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PKPDsim

PKPDsim is a library for numerical integration of ODE systems, in particular pharmacokinetic-pharmacodynamic (PK-PD) mixed-effects models.

Installation

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

The CRAN version of PKPDsim can be installed using:

install.packages("PKPDsim")

The development version of PKPDsim can be installed using:

devtools::install_github("InsightRX/PKPDsim")

A number of models from the literature have been made available for use in PKPD simulations. To see which models are available for installation, run:

available_default_literature_models()

You can install these models as packages using the following commands:

# To install a single model:
install_default_literature_model("pk_busulfan_mccune")
# To install all supplied models:
install_default_literature_model("all")

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('PKPDsim')

Monthly Downloads

730

Version

1.4.0

License

MIT + file LICENSE

Issues

Pull Requests

Stars

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Repository

https://github.com/InsightRX/PKPDsim

Homepage

https://insightrx.github.io/PKPDsim/

Maintainer

Ron Keizer

Last Published

August 19th, 2024

Functions in PKPDsim (1.4.0)

First-order absorption- 2 compartment

calc_auc_analytic

Convenience function to calculate the AUC based on PK model parameters at any given moment, for linear iv models.

available_default_literature_models

See models from the literature available for installation

advan_process_infusion_doses

Add column RATEALL to ADVAN-style dataset to handle infusions

calc_ss_analytic

Returns the state of a linear PK system at steady state (trough) using analytics equations (so for linear PK systems only).

Add residual variability to the dependent variable

calculate_parameters

Calculate model-specific variables using a dummy call to sim_ode()

Calculate derivative

bioavailability_to_R_code

Transforms bioavailability specs into appropriate R code

covariate_last_obs_only

Use only last observed covariate values

covariates_table_to_list

Convert covariate table specified as data.frame

apply_duration_scale

Apply infusion duration scale to a regimen

check_mixture_model

Check that mixture model is specified in right format and within constraints (1 parameter, 2 groups)

get_fixed_parameters

Get fixed parameters from model definition.

compile_sim_cpp

Compile ODE model to c++ function

get_ode_model_size

Get the number of states in the ODE from the code code C++ code for model

covariate function builder

create_event_table

Create an event table

detect_ode_syntax

Auto-detect the syntax for the ODE code

Functions for getting information about a model

Apply lagtime to a regimen

check_obs_input

Checks obs input for valid combinations of cmt, var, scale

ifelse function but then based on whether value is NULL or not

get_parameters_from_code

Get model parameters from code

is_positive_definite

Is matrix positive definite

install_default_literature_model

Install default literature model

Fill in NAs with the previous non-missing value

Load model definition from API, and compile to R library

is_newer_package

Check if package number is different from currently installed, and provide some messaging.

More powerful multivariate normal sampling function

analytical_eqn_wrapper

Wrapper for using analytical equations with PKPD regimens

check_iov_specification

Checks that IOV was specified appropriately

create_obs_data

Create obs data

lower_triangle_mat_size

Size of the lower triangle of the matrix

join_cov_and_par

Combines covariates and parameters into a single list, useful for reparametrization of the model.

Join two dosing regimens

Create a regimen from NONMEM data

new_covariate_model

covariate model function

Create new ODE model

Print function for PKPDsim regimen

get_t_obs_from_regimen

Extract sensible default observation times from a specified regimen

Get expected variance/sd/ci of dependent variable based on PKPDsim model, parameters, and regimen

Probabilistically model adherence

Create lower-diagonal omega matrix from CV for parameter estimates

search_replace_in_file

Find string and replace in file

Reparametrize model parameters using a reparametrization defined within the model.

nlmixr_parse_parameters

Function to parse parameters for a model into a structure used by nlmixr

Dose regimen for sim_ode

read_model_json

Read model definition from JSON

Merge two regimens together.

Print function for PKPDsim simulation function

parse_obs_types

Parse observation types to simulation code

define_tdm_init_model

defines C code for TDM before dose conditions

Convert a table to a list

Remove n doses (from tail) of PKPDsim regimen

triangle_to_full

Convert triangle omega matrix to full omega matrix

vector_to_R_code

Transform a vector into a string that evaluates to the same vector

pkpdsim_to_nlmixr

Convert a model generated with PKPDsim to an object for nlmixr

Return a list in R syntax

Deprecated function, renamed to sim()

Simulate ODE and create a Shiny app

Only core function of the simulation function, always just returns observations. Mostly useful for estimations / optimal design. Has no checks (for speed)!

Simulate ODE or analytical equation

print.covariate

Print function for PKPDsim covariate object

Convert PKPDsim regimen to NONMEM table (doses only)

Remove n doses (from start) of PKPDsim regimen

shift_state_indices

R starts counting vector indices at 1, c++ starts at 0, so reduce all state numbers in the Cpp function definition by 1

Test if model still in memory

Current time in UTC

Translate a model from/to various PKPD simulators

ThreeCompIVinfusionMetab

3-compartment IV infusion with first-order metabolite formation

Put vector values in quotes

add_ruv_to_quantile

Calculate the increase in a specific quantile for a distribution on y when residual variability is added

adherence_markov

Markov adherence model

adherence_binomial

Binomial adherence

ThreeCompIVinfusion

IV infusion- 3 compartment

ADVAN-style equations

ThreeCompIVbolus

IV bolus- 3 compartment

IV bolus- 2 compartment

PKPDsim-package

PKPDsim package

TwoCompIVinfusion

IV infusion- 2 compartment

first-order absorption 1 compartment

ThreeCompOralMetab

first-order absorption- 3 compartment-Metabolite

OneCompIVinfusion

IV infusion- 1 compartment

first-order absorption- 3 compartment

ADVAN-style functions to calculate linear PK systems

advan_create_data

Create ADVAN-style dataset

advan_parse_output

Internal function to parse the raw output from ADVAN-style functions