nlmixr2 r-universe repositoryhttps://nlmixr2.r-universe.devPackage updated in nlmixr2cranlike-server 0.18.56https://github.com/nlmixr2.png?size=400nlmixr2 r-universe repositoryhttps://nlmixr2.r-universe.devMon, 09 Sep 2024 03:28:32 GMT[nlmixr2] babelmixr2 0.1.3matthew.fidler@gmail.com (Matthew Fidler)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://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>.
When 'lixoftConnectors' is available, 'Monolix' can be run
directly instead of setting up command line usage.https://github.com/r-universe/nlmixr2/actions/runs/10766424934Mon, 09 Sep 2024 03:28:32 GMTbabelmixr20.1.3successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/babelmixr2new-estimation.Rmdnew-estimation.htmlCreating a New Estimation Method2022-10-22 23:55:042023-05-24 15:56:40running-pknca.Rmdrunning-pknca.htmlObtain initial estimates and unit conversions with PKNCA2023-10-22 16:53:172023-10-22 16:53:17[nlmixr2] rxode2 3.0.0matthew.fidler@gmail.com (Matthew L. Fidler)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 information is available in the
inst/COPYRIGHTS.https://github.com/r-universe/nlmixr2/actions/runs/10760590009Sun, 08 Sep 2024 13:55:16 GMTrxode23.0.0successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/rxode2rxode2-syntax.Rmdrxode2-syntax.htmlrxode2 ODE solving syntax2021-12-01 07:08:212023-08-28 03:41:04[nlmixr2] nlmixr2est 3.0.0matthew.fidler@gmail.com (Matthew Fidler)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>).https://github.com/r-universe/nlmixr2/actions/runs/10748206438Sat, 07 Sep 2024 02:35:52 GMTnlmixr2est3.0.0successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2est[nlmixr2] nlmixr2lib 0.2.0.9000wdenney@humanpredictions.com (Bill Denney)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.https://github.com/r-universe/nlmixr2/actions/runs/10702538221Wed, 04 Sep 2024 12:59:26 GMTnlmixr2lib0.2.0.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2libcreate-model-library.Rmdcreate-model-library.htmlCreating a model library2022-09-16 15:36:082024-06-29 00:52:44list-of-models.Rmdlist-of-models.htmlList of models2023-04-22 01:05:012023-04-22 01:05:01[nlmixr2] lotri 1.0.0matthew.fidler@gmail.com (Matthew L. Fidler)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'.https://github.com/r-universe/nlmixr2/actions/runs/10641965525Sat, 31 Aug 2024 02:35:04 GMTlotri1.0.0successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/lotrilotri-motivation.Rmdlotri-motivation.htmlLotri Motivation2019-05-10 03:04:322022-06-18 01:05:53[nlmixr2] PreciseSums 0.7matthew.fidler@gmail.com (Matthew Fidler)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.https://github.com/r-universe/nlmixr2/actions/runs/10548416052Sun, 25 Aug 2024 16:18:26 GMTPreciseSums0.7successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/PreciseSums[nlmixr2] n1qn1 6.0.1-12matthew.fidler@gmail.com (Matthew Fidler)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.https://github.com/r-universe/nlmixr2/actions/runs/10498873165Wed, 21 Aug 2024 21:49:23 GMTn1qn16.0.1-12successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/n1qn1c[nlmixr2] lbfgsb3c 2024-3.5matthew.fidler@gmail.com (Matthew L Fidler)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.https://github.com/r-universe/nlmixr2/actions/runs/10498872900Wed, 21 Aug 2024 18:06:25 GMTlbfgsb3c2024-3.5successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/lbfgsb3clbfgsb3c.Rmdlbfgsb3c.htmllbfgsb3c: Using the 2011 version of L-BFGS-B.2019-03-22 20:20:132023-11-28 03:58:07[nlmixr2] dparser 1.3.1-12matthew.fidler@gmail.com (Matthew Fidler)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.https://github.com/r-universe/nlmixr2/actions/runs/10461047572Mon, 19 Aug 2024 21:03:01 GMTdparser1.3.1-12successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/dparser-R[nlmixr2] nonmem2rx 0.1.4.9000matthew.fidler@gmail.com (Matthew Fidler)'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.https://github.com/r-universe/nlmixr2/actions/runs/10767370561Sat, 10 Aug 2024 22:24:09 GMTnonmem2rx0.1.4.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nonmem2rximport-nonmem.Rmdimport-nonmem.htmlImporting NONMEM into rxode22023-05-11 05:43:002023-12-12 03:58:39[nlmixr2] nlmixr2rpt 0.2.0john.m.harrold@gmail.com (John Harrold)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).https://github.com/r-universe/nlmixr2/actions/runs/10518842533Wed, 24 Jul 2024 01:53:46 GMTnlmixr2rpt0.2.0successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2rptAccessing_Figures_and_Tables.RmdAccessing_Figures_and_Tables.htmlAccessing Figures and Tables2021-10-17 02:35:332022-09-09 22:22:31Reporting_nlmixr_Fit_Results.RmdReporting_nlmixr_Fit_Results.htmlReporting nlmixr2 Fit Results2021-10-13 02:12:382024-07-24 01:53:46[nlmixr2] nlmixr2 2.1.2matthew.fidler@gmail.com (Matthew Fidler)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>).https://github.com/r-universe/nlmixr2/actions/runs/10437224599Wed, 17 Jul 2024 19:21:03 GMTnlmixr22.1.2successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2[nlmixr2] nlmixr2plot 2.0.9matthew.fidler@gmail.com (Matthew Fidler)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.https://github.com/r-universe/nlmixr2/actions/runs/10415291014Wed, 17 Jul 2024 19:19:05 GMTnlmixr2plot2.0.9successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2plot[nlmixr2] nlmixr2extra 2.0.10matthew.fidler@gmail.com (Matthew Fidler)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.https://github.com/r-universe/nlmixr2/actions/runs/10370198138Wed, 17 Jul 2024 19:18:06 GMTnlmixr2extra2.0.10successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2extra[nlmixr2] nlmixr2targets 0.0.0.9000wdenney@humanpredictions.com (Bill Denney)'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.https://github.com/r-universe/nlmixr2/actions/runs/10429669135Wed, 20 Mar 2024 14:59:33 GMTnlmixr2targets0.0.0.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2targetsestimating.Rmdestimating.htmlEstimating nlmixr2 models with 'nlmixr2targets'2024-03-08 11:37:012024-03-20 14:59:33[nlmixr2] nlmixr2data 2.0.9matthew.fidler@gmail.com (Matthew Fidler)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>).https://github.com/r-universe/nlmixr2/actions/runs/10627007025Wed, 31 Jan 2024 19:55:31 GMTnlmixr2data2.0.9successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2data[nlmixr2] rxode2ll 2.0.11.9000matthew.fidler@gmail.com (Matthew L. Fidler)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.https://github.com/r-universe/nlmixr2/actions/runs/10677418382Wed, 29 Mar 2023 15:31:51 GMTrxode2ll2.0.11.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/rxode2ll[nlmixr2] xpose.nlmixr2 0.4.0justin.wilkins@occams.com (Justin Wilkins)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.https://github.com/r-universe/nlmixr2/actions/runs/10731709034Tue, 07 Jun 2022 13:04:34 GMTxpose.nlmixr20.4.0successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/xpose.nlmixr2