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clinPK: Clinical Pharmacokinetics Toolkit

Overview

The clinPK package provides equations commonly used in clinical pharmacokinetics and clinical pharmacology, such as equations for dose individualization, compartmental pharmacokinetics, drug exposure, anthropomorphic calculations, clinical chemistry, and conversion of common clinical parameters. Where possible and relevant, it provides multiple published and peer-reviewed equations within the respective R function.

Installation

The development version of clinPK always has the most up-to-date improvements and bug fixes. We aim to release clinPK on CRAN at least once a year, depending on the number and impact of updates made to the development version.

The CRAN version of clinPK can be installed using:

install.packages("clinPK")

The development version of clinPK can be installed using:

devtools::install_github("InsightRX/clinPK")

Contributing

We welcome input from the community:

If you think you have encountered a bug, please submit an issue on the GitHub

page. Please include a reproducible example of the unexpected behavior.

Please open a pull request if you have a fix or updates that would improve the package. If you're not sure if your proposed

changes are useful or within scope of the package, feel free to contact one of the authors of this package.

Disclaimer

The functionality in this R package is provided "as is". While its authors adhere to software development best practices, the software may still contain unintended errors.

InsightRX Inc. and the authors of this package can not be held liable for any damages resulting from any use of this software. By the use of this software package, the user waives all warranties, expressed or implied, including any warranties to the accuracy, quality or suitability of InsightRX for any particular purpose, either medical or non-medical.

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Version

Install

install.packages('clinPK')

Monthly Downloads

338

Version

0.13.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/InsightRX/clinPK

Homepage

https://insightrx.github.io/clinPK/

Maintainer

Ron Keizer

Last Published

February 23rd, 2024

Functions in clinPK (0.13.0)

Estimate serum creatinine

Calculate half-life based on two points

calc_neutropenia_grade

Calculate neutropenia grade from ANC

Convert dose to expected AUCinf or AUCt for 1 compartment linear PK model

Calculate fat-free mass

Calculate lean body weight

convert_creat_assay

Convert serum creatinine from various assays to Jaffe

convert_flow_unit

Convert flow (e.g. clearance) from / to units

Convert lbs to kg

convert_creat_unit

Convert creatinine to different unit

Convert cm to inch

Calculate mean between two values in a vector Used in NCA for calculation of mean between two or more timepoints.

Convert kg to oz

pct_weight_for_age

Percentile weight for age for children

Calculate AKI stage according to KDIGO criteria

Convert oz to kg

Convert kg to lbs

Convert molar to concentration

check_covs_available

Checks whether required covariates for eGFR calculations are present

Returns parameters needed to calculate eGFR according to the method specified.

pk_1cmt_inf_dose_from_cmax

Calculate dose to achieve steady state Cmax for 1-compartmental PK model with infusion dosing at steady state

Perform an NCA based on a NONMEM-style dataset

Concentration predictions for 1-compartmental PK model after single or multiple bolus doses

pk_2cmt_bolus_ss

Concentration predictions for 2-compartmental PK model, bolus dosing at steady state

pk_1cmt_inf_dose_for_range

Calculate dose based on a given AUC24, Cmax, and Cmin, assuming 1-compartment model

Check if values in vector are empty

Helper function to grab the conversion factor from an input unit and given list

calc_kel_single_tdm

Calculate elimination rate when given a single TDM sample

pk_2cmt_bolus_dose_from_cmin

Calculate dose to achieve steady state trough for 2-compartmental PK model bolus dosing at steady state

pk_1cmt_inf_cmax_ss

Cmax for linear 1-compartment PK model at steady state

pk_1cmt_inf_cmin_ss

Cmin (trough) for linear 1-compartment PK model at steady state

Concentration predictions for 2-compartmental PK model, single or multiple bolus doses

