R-universe - mattfidler (Matthew Fidler)

rxode2 - Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The vendored 'SUNDIALS' 'CVODE' sources and headers are released under the BSD-3-Clause license. The information is available in the inst/COPYRIGHTS.

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openblascppopenmp

13.44 score 67 stars 19 dependents 4.7k scripts 4.1k downloads

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>).

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openblascppopenmp

10.93 score 15 stars 13 dependents 94 scripts 2.6k downloads

lotri - 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'.

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openblascppopenmp

9.48 score 7 stars 20 dependents 41 scripts 3.2k downloads

nlmixr2 - Nonlinear Mixed Effects Models in Population PK/PD

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9.03 score 102 stars 2 dependents 403 scripts 1.9k downloads

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.

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nlmixr2nonmempharmacometricsrxode2cpp

8.14 score 16 stars 2 dependents 56 scripts 969 downloads

lbfgsb3c - 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.

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cppopenmp

7.73 score 1 stars 26 dependents 35 scripts 4.9k downloads

nlmixr2plot - Nonlinear Mixed Effects Models in Population PK/PD, Plot Functions

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7.13 score 3 stars 4 dependents 16 scripts 1.9k downloads

nlmixr2extra - Nonlinear Mixed Effects Models in Population PK/PD, Extra Support Functions

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openblascpp

7.08 score 7 stars 6 dependents 23 scripts 2.0k downloads

rxode2ll - Log-Likelihood Functions for 'rxode2'

Provides the log-likelihoods with gradients from 'stan' (Carpenter et al (2015), <doi:10.48550/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.

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cppopenmp

6.76 score 3 stars 20 dependents 1 scripts 2.1k downloads

nlmixr2data - 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>).

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6.61 score 7 stars 16 dependents 52 scripts 1.6k downloads

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'. It also converts 'nlmixr2'/'rxode2' models to 'PopED' optimal design databases (Fidler et al (2024) <doi:10.70534/XUMG6226>). 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.

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monolixnonmempharmacometricscpp

6.56 score 16 stars 125 scripts 717 downloads

RcppTrust - Thread-Safe C++ Trust Region Optimizers

Thread-safe C++ trust region optimizers, each exposed both as an R function and as a C-callable entry point (with function pointers registered for other packages to call without linking against this package's shared library) so they can be used from parallel C++ code such as in 'nlmixr2est'. Includes a port of the two-derivative trust region algorithm in the 'trust' package by Charles J. Geyer; a port of the Steihaug truncated conjugate-gradient trust region method from the 'basin' Rust crate (Steihaug (1983) <doi:10.1137/0720042>); and ports of M. J. D. Powell's derivative-free BOBYQA (Powell (2009), Report DAMTP 2009/NA06) and NEWUOA (Powell (2006) <doi:10.1007/0-387-30065-1_16>) Fortran 77 code <https://github.com/libprima/prima/tree/main/fortran/original>, as modified and distributed in the 'minqa' package, whose R interface is reproduced.

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optimizationtrustopenblascppopenmp

5.86 score 8 dependents 278 downloads

dparser - Port of 'Dparser' Package

A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita (1987) algorithm. (Paper can be found at <https://aclanthology.org/P84-1073.pdf>). The original 'dparser' package documentation can be found at <https://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like rxode2's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use #include <dparser.h>. This also provides a R-based port of the make_dparser <https://dparser.sourceforge.net/d/make_dparser.cat> command called mkdparser(). Additionally you can parse an arbitrary grammar within R using the dparse() function, which works on most OSes and is mainly for grammar testing. The fastest parsing, of course, occurs at the C level, and is suggested.

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5.85 score 4 stars 20 dependents 5 scripts 2.4k downloads

n1qn1 - 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.

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openblascpp

4.85 score 1 stars 16 dependents 6 scripts 1.5k downloads

PreciseSums - Accurate Floating Point Sums and Products

Most of the time floating point arithmetic does approximately the right thing. When adding sums or having products of numbers that greatly differ in magnitude, the floating point arithmetic may be incorrect. This package implements the Kahan (1965) sum <doi:10.1145/363707.363723>, Neumaier (1974) sum <doi:10.1002/zamm.19740540106>, pairwise-sum (adapted from 'NumPy', See Castaldo (2008) <doi:10.1137/070679946> for a discussion of accuracy), and arbitrary precision sum (adapted from the fsum in 'Python' ; Shewchuk (1997) <https://people.eecs.berkeley.edu/~jrs/papers/robustr.pdf>). In addition, products are changed to long double precision for accuracy, or changed into a log-sum for accuracy.

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4.75 score 1 stars 23 dependents 6 scripts 1.6k downloads

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').

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monolixnlmixr2pharmacometricsrxode2cpp

4.58 score 2 stars 1 dependents 21 scripts 533 downloads

nlmixr2nn - Neural-Network ODEs for 'rxode2' and 'nlmixr2'

Embed neural networks inside ordinary differential equation right-hand sides for 'rxode2' and 'nlmixr2'. Networks are exposed as compiled 'rxode2' custom functions that supply the network value and its analytic input derivatives, allowing larger networks than the per-weight code-generation approach of 'pmxNODE'.

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cpp

4.02 score

rxode2lincmt - Linear Compartment Model Solutions and Gradients for 'rxode2'

Analytic one, two and three compartment linear pharmacokinetic solutions with their parameter gradients from 'stan' automatic differentiation (Carpenter et al (2015) <doi:10.48550/arXiv.1509.07164>), eigen decompositions and derived-parameter conversions used by 'rxode2' (Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>). Split out of 'rxode2' so its installation does not compile 'stan' AD items which made it take too long to compile by itself. The closed-form solutions follow the idea of the 'wnl' package (Bae, <https://CRAN.R-project.org/package=wnl>), though the implementation here is different.

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cpp

3.22 score 11 dependents

rxode2lincmt - Linear Compartment Model Solutions and Gradients for 'rxode2'

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cpp

1.70 score