mattfidler r-universe repositoryhttps://mattfidler.r-universe.devPackage updated in mattfidlercranlike-server 0.17.42https://github.com/mattfidler.png?size=400mattfidler r-universe repositoryhttps://mattfidler.r-universe.devMon, 01 Jul 2024 13:12:51 GMT[nlmixr2] rxode2parse 2.0.19.9000matthew.fidler@gmail.com (Matthew L. Fidler)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'.https://github.com/r-universe/nlmixr2/actions/runs/9745139208Mon, 01 Jul 2024 13:12:51 GMTrxode2parse2.0.19.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/rxode2parse[nlmixr2] rxode2 2.1.3.9000matthew.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/9722482043Sat, 29 Jun 2024 06:30:26 GMTrxode22.1.3.9000successhttps://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] lotri 0.4.4.9000matthew.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.https://github.com/r-universe/nlmixr2/actions/runs/9661499385Tue, 25 Jun 2024 11:18:07 GMTlotri0.4.4.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/lotrilotri-motivation.Rmdlotri-motivation.htmlLotri Motivation2019-05-10 03:04:322022-06-18 01:05:53[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/9834221557Sat, 08 Jun 2024 13:44:38 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] nlmixr2est 2.2.2.9000matthew.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/9824881309Fri, 07 Jun 2024 12:18:56 GMTnlmixr2est2.2.2.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2est[nlmixr2] rxode2random 2.1.1.9000matthew.fidler@gmail.com (Matthew L. Fidler)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'.https://github.com/r-universe/nlmixr2/actions/runs/9824348031Fri, 07 Jun 2024 03:26:01 GMTrxode2random2.1.1.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/rxode2random[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/9721791327Thu, 30 May 2024 12:43:26 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/9720780369Thu, 30 May 2024 01:36:35 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/9691186962Tue, 28 May 2024 12:23:18 GMTnlmixr2extra2.0.10successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2extra[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/9655600913Sun, 26 May 2024 02:07:54 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] rxode2et 2.0.13matthew.fidler@gmail.com (Matthew L. Fidler)Provides the event table and support functions 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'.https://github.com/r-universe/nlmixr2/actions/runs/9655469132Sat, 25 May 2024 23:55:55 GMTrxode2et2.0.13successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/rxode2et[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/9738708676Wed, 31 Jan 2024 19:55:31 GMTnlmixr2data2.0.9successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/nlmixr2data[nlmixr2] dparser 1.3.1-11matthew.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/9815982695Sat, 09 Dec 2023 13:53:28 GMTdparser1.3.1-11successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/dparser-R[ggpmxdevelopment] ggPMX 1.2.11.9000matt.fidler@novartis.com (Matthew Fidler)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.https://github.com/r-universe/ggpmxdevelopment/actions/runs/9690439802Thu, 30 Nov 2023 16:06:25 GMTggPMX1.2.11.9000successhttps://ggpmxdevelopment.r-universe.devhttps://github.com/ggpmxdevelopment/ggpmxggPMX-guide.RmdggPMX-guide.htmlggPMX - User Guide2019-04-25 05:48:292023-11-30 11:47:07[nlmixr2] PreciseSums 0.6matthew.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/9656103397Fri, 21 Apr 2023 17:53:37 GMTPreciseSums0.6successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/PreciseSums[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/9707801017Wed, 29 Mar 2023 15:31:51 GMTrxode2ll2.0.11.9000successhttps://nlmixr2.r-universe.devhttps://github.com/nlmixr2/rxode2ll