Package: PKPDsim 1.4.0

Ron Keizer

PKPDsim: Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations

Simulate dose regimens for pharmacokinetic-pharmacodynamic (PK-PD) models described by differential equation (DE) systems. Simulation using ADVAN-style analytical equations is also supported (Abuhelwa et al. (2015) <doi:10.1016/j.vascn.2015.03.004>).

Authors:Ron Keizer [aut, cre], Jasmine Hughes [aut], Dominic Tong [aut], Kara Woo [aut], Jordan Brooks [aut], InsightRX [cph, fnd]

PKPDsim_1.4.0.tar.gz
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PKPDsim.pdf |PKPDsim.html✨
PKPDsim/json (API)
NEWS

# Install 'PKPDsim' in R:
install.packages('PKPDsim', repos = c('https://insightrx.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/insightrx/pkpdsim/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

odepharmacodynamicspharmacokineticspharmacometrics

65 exports 30 stars 3.38 score 15 dependencies 85 scripts 1.1k downloads

Last updated 29 days agofrom:458c026d81. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 19 2024
R-4.5-win-x86_64NOTEAug 19 2024
R-4.5-linux-x86_64NOTEAug 19 2024
R-4.4-win-x86_64NOTEAug 19 2024
R-4.4-mac-x86_64NOTEAug 19 2024
R-4.4-mac-aarch64NOTEAug 19 2024
R-4.3-win-x86_64NOTEAug 19 2024
R-4.3-mac-x86_64NOTEAug 19 2024
R-4.3-mac-aarch64NOTEAug 19 2024

Exports:add_quotesadd_ruvadd_ruv_to_quantileadherence_binomialadherence_markovadvanadvan_create_dataadvan_parse_outputadvan_process_infusion_dosesapply_duration_scaleapply_lagtimeavailable_default_literature_modelscalc_auc_analyticcalc_ss_analyticcalculate_parameterscompile_sim_cppcovariate_last_obs_onlycovariates_table_to_listcv_to_omegadetect_ode_syntaxf_covget_model_auc_compartmentget_model_covariatesget_model_fixed_parametersget_model_iovget_model_linearityget_model_parametersget_model_structureget_ode_model_sizeget_parameters_from_codeget_var_yifelse0install_default_literature_modelis_positive_definitejoin_cov_and_parjoin_regimenmerge_regimenmodel_from_apimodel_librarymvrnorm2na_locfnew_adherencenew_covariatenew_covariate_modelnew_ode_modelnew_regimennlmixr_parse_parametersnm_to_regimenpkpdsim_to_nlmixrpop_regimenprint_listread_model_jsonregimen_to_nmreparametrizesearch_replace_in_fileshift_regimensimsim_coresim_odesim_ode_shinytable_to_listtest_modeltest_pointertranslate_odetriangle_to_full

Dependencies:BHclidata.tablegluejsonlitelifecyclemagrittrMASSrandtoolboxRcpprlangrngWELLstringistringrvctrs

Absorption models

Rendered fromexample-absorption-models.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2023-03-02
Started: 2022-06-15

Covariates

Rendered fromcovariates.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2024-07-31
Started: 2022-06-15

Export model

Rendered fromexport-model.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2022-06-15
Started: 2022-06-15

Model

Rendered frommodel.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2024-07-31
Started: 2022-06-15

Output

Rendered fromoutput.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2022-06-15
Started: 2022-06-15

Parameters

Rendered fromparameters.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2022-06-15
Started: 2022-06-15

Regimen

Rendered fromregimen.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2024-07-31
Started: 2022-06-15

Simulation

Rendered fromsimulation.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2022-06-15
Started: 2022-06-15

Speed

Rendered fromspeed.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2022-06-15
Started: 2022-06-15

