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 publication2017-02-27 08:15:20
MaintainerBill Denney <wdenney@humanpredictions.com>
LicenseAGPL-3
Version0.8.1
https://github.com/billdenney/pknca

View on CRAN

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

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

Files

PKNCA
PKNCA/inst
PKNCA/inst/CITATION
PKNCA/inst/doc
PKNCA/inst/doc/Options-for-Controlling-PKNCA.R
PKNCA/inst/doc/Options-for-Controlling-PKNCA.Rmd
PKNCA/inst/doc/Superposition.Rmd
PKNCA/inst/doc/Data-Cleaning-in-PKNCA.html
PKNCA/inst/doc/Superposition.html
PKNCA/inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.R
PKNCA/inst/doc/Superposition.R
PKNCA/inst/doc/Selection-of-Calculation-Intervals.R
PKNCA/inst/doc/Writing-Parameter-Functions.Rmd
PKNCA/inst/doc/Introduction-and-Usage.Rmd
PKNCA/inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd
PKNCA/inst/doc/Introduction-and-Usage.html
PKNCA/inst/doc/Selection-of-Calculation-Intervals.html
PKNCA/inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.html
PKNCA/inst/doc/Introduction-and-Usage.R
PKNCA/inst/doc/Writing-Parameter-Functions.R
PKNCA/inst/doc/Writing-Parameter-Functions.html
PKNCA/inst/doc/Example-theophylline.html
PKNCA/inst/doc/Options-for-Controlling-PKNCA.html
PKNCA/inst/doc/Data-Cleaning-in-PKNCA.Rmd
PKNCA/inst/doc/Selection-of-Calculation-Intervals.Rmd
PKNCA/tests
PKNCA/tests/testthat.R
PKNCA/tests/testthat
PKNCA/tests/testthat/test-interpolate.conc.R
PKNCA/tests/testthat/test-check.intervals.R
PKNCA/tests/testthat/test-pk.calc.simple.R
PKNCA/tests/testthat/test-001-add.interval.col.R
PKNCA/tests/testthat/test-merge.R
PKNCA/tests/testthat/test-class-PKNCAdose.R
PKNCA/tests/testthat/test-cleaners.R
PKNCA/tests/testthat/test-provenance.R
PKNCA/tests/testthat/test-class-PKNCAresults.R
PKNCA/tests/testthat/test-exclude.R
PKNCA/tests/testthat/test-class-PKNCAconc.R
PKNCA/tests/testthat/test-class-PKNCAdata.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-class-general.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/provenance.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/class-PKNCAdata.R PKNCA/R/pk.calc.c0.R PKNCA/R/pk.calc.all.R PKNCA/R/tss.R PKNCA/R/class-PKNCAresults.R PKNCA/R/002-pk.business.rules.R PKNCA/R/class-general.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/class-PKNCAconc.R PKNCA/R/general.functions.R PKNCA/R/merge.R PKNCA/R/class-PKNCAdose.R PKNCA/R/exclude.R PKNCA/R/pk.calc.simple.R PKNCA/R/auc.R PKNCA/R/interpolate.conc.R
PKNCA/vignettes
PKNCA/vignettes/Options-for-Controlling-PKNCA.Rmd
PKNCA/vignettes/Superposition.Rmd
PKNCA/vignettes/Writing-Parameter-Functions.Rmd
PKNCA/vignettes/Introduction-and-Usage.Rmd
PKNCA/vignettes/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd
PKNCA/vignettes/PKNCA-ISoP_Study_Group-2016-05-25.pptx
PKNCA/vignettes/2015_ACoP_PKNCA_poster.pdf
PKNCA/vignettes/Data-Cleaning-in-PKNCA.Rmd
PKNCA/vignettes/Selection-of-Calculation-Intervals.Rmd
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/split.PKNCAconc.Rd PKNCA/man/exclude.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/addProvenance.Rd PKNCA/man/PKNCAdose.Rd PKNCA/man/pk.tss.monoexponential.population.Rd PKNCA/man/pk.calc.deg.fluc.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/PKNCA.options.describe.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/check.conversion.Rd PKNCA/man/signifString.Rd PKNCA/man/pk.tss.monoexponential.Rd PKNCA/man/pk.calc.swing.Rd PKNCA/man/setRoute.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/merge.splitlist.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/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/checkProvenance.Rd PKNCA/man/check.interval.specification.Rd PKNCA/man/pk.calc.cav.Rd PKNCA/man/PKNCA.choose.option.Rd PKNCA/man/get.parameter.deps.Rd PKNCA/man/check.interval.deps.Rd PKNCA/man/pk.calc.cmax.Rd PKNCA/man/clean.conc.blq.Rd PKNCA/man/setExcludeColumn.Rd PKNCA/man/getData.PKNCAconc.Rd PKNCA/man/pk.calc.ptr.Rd PKNCA/man/setDuration.Rd PKNCA/man/print.PKNCAconc.Rd PKNCA/man/PKNCA.set.summary.Rd PKNCA/man/print.provenance.Rd PKNCA/man/getColumnValueOrNot.Rd PKNCA/man/pk.nca.interval.Rd

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