
pk.calc.clast.obs Man page Source code
pk.calc.cmax Man page Source code
pk.calc.cmin Man page Source code
pk.calc.ctrough Man page Source code
pk.calc.deg.fluc Man page Source code
pk.calc.f Man page Source code
pk.calc.half.life Man page Source code
pk.calc.kel Man page Source code
pk.calc.kel.obs Man page Source code
pk.calc.kel.pred Man page Source code
pk.calc.mrt Man page Source code
pk.calc.mrt.last Man page Source code
pk.calc.mrt.obs Man page Source code
pk.calc.mrt.pred Man page Source code
pk.calc.ptr Man page Source code
pk.calc.swing Man page Source code
pk.calc.tfirst Man page Source code
pk.calc.thalf.eff Man page Source code
pk.calc.thalf.eff.obs Source code
pk.calc.thalf.eff.pred Source code
pk.calc.tlag Man page Source code
pk.calc.tlast Man page Source code
pk.calc.tmax Man page Source code
pk.calc.vd Man page Source code
pk.calc.vd.obs Man page Source code
pk.calc.vd.pred Man page Source code
pk.calc.vss Man page Source code
pk.calc.vss.obs Man page Source code
pk.calc.vss.pred Man page Source code
pk.calc.vz Man page Source code
pk.calc.vz.obs Man page Source code
pk.calc.vz.pred Man page Source code
pk.nca Man page Source code
pk.nca.interval Man page Source code
pk.nca.intervals Source code
pk.tss Man page Source code
pk.tss.data.prep Man page Source code
pk.tss.monoexponential Man page Source code
pk.tss.monoexponential.individual Man page Source code
pk.tss.monoexponential.population Man page Source code
pk.tss.stepwise.linear Man page Source code
plot.PKNCAconc Man page Source code
plot.PKNCAdata Man page Source code
print.PKNCAconc Man page Source code
print.PKNCAdata Man page Source code
print.PKNCAdose Man page Source code
print.parseFormula Source code
print.provenance Man page Source code
roundString Man page Source code
roundingSummarize Man page Source code
set.name.matching Source code
setDuration Man page Source code
setDuration.PKNCAdose Man page Source code
setExcludeColumn Man page Source code
setRoute Man page Source code
setRoute.PKNCAdose Man page Source code
signifString Man page Source code
sort.interval.cols Man page Source code
split.PKNCAconc Man page Source code
split.PKNCAdata Man page Source code
split.PKNCAdose Man page
summary.PKNCAconc Man page Source code
summary.PKNCAdata Man page Source code
summary.PKNCAdose Man page
summary.PKNCAresults Man page Source code
superposition Man page Source code
superposition.PKNCAconc Man page Source code
superposition.numeric Man page Source code
tss.monoexponential.generate.formula Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/Options-for-Controlling-PKNCA.R
inst/doc/Options-for-Controlling-PKNCA.Rmd
inst/doc/Superposition.Rmd
inst/doc/Data-Cleaning-in-PKNCA.html
inst/doc/Superposition.html
inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.R
inst/doc/Superposition.R
inst/doc/Selection-of-Calculation-Intervals.R
inst/doc/Writing-Parameter-Functions.Rmd
inst/doc/Introduction-and-Usage.Rmd
inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd
inst/doc/Introduction-and-Usage.html
inst/doc/Selection-of-Calculation-Intervals.html
inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.html
inst/doc/Introduction-and-Usage.R
inst/doc/Writing-Parameter-Functions.R
inst/doc/Writing-Parameter-Functions.html
inst/doc/Example-theophylline.html
inst/doc/Options-for-Controlling-PKNCA.html
inst/doc/Data-Cleaning-in-PKNCA.Rmd
inst/doc/Selection-of-Calculation-Intervals.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-interpolate.conc.R
tests/testthat/test-check.intervals.R
tests/testthat/test-pk.calc.simple.R
tests/testthat/test-001-add.interval.col.R
tests/testthat/test-merge.R
tests/testthat/test-class-PKNCAdose.R
tests/testthat/test-cleaners.R
tests/testthat/test-provenance.R
