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>).
Last updated 25 days ago
8.19 score 39 stars 2 packages 98 scripts 1.8k downloadsnlmixr2est - 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>).
Last updated 1 days ago
7.92 score 7 stars 8 packages 20 scripts 1.7k downloadslotri - A Simple Way to Specify Symmetric, Block Diagonal Matrices
Provides a simple mechanism to specify a symmetric block diagonal matrices (often used for covariance matrices). This is based on the domain specific language implemented in 'nlmixr2' but expanded to create matrices in R generally instead of specifying parts of matrices to estimate. It has expanded to include some matrix manipulation functions that are generally useful for 'rxode2' and 'nlmixr2'.
Last updated 27 days ago
7.72 score 5 stars 13 packages 18 scripts 2.1k downloadslbfgsb3c - Limited Memory BFGS Minimizer with Bounds on Parameters with optim() 'C' Interface
Interfacing to Nocedal et al. L-BFGS-B.3.0 (See <http://users.iems.northwestern.edu/~nocedal/lbfgsb.html>) limited memory BFGS minimizer with bounds on parameters. This is a fork of 'lbfgsb3'. This registers a 'R' compatible 'C' interface to L-BFGS-B.3.0 that uses the same function types and optimization as the optim() function (see writing 'R' extensions and source for details). This package also adds more stopping criteria as well as allowing the adjustment of more tolerances.
Last updated 30 days ago
7.55 score 15 packages 16 scripts 4.1k downloadsbabelmixr2 - 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.
Last updated 1 hours ago
monolixnonmempharmacometrics
6.63 score 8 stars 41 scripts 698 downloadsnlmixr2lib - A Model Library for 'nlmixr2'
A model library for 'nlmixr2'. The models include (and plan to include) pharmacokinetic, pharmacodynamic, and disease models used in pharmacometrics. Where applicable, references for each model are included in the meta-data for each individual model. The package also includes model composition and modification functions to make model updates easier.
Last updated 11 days ago
6.24 score 5 stars 6 scripts 426 downloadsnlmixr2extra - Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions
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>). This package is for support functions like preconditioned fits <doi:10.1208/s12248-016-9866-5>, boostrap and stepwise covariate selection.
Last updated 30 days ago
5.57 score 3 stars 4 packages 10 scripts 1.7k downloadsnlmixr2data - Nonlinear Mixed Effects Models in Population PK/PD, Data
Datasets for 'nlmixr2' and 'rxode2'. 'nlmixr2' is used for fitting and comparing 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>).
Last updated 9 months ago
5.08 score 3 stars 9 packages 6 scripts 1.5k downloadsnlmixr2plot - Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions
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>). This package is for 'ggplot2' plotting methods for 'nlmixr2' objects.
Last updated 30 days ago
4.82 score 2 stars 3 packages 6 scripts 1.5k downloadsnlmixr2rpt - Templated Word and PowerPoint Reporting of 'nlmixr2' Fitting Results
This allows you to generate reporting workflows around 'nlmixr2' analyses with outputs in Word and PowerPoint. You can specify figures, tables and report structure in a user-definable 'YAML' file. Also you can use the internal functions to access the figures and tables to allow their including in other outputs (e.g. R Markdown).
Last updated 29 days ago
4.75 score 2 stars 14 scripts 262 downloadsrxode2ll - Log-Likelihood Functions for 'rxode2'
Provides the log-likelihoods with gradients from 'stan' (Carpenter et al (2015), <arXiv:1509.07164>) needed for generalized log-likelihood estimation in 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). This is split of to reduce computational burden of recompiling 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) which runs the 'nlmixr2' models during estimation.
Last updated 2 years ago
4.71 score 2 stars 12 packages 1 scripts 1.4k downloadsn1qn1 - Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS Optimization
Provides 'Scilab' 'n1qn1'. This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian. If the Hessian is near enough the truth in optimization it can speed up the optimization problem. The algorithm is described in the 'Scilab' optimization documentation located at <https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>. This version uses manually modified code from 'f2c' to make this a C only binary.
Last updated 2 months ago
4.26 score 1 stars 9 packages 4 scripts 1.4k downloadsrxode2parse - Parsing and Code Generation Functions for 'rxode2'
Provides the parsing needed for 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>). It also provides the 'stan' based advan linear compartment model solutions with gradients (Carpenter et al (2015), <doi:10.48550/arXiv.1509.07164>) needed in 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). This split will reduce computational burden of recompiling 'rxode2'.
Last updated 25 days ago
archivedpackagesr-universe
3.54 score 5 stars 2 packages 1 scripts 2.3k downloadsrxode2random - Random Number Generation Functions for 'rxode2'
Provides the random number generation (in parallel) needed for 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) and 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>). This split will reduce computational burden of recompiling 'rxode2'.
Last updated 28 days ago
archivedpackagesr-universe
3.41 score 5 stars 2 packages 2 scripts 1.7k downloadsxpose.nlmixr2 - Graphical Diagnostics for Pharmacometric Models: Extension to 'nlmixr2'
Extension to 'xpose' to support 'nlmixr2'. Provides functions to import 'nlmixr2' fit data into an 'xpose' data object, allowing the use of 'xpose' for 'nlmixr2' model diagnostics.
Last updated 2 years ago
3.32 score 1 stars 1 packages 35 scripts 335 downloadsnlmixr2targets - Targets for 'nlmixr2' Pipelines
'nlmixr2' often has long runtimes. A pipeline toolkit tailored to 'nlmixr2' workflows leverages 'targets' and 'nlmixr2' to ease reproducible workflows. 'nlmixr2targets' ensures minimal rework in model development with 'nlmixr2' and 'targets' by simplifying and standardizing models and datasets.
Last updated 7 months ago
3.18 score 6 scripts