Package: magi 1.2.5

magi: MAnifold-Constrained Gaussian Process Inference

Provides fast and accurate inference for the parameter estimation problem in Ordinary Differential Equations, including the case when there are unobserved system components. Implements the MAGI method (MAnifold-constrained Gaussian process Inference) of Yang, Wong, and Kou (2021) <doi:10.1073/pnas.2020397118>. A user guide is provided by the accompanying software paper Wong, Yang, and Kou (2024) <doi:10.18637/jss.v109.i04>.

Authors:Shihao Yang [aut, cre], Samuel W.K. Wong [aut], S.C. Kou [ctb, cph]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
magi/json (API)

# Install 'magi' in R:

install.packages('magi', repos = c('https://shihao-yang.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

FNdat - Dataset of noisy observations from the FitzHugh-Nagumo (FN) equations

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

openblas cpp

3.50 score 63 scripts 272 downloads 23 exports 12 dependencies

Last updated from:c7529470be. Checks:12 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	573
linux-devel-x86_64	OK	290
source / vignettes	OK	342
linux-release-arm64	OK	588
linux-release-x86_64	OK	279
macos-release-arm64	OK	256
macos-release-x86_64	OK	509
macos-oldrel-arm64	OK	239
macos-oldrel-x86_64	OK	583
windows-devel	OK	360
windows-release	OK	354
windows-oldrel	OK	356
wasm-release	FAIL	199

Exports:calCov fnmodelDtheta fnmodelDx fnmodelODE gpcov gpmean gpsmoothing gpsmoothllik hes1logmodelDtheta hes1logmodelDx hes1logmodelODE hes1modelDtheta hes1modelDx hes1modelODE is.magioutput magioutput MagiPosterior MagiSolver ptransmodelDtheta ptransmodelDx ptransmodelODE setDiscretization testDynamicalModel

Dependencies:BH cli deSolve glue gridBase gridExtra gtable lifecycle Rcpp RcppArmadillo rlang roptim

magi-vignette

Basic usage example: Fitzhugh-Nagumo equations | Example with an unobserved component and asynchronous observations: Hes1 system | Example with time-dependency in ODE: HIV model with oscillating infection rate

Rendered frommagi-vignette.Rmdusingknitr::rmarkdown

Last update: 2024-05-06
Started: 2021-07-27

Help page	Topics
Calculate stationary Gaussian process kernel	calCov
Dataset of noisy observations from the FitzHugh-Nagumo (FN) equations	FNdat
The FitzHugh-Nagumo (FN) equations	fnmodelDtheta fnmodelDx fnmodelODE
Conditional covariance of Gaussian process given observations	gpcov
Conditional mean of Gaussian process given observations	gpmean
Gaussian process smoothing	gpsmoothing
Marginal log-likelihood for Gaussian process smoothing	gpsmoothllik
Hes1 equations: oscillation of mRNA and protein levels	hes1logmodelDtheta hes1logmodelDx hes1logmodelODE hes1modelDtheta hes1modelDx hes1modelODE
MagiSolver output ('magioutput') object	is.magioutput magioutput
'magi': MAnifold-Constrained Gaussian Process Inference	magi
MAGI posterior density	MagiPosterior
MAnifold-constrained Gaussian process Inference (MAGI)	MagiSolver
Generate plots from 'magioutput' object	plot.magioutput
Protein transduction model	ptransmodelDtheta ptransmodelDx ptransmodelODE
Set discretization level	setDiscretization
Summary of parameter estimates from 'magioutput' object	summary.magioutput
Test dynamic system model specification	testDynamicalModel

Package: magi 1.2.5

magi: MAnifold-Constrained Gaussian Process Inference

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)