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.


The PKNCA R package is designed to perform all noncompartmental analysis (NCA) calculations for pharmacokinetic (PK) data. The package is broadly separated into two parts (calculation and summary) with some additional housekeeping functions.

The primary and secondary goals of the PKNCA package are to 1) only give correct answers to the specific questions being asked and 2) automate as much as possible to simplify the task of the analyst. When automation would leave ambiguity or make a choice that the analyst may have an alternate preference for, it is either not used or is possible to override.

Note that backward compatibility will not be guaranteed until version 1.0. Argument and function changes will continue until then. These will be especially noticable around the inclusion of IV NCA parameters and additional specifications of the dosing including dose amount and route.

To install the development version from github, install the devtools package and then type the following commands:

library(devtools)
install_github("billdenney/pknca")

Calculating parameters

# Load the package
library(PKNCA)
# Set the business rule options with the PKNCA.options() function
# Load your concentration-time data
myrawconcdata <- read.csv("myconc.csv", stringsAsFactors=FALSE)
# Load your dose data
myrawdosedata <- read.csv("mydose.csv", stringsAsFactors=FALSE)
# Put your concentration data into a PKNCAconc object
myconc <- PKNCAconc(data=myrawconcdata,
                    formula=conc~time|treatment+subject/analyte)
# Put your dose data into a PKNCAdose object
mydose <- PKNCAdose(data=myrawdosedata,
                    formula=dose~time|treatment+subject)
# Combine the two (and automatically determine the intervals of
# interest
mydata <- PKNCAdata(myconc, mydose)
# Compute the NCA parameters
myresults <- pk.nca(mydata)
# Summarize the results
summary(myresults)

More help is available in the function help files, and be sure to look at the PKNCA.options function for many choices to make PKNCA conform to your company's business rules for calculations and summarization.

Feature requests

Please use the github issues page (https://github.com/billdenney/pknca/issues) to make feature requests and bug reports.

News

Note that backward compatibility will not be guaranteed until version 1.0. Argument and function changes will continue until then. These will be especially noticable around the inclusion of IV NCA parameters and additional specifications of the dosing including dose amount and route.

PKNCA 0.7.1

  • Updated vignettes
  • Standardize rounding and significance with missing values in signifString and roundString
  • Enable wide data output with as.data.frame(PKNCAresults, out.format="wide")
  • Correct calculation of Vz
  • Various CRAN-related cleanups

PKNCA 0.7

  • Features added
    • Additional PK parameters to support IV dosing added
    • Fix #11, Intervals can be specified manually, and will apply across appropriate parts of the grouping variables
    • Enable dose and dose.time as parameters to NCA calculations
    • More NCA parameters are calculated, especially related to IV dosing
    • Fix #8, Reporting times for time-based parameters are now within the current interval rather than since first dose (e.g. Tmax on day 14 should be between 0 and 24 not 2724+c(0, 24))
    • Added several vignettes
  • Bugs fixed
    • Dosing without concentration is probably placebo; warn and continue
    • Fix #6, make merge.splitByData work with more than one dosing level
    • Export some generic classes that were not previously exported to simplify their use
    • Superposition extensions when lambda.z cannot be calculated
    • Significance rounding into character strings works when the rounding moves up one order of magnitude.
    • Fix #9, summarization of parameters that are not calculated show not calculated instead of missing.

PKNCA 0.6

First release targeting CRAN

Reference manual

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install.packages("PKNCA")

0.8.1 by Bill Denney, 9 months ago


https://github.com/billdenney/pknca


Report a bug at https://github.com/billdenney/pknca/issues


Browse source code at https://github.com/cran/PKNCA


Authors: Bill Denney [aut, cre], Clare Buckeridge [aut], Sridhar Duvvuri [ctb]


Documentation:   PDF Manual  


Task views: Analysis of Pharmacokinetic Data


AGPL-3 license


Imports dplyr, digest, plyr, nlme, parallel, lattice, stats, tidyr, utils

Suggests knitr, testthat, ggplot2


Imported by polyPK.


See at CRAN