Convert concentration to molar

convert_albumin_unit

Convert albumin from / to units

convert_bilirubin_unit

Convert bilirubin from / to units

pk_2cmt_inf_cmin_ss

Cmin (trough) for 2-compartmental PK model, bolus dosing at steady state

pk_2cmt_bolus_cmax_ss

Cmax for 2-compartmental PK model, bolus dosing at steady state

convert_conc_unit

Convert concentration units

print.nca_output

Print function for output from nca()

pct_bmi_for_age

Percentile BMI for age for children

Read WHO growth tables

relative2absolute_bsa

Convert quantity expressed relative to BSA to absolute units

NCA core function to perform linear trapezoid calculations for post-infusion

Convert any weight unit to kg

pk_1cmt_bolus_ss

Concentration predictions for 1-compartmental PK model with bolus dosing at steady state

Concentration predictions for 1-compartmental PK model after single or multiple bolus doses

Convert inch to cm

pk_1cmt_inf_dose_from_cmin

Calculate dose to achieve steady state trough for 1-compartmental PK model with infusion dosing at steady state

pk_1cmt_bolus_dose_from_cmax

Calculate dose to achieve steady state Cmax for 1-compartmental PK model bolus dosing at steady state

pk_1cmt_bolus_dose_from_cmin

Calculate dose to achieve steady state trough for 1-compartmental PK model bolus dosing at steady state

Concentration predictions for 2-compartmental PK model with infusion dosing at steady state

Less-than-or-equal-to with a little room for floating point precision issues

NCA core function to perform log-linear trapezoid calculations for post-infusion

pk_2cmt_inf_dose_from_cmax

Calculate dose to achieve steady state Cmax for 2-compartmental PK model with infusion dosing at steady state

pk_1cmt_bolus_cmax_ss

Cmax for linear 1-compartment PK model at steady state, bolus dosing

pk_2cmt_bolus_cmin_ss

Cmin (trough) for 2-compartmental PK model, bolus dosing at steady state

pk_1cmt_bolus_cmin_ss

Cmin (trough) for linear 1-compartment PK model at steady state, bolus dosing

Remove less-than/greater-than symbols and convert to numeric

Calculate kinetic GFR

pk_2cmt_inf_dose_from_cmin

Calculate dose to achieve steady state trough for 2-compartmental PK model with infusion dosing at steady state

Time to steady state In either time units or number of doses

Concentration predictions for 2-compartmental PK model with infusion dosing at steady state

find_nearest_interval

Generic function to calculate the interval nearest to a possible dosing interval

Calculate fraction of steady state at particular time after start of dosing

pct_height_for_age

Percentile height for age for children

Greater-than-or-equal-to with a little room for floating point precision issues

find_nearest_dose

Generic function to calculate the dose nearest to a specific dose unit increment

Concentration predictions for 1-compartmental oral PK model after single or multiple bolus doses

Concentration predictions for 2-compartmental PK model, single or multiple infusions

Calculate terminal half-life for 1-compartment model

pct_for_age_generic

Percentile height or weight for age for children

pk_2cmt_inf_cmax_ss

Cmax (trough) for 2-compartmental PK model, bolus dosing at steady state

Calculate half-life(s) for 2-compartment model

pk_2cmt_bolus_dose_from_cmax

Calculate dose to achieve steady state Cmax for 2-compartmental PK model bolus dosing at steady state

pk_2cmt_t12_interval

Calculate average half-life for 2-compartment model during a specific interval

Add residual variability to data

calc_amts_for_conc

Calculate the amounts in all compartments in a compartmental PK system based on a given concentration in the central compartment, and assuming steady state.

calc_baseline_scr

Calculate baseline sCr

Convert AUCtau or AUCt to dose (for 1-compartment linear PK model)

accumulation_ratio

Calculate accumulation ratio This is the ratio of drug concentration or AUC at steady state over concentrations after single dose

Calculate adjusted body weight (ABW)

factors or characters to numeric

Calculate AKI stage

absolute2relative_bsa

Convert quantity expressed in absolute units relative to normalized BSA

Calculate ideal body weight in kg for children and adults

Estimate serum creatinine in neonates

calc_egfr_cystatin

Calculate eGFR based on Cystatin C measurements

Calculate body surface area

calc_dosing_weight

Calculate commonly used "dosing weight"

calc_carboplatin_calvert

Calvert equation for carboplatin

calc_kel_double_tdm

Calculate elimination rate when given two TDM samples