Showing 11 of total 11 results (show query)
uupharmacometrics
xpose:Diagnostics for Pharmacometric Models
Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.
Maintained by Benjamin Guiastrennec. Last updated 3 months ago.
diagnosticsggplot2nonmempharmacometricsxpose
62 stars 11.02 score 183 scripts 6 dependents
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 6 months ago.
nlmeoptimal-designpharmacodynamicspharmacokineticspharmacometricspkpdpopulationpopulation-model
33 stars 9.58 score 300 scripts 1 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 1 months ago.
odepharmacodynamicspharmacokineticspharmacometricscpp
36 stars 9.44 score 100 scripts
nmautoverse
NMdata:Preparation, Checking and Post-Processing Data for PK/PD Modeling
Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.
Maintained by Philip Delff. Last updated 7 days ago.
17 stars 7.72 score 88 scripts 2 dependentsuupharmacometrics
xpose4:Diagnostics for Nonlinear Mixed-Effect Models
A model building aid for nonlinear mixed-effects (population) model analysis using NONMEM, facilitating data set checkout, exploration and visualization, model diagnostics, candidate covariate identification and model comparison. The methods are described in Keizer et al. (2013) <doi:10.1038/psp.2013.24>, and Jonsson et al. (1999) <doi:10.1016/s0169-2607(98)00067-4>.
Maintained by Andrew C. Hooker. Last updated 1 years ago.
diagnosticsnonmempharmacometricspopulation-modelxpose
36 stars 7.31 score 315 scripts
nlmixr2
nonmem2rx:Converts 'NONMEM' Models to 'rxode2'
'NONMEM' has been a tool for running nonlinear mixed effects models since the 80s and is still used today (Bauer 2019 <doi:10.1002/psp4.12404>). This tool allows you to convert 'NONMEM' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) and with simple models 'nlmixr2' syntax (Fidler et al (2019) <doi:10.1002/psp4.12445>). The 'nlmixr2' syntax requires the residual specification to be included and it is not always translated. If available, the 'rxode2' model will read in the 'NONMEM' data and compare the simulation for the population model ('PRED') individual model ('IPRED') and residual model ('IWRES') to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'NONMEM' and can convert the objects converted from 'nonmem2rx' to a full 'nlmixr2' fit.
Maintained by Matthew Fidler. Last updated 4 months ago.
nlmixr2nonmempharmacometricsrxode2cpp
12 stars 6.46 score 23 scripts 1 dependentsnlmixr2
babelmixr2:Use 'nlmixr2' to Interact with Open Source and Commercial Software
Run other estimation and simulation software via the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) interface including 'PKNCA', 'NONMEM' and 'Monolix'. While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When 'lixoftConnectors' is available, 'Monolix' can be run directly instead of setting up command line usage.
Maintained by Matthew Fidler. Last updated 21 days ago.
monolixnonmempharmacometricscpp
9 stars 6.11 score 53 scripts
certara
Certara.R:Easily Install Pharmacometric Packages and Shiny Applications Developed by Certara
A convenient set of wrapper functions to install pharmacometric packages and Shiny applications developed by Certara PMX and Integrated Drug Development (iDD). The functions ensure the successful installation of packages from non-standard repositories.
Maintained by James Craig. Last updated 5 months ago.
14 stars 4.45 score 2 scriptsnlmixr2
monolix2rx:Converts 'Monolix' Models to 'rxode2'
'Monolix' is a tool for running mixed effects model using 'saem'. This tool allows you to convert 'Monolix' models to 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) using the form compatible with 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). If available, the 'rxode2' model will read in the 'Monolix' data and compare the simulation for the population model individual model and residual model to immediately show how well the translation is performing. This saves the model development time for people who are creating an 'rxode2' model manually. Additionally, this package reads in all the information to allow simulation with uncertainty (that is the number of observations, the number of subjects, and the covariance matrix) with a 'rxode2' model. This is complementary to the 'babelmixr2' package that translates 'nlmixr2' models to 'Monolix' and can convert the objects converted from 'monolix2rx' to a full 'nlmixr2' fit. While not required, you can get/install the 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When 'lixoftConnectors' is available, 'Monolix' can be used to load its model library instead manually setting up text files (which only works with old versions of 'Monolix').
Maintained by Matthew Fidler. Last updated 4 months ago.
monolixnlmixr2pharmacometricsrxode2cpp
1 stars 4.40 score 14 scripts 1 dependents
asancpt
caffsim:Simulation of Plasma Caffeine Concentrations by Using Population Pharmacokinetic Model
Simulate plasma caffeine concentrations using population pharmacokinetic model described in Lee, Kim, Perera, McLachlan and Bae (2015) <doi:10.1007/s00431-015-2581-x> and the package was published <doi:10.12793/tcp.2017.25.3.141>.
Maintained by Sungpil Han. Last updated 5 years ago.
caffeinemedicinemonte-carlo-simulationpharmacokineticspharmacometricstoxicology
9 stars 3.77 score 13 scripts