PKNCA: Perform Pharmacokinetic Non-Compartmental Analysis

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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.

Author
Bill Denney [aut, cre], Clare Buckeridge [aut], Sridhar Duvvuri [ctb]
Date of publication
2016-08-15 16:28:48
Maintainer
Bill Denney <wdenney@humanpredictions.com>
License
AGPL-3
Version
0.7.1
URLs

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