Readme and manuals

Help Manual

Help pageTopics
Put vector values in quotesadd_quotes
Add residual variability to the dependent variableadd_ruv
Calculate the increase in a specific quantile for a distribution on y when residual variability is addedadd_ruv_to_quantile
Binomial adherenceadherence_binomial
Markov adherence modeladherence_markov
ADVAN-style functions to calculate linear PK systemsadvan
Create ADVAN-style datasetadvan_create_data
Internal function to parse the raw output from ADVAN-style functionsadvan_parse_output
Add column RATEALL to ADVAN-style dataset to handle infusionsadvan_process_infusion_doses
Apply infusion duration scale to a regimenapply_duration_scale
Apply lagtime to a regimenapply_lagtime
See models from the literature available for installationavailable_default_literature_models
Convenience function to calculate the AUC based on PK model parameters at any given moment, for linear iv models.calc_auc_analytic
Calculate derivativecalc_dydP
Returns the state of a linear PK system at steady state (trough) using analytics equations (so for linear PK systems only).calc_ss_analytic
Calculate model-specific variables using a dummy call to sim_ode()calculate_parameters
Checks obs input for valid combinations of cmt, var, scalecheck_obs_input
Compile ODE model to c++ functioncompile_sim_cpp
Use only last observed covariate valuescovariate_last_obs_only
Convert covariate table specified as data.framecovariates_table_to_list
Create lower-diagonal omega matrix from CV for parameter estimatescv_to_omega
Auto-detect the syntax for the ODE codedetect_ode_syntax
covariate function builderf_cov
Get fixed parameters from model definition.get_fixed_parameters
Functions for getting information about a modelget_model_auc_compartment get_model_covariates get_model_fixed_parameters get_model_info get_model_iov get_model_linearity get_model_parameters get_model_structure
Get the number of states in the ODE from the code code C++ code for modelget_ode_model_size
Get model parameters from codeget_parameters_from_code
Get expected variance/sd/ci of dependent variable based on PKPDsim model, parameters, and regimenget_var_y
ifelse function but then based on whether value is NULL or notifelse0
Install default literature modelinstall_default_literature_model
Is matrix positive definiteis_positive_definite
Combines covariates and parameters into a single list, useful for reparametrization of the model.join_cov_and_par
Join two dosing regimensjoin_regimen
Size of the lower triangle of the matrixlower_triangle_mat_size
Merge two regimens together.merge_regimen
Load model definition from API, and compile to R librarymodel_from_api
Model librarymodel_library
More powerful multivariate normal sampling functionmvrnorm2
Fill in NAs with the previous non-missing valuena_locf
Probabilistically model adherencenew_adherence
New covariatenew_covariate
covariate model functionnew_covariate_model
Create new ODE modelnew_ode_model
Dose regimen for sim_odenew_regimen
Function to parse parameters for a model into a structure used by nlmixrnlmixr_parse_parameters
Create a regimen from NONMEM datanm_to_regimen
PK datasetpkdata
Convert a model generated with PKPDsim to an object for nlmixrpkpdsim_to_nlmixr
Remove n doses (from tail) of PKPDsim regimenpop_regimen
Return a list in R syntaxprint_list
Read model definition from JSONread_model_json
Convert PKPDsim regimen to NONMEM table (doses only)regimen_to_nm
Reparametrize model parameters using a reparametrization defined within the model.reparametrize
Find string and replace in filesearch_replace_in_file
Remove n doses (from start) of PKPDsim regimenshift_regimen
Simulate ODE or analytical equationsim
Only core function of the simulation function, always just returns observations. Mostly useful for estimations / optimal design. Has no checks (for speed)!sim_core
Deprecated function, renamed to 'sim()'sim_ode
Simulate ODE and create a Shiny appsim_ode_shiny
Convert a table to a listtable_to_list
Test a modeltest_model
Test if model still in memorytest_pointer
Translate a model from/to various PKPD simulatorstranslate_ode
Convert triangle omega matrix to full omega matrixtriangle_to_full