Package: uqsa
Type: Package
Title: Uncertainty Quantification and Global Sensitivity Analysis
Version: 0.8.3
Authors@R: c(
    person("Alexandra","Jauhiainen",email="Alexandra.Jauhiainen@astrazeneca.com",role=c("aut")),
    person("Olivia","Eriksson",email="olivia@kth.se",role=c("aut","ctb","cph")),
    person("Federica","Milinanni",email="fedmil@kth.se",role="aut"),
    person("Andrei","Kramer",email="andreikr@kth.se",role=c("cre")))
Description: In the field of systems biology, chemical reaction
        networks are modeled in various ways, two of those are: (i)
        stochastic simulations (e.g. Gillespie algorithm) and (ii)
        ordinary differential equations. In this package we use a
        simple tabular model description of reaction systems and
        automatically generate C code for either solver type. We use
        the ordinary differential equation solvers from the GNU
        Scientific Library and provide an interface that deals with
        lists of simulation experiments. Each simulation experiment
        contains both the data, and instructions for the model to
        replicate the data. We use approximate Bayesian computation
        methods (combined with Markov chain Monte Carlo and sequential
        Monte Carlo, particle filters) as well as classic methods such
        as Random Walk Metropolis (Gaussian transition kernel) and
        Simplified Manifold Metropolis adjusted Langevin algorithm for
        a Bayesian investigation of the model´s parameter space.
        Experiments can be evaluated in a sequence; intermediate
        probability densities are modeled using the 'VineCopula'
        package. The package is also intended to be useful in an HPC
        environment, with some functions that use 'pbdMPI'
        capabilities.
Language: en-US
License: GPL (>=3)
Encoding: UTF-8
Depends: R (>= 4.1)
Imports: stats, methods, parallel, Ryacas, VineCopula, MASS, errors,
        mvtnorm, digest, colorspace, pracma, cli
Suggests: ks, remotes, pbdMPI, ggplot2, testthat (>= 3.0.0), knitr,
        rmarkