Showing 13 of total 13 results (show query)
andrewhooker
PopED:Population (and Individual) Optimal Experimental Design
Optimal experimental designs for both population and individual studies based on nonlinear mixed-effect models. Often this is based on a computation of the Fisher Information Matrix. This package was developed for pharmacometric problems, and examples and predefined models are available for these types of systems. The methods are described in Nyberg et al. (2012) <doi:10.1016/j.cmpb.2012.05.005>, and Foracchia et al. (2004) <doi:10.1016/S0169-2607(03)00073-7>.
Maintained by Andrew C. Hooker. Last updated 5 months ago.
nlmeoptimal-designpharmacodynamicspharmacokineticspharmacometricspkpdpopulationpopulation-model
15.5 match 33 stars 9.58 score 300 scripts 1 dependents
john-harrold
ubiquity:PKPD, PBPK, and Systems Pharmacology Modeling Tools
Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Maintained by John Harrold. Last updated 16 days ago.
14.4 match 13 stars 7.14 score 33 scripts
novartis
xgxr:Exploratory Graphics for Pharmacometrics
Supports a structured approach for exploring PKPD data <https://opensource.nibr.com/xgx/>. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Maintained by Andrew Stein. Last updated 1 years ago.
6.0 match 13 stars 7.76 score 105 scripts 5 dependents
insightrx
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>).
Maintained by Ron Keizer. Last updated 19 days ago.
odepharmacodynamicspharmacokineticspharmacometricscpp
1.8 match 36 stars 9.47 score 100 scripts
marclavielle
Rsmlx:R Speaks 'Monolix'
Provides methods for model building and model evaluation of mixed effects models using 'Monolix' <https://monolix.lixoft.com>. 'Monolix' is a software tool for nonlinear mixed effects modeling that must have been installed in order to use 'Rsmlx'. Among other tasks, 'Rsmlx' provides a powerful tool for automatic PK model building, performs statistical tests for model assessment, bootstrap simulation and likelihood profiling for computing confidence intervals. 'Rsmlx' also proposes several automatic covariate search methods for mixed effects models.
Maintained by Chloe Bracis. Last updated 9 months ago.
4.0 match 4 stars 3.96 score 19 scripts
iame-researchcenter
PFIM:Population Fisher Information Matrix
Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>, Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>, Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>, Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>, Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.
Maintained by Romain Leroux. Last updated 5 months ago.
5.2 match 2.78 score 9 scripts
nlmixr2
nlmixr2:Nonlinear Mixed Effects Models in Population PK/PD
Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Maintained by Matthew Fidler. Last updated 24 days ago.
1.7 match 50 stars 8.45 score 120 scripts 3 dependentsnlmixr2
nlmixr2est:Nonlinear Mixed Effects Models in Population PK/PD, Estimation Routines
Fit and compare nonlinear mixed-effects models in differential equations with flexible dosing information commonly seen in pharmacokinetics and pharmacodynamics (Almquist, Leander, and Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation solving is by compiled C code provided in the 'rxode2' package (Wang, Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Maintained by Matthew Fidler. Last updated 25 days ago.
1.7 match 9 stars 8.26 score 26 scripts 9 dependents
ahgroup
DSAIRM:Dynamical Systems Approach to Immune Response Modeling
Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.
Maintained by Andreas Handel. Last updated 8 months ago.
2.0 match 34 stars 6.19 score 23 scripts
ggpmxdevelopment
ggPMX:'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models
At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling activities in order to reduce the overall effort required for generating such plots. For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox, called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP <doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>. When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required Chart Data instead of exporting it from the 'Monolix' gui.
Maintained by Matthew Fidler. Last updated 1 years ago.
1.7 match 39 stars 7.23 score 80 scripts
stephen-amori
apmx:Automated Population Pharmacokinetic Dataset Assembly
Automated methods to assemble population PK (pharmacokinetic) and PKPD (pharmacodynamic) datasets for analysis in 'NONMEM' (non-linear mixed effects modeling) by Bauer (2019) <doi:10.1002/psp4.12404>. The package includes functions to build datasets from SDTM (study data tabulation module) <https://www.cdisc.org/standards/foundational/sdtm>, ADaM (analysis dataset module) <https://www.cdisc.org/standards/foundational/adam>, or other dataset formats. The package will combine population datasets, add covariates, and create documentation to support regulatory submission and internal communication.
Maintained by Stephen Amori. Last updated 1 years ago.
0.5 match 5 stars 4.40 score 10 scripts
cran
ncappc:NCA Calculations and Population Model Diagnosis
A flexible tool that can perform (i) traditional non-compartmental analysis (NCA) and (ii) Simulation-based posterior predictive checks for population pharmacokinetic (PK) and/or pharmacodynamic (PKPD) models using NCA metrics.
Maintained by Andrew C. Hooker. Last updated 7 years ago.
0.5 match 2.70 score