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pmxTools

Pharmacometric Tools for Modeling & Simulation

Developed by Justin Wilkins, Bill Denney and Rik Schoemaker, with contributions from a host of others.

Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero- and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008) http://lixoft.com/wp-content/uploads/2016/03/PKPDlibrary.pdf); parametric simulation from NONMEM-generated parameter estimates and other output; and parsing, tabulating and plotting results generated by Perl-speaks-NONMEM (PsN).

To install:

devtools::install_github("kestrel99/pmxTools")

or download directly from CRAN.

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Version

Install

install.packages('pmxTools')

Monthly Downloads

420

Version

1.2.1

License

GPL-2

Issues

4

Pull Requests

3

Stars

32

Forks

10

Maintainer

Justin Wilkins

Last Published

August 26th, 2020

Functions in pmxTools (1.2.1)

calc_ss_1cmt

Calculate C(t) for a 1-compartment linear model at steady-state
calc_sd_2cmt

Calculate C(t) for a 1-compartment linear model
get_theta

Extract structural model parameter estimates and associated information from a NONMEM output object.
calc_sd_3cmt

Calculate C(t) for a 1-compartment linear model
gm

Calculate geometric mean
gcv_convert

Convert geometric variance or standard deviation to a geometric coefficient of variation
plot_nmprogress

Plot NONMEM parameter estimation by iteration.
calc_ss_3cmt

Calculate C(t) for a 3-compartment linear model at steady-state
plot_scm

Visualize PsN SCM output.
rnm

Read NONMEM 7.2+ output into an R object.
read_nm

Read NONMEM 7.2+ output into a list of lists.
sample_sigma

Sample from the multivariate normal distribution using the SIGMA variance-covariance matrix to generate new sets of simulated EPSILONs from NONMEM output.
read_nm_all

Read all NONMEM files for a single NONMEM run.
calc_ss_2cmt

Calculate C(t) for a 2-compartment linear model at steady-state
pk_curve

Provide concentration-time curves.
pcv

Calculate percentage coefficient of variation
sample_omega

Sample from the multivariate normal distribution using the OMEGA variance-covariance matrix to generate new sets of simulated ETAs from NONMEM output.
get_auc

Calculate the area under the curve (AUC) for each subject over the time interval for dependent variables (dv) using the trapezoidal rule.
get_omega

Extract variability parameter estimates from a NONMEM output object.
get_est_table

Create a table of model parameter estimates from a NONMEM output object.
get_shrinkage

Extract shrinkage estimates from a NONMEM output object.
sample_uncert

Sample from the multivariate normal distribution to generate new sets of parameters from NONMEM output.
get_probinfo

Extract problem and estimation information from a NONMEM output object.
get_sigma

Extract residual variability parameter estimates from a NONMEM output object.
read_nm_multi_table

Read (single or) multiple NONMEM tables from a single file
read_nm_std_ext

Read a standard NONMEM extension file
read_scm

Read PsN SCM output into a format suitable for further use.
read_nmtables

Reads NONMEM output tables.
read_nmext

Read NONMEM output into a list.
read_nmcov

Read in the NONMEM variance-covariance matrix.
table_rtf

Read NONMEM output into a list.
calc_derived

Calculate derived pharmacokinetic parameters for a 1-, 2-, or 3-compartment linear model.
calc_sd_1cmt

Calculate C(t) for a 1-compartment linear model