tests/testthat/test-class-PKNCAresults.R
tests/testthat/test-exclude.R
tests/testthat/test-class-PKNCAconc.R
tests/testthat/test-class-PKNCAdata.R
tests/testthat/test-time.to.steady.state.R
tests/testthat/test-general.functions.R
tests/testthat/test-pk.business.rules.R
tests/testthat/test-pk.calc.all.R
tests/testthat/test-auc.R
tests/testthat/test-superpostion.R
tests/testthat/test-PKNCA.options.R
tests/testthat/test-class-general.R
tests/testthat/test-AIC.list.R
tests/testthat/test-parseFormula.R
tests/testthat/test-choose-intervals.R
tests/testthat/test-pk.calc.c0.R
tests/testthat/test-half.life.R
tests/testthat/generate.data.R
NAMESPACE
NEWS.md
R
R/parseFormula.R
R/provenance.R
R/superposition.R
R/AIC.list.R
R/tss.stepwise.linear.R
R/001-add.interval.col.R
R/tss.monoexponential.R
R/class-PKNCAdata.R
R/pk.calc.c0.R
R/pk.calc.all.R
R/tss.R
R/class-PKNCAresults.R
R/002-pk.business.rules.R
R/class-general.R
R/check.intervals.R
R/cleaners.R
R/PKNCA.R
R/half.life.R
R/PKNCA.options.R
R/choose.intervals.R
R/class-PKNCAconc.R
R/general.functions.R
R/merge.R
R/class-PKNCAdose.R
R/exclude.R
R/pk.calc.simple.R
R/auc.R
R/interpolate.conc.R
vignettes
vignettes/Options-for-Controlling-PKNCA.Rmd
vignettes/Superposition.Rmd
vignettes/Writing-Parameter-Functions.Rmd
vignettes/Introduction-and-Usage.Rmd
vignettes/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd
vignettes/PKNCA-ISoP_Study_Group-2016-05-25.pptx
vignettes/2015_ACoP_PKNCA_poster.pdf
vignettes/Data-Cleaning-in-PKNCA.Rmd
vignettes/Selection-of-Calculation-Intervals.Rmd
vignettes/PKNCA-ISoP_New_England-2016-03-31.pptx
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/pk.calc.mrt.Rd
man/pk.calc.half.life.Rd
man/check.conc.time.Rd
man/pk.calc.kel.Rd
man/parseFormula.Rd
man/as.data.frame.PKNCAresults.Rd
man/split.PKNCAconc.Rd
man/exclude.Rd
man/geomean.Rd
man/pk.calc.auxc.Rd
man/pk.tss.data.prep.Rd
man/pk.calc.tmax.Rd
man/pk.nca.Rd
man/plot.PKNCAconc.Rd
man/business.mean.Rd
man/addProvenance.Rd
man/PKNCAdose.Rd
man/pk.tss.monoexponential.population.Rd
man/pk.calc.deg.fluc.Rd
man/print.PKNCAdata.Rd
man/pk.calc.c0.Rd
man/summary.PKNCAresults.Rd
man/pk.calc.ctrough.Rd
man/PKNCAconc.Rd
man/PKNCA.options.describe.Rd
man/pk.calc.clast.obs.Rd
man/getDepVar.Rd
man/choose.auc.intervals.Rd
man/find.tau.Rd
man/AIC.list.Rd
man/pk.calc.vss.Rd
man/check.conversion.Rd
man/signifString.Rd
man/pk.tss.monoexponential.Rd
man/pk.calc.swing.Rd
man/setRoute.Rd
man/superposition.Rd
man/PKNCAdata.Rd
man/sort.interval.cols.Rd
man/pk.tss.stepwise.linear.Rd
man/roundingSummarize.Rd
man/get.first.model.Rd
man/clean.conc.na.Rd
man/merge.splitlist.Rd
man/getIndepVar.Rd
man/roundString.Rd
man/pk.tss.monoexponential.individual.Rd
man/pk.calc.tlast.Rd
man/pk.calc.cl.Rd
man/adj.r.squared.Rd
man/findOperator.Rd
man/getGroups.PKNCAconc.Rd
man/formula.PKNCAconc.Rd
man/interp.extrap.conc.Rd
man/pk.calc.vd.Rd
man/PKNCA.Rd
man/pk.calc.f.Rd
man/formula.parseFormula.Rd
man/pk.calc.thalf.eff.Rd
man/get.interval.cols.Rd
man/pk.calc.aucpext.Rd
man/summary.PKNCAdata.Rd
man/PKNCA.options.Rd
man/pk.calc.tlag.Rd
man/add.interval.col.Rd
man/tss.monoexponential.generate.formula.Rd
man/pk.calc.vz.Rd
man/get.best.model.Rd
man/model.frame.PKNCAconc.Rd
man/pk.business.Rd
man/PKNCAresults.Rd
man/pk.tss.Rd
man/checkProvenance.Rd
man/check.interval.specification.Rd
man/pk.calc.cav.Rd
man/PKNCA.choose.option.Rd
man/get.parameter.deps.Rd
man/check.interval.deps.Rd
man/pk.calc.cmax.Rd
man/clean.conc.blq.Rd
man/setExcludeColumn.Rd
man/getData.PKNCAconc.Rd
man/pk.calc.ptr.Rd
man/setDuration.Rd
man/print.PKNCAconc.Rd
man/PKNCA.set.summary.Rd
man/print.provenance.Rd
man/getColumnValueOrNot.Rd
man/pk.nca.interval.Rd
PKNCA documentation built on May 20, 2017, 1:56 a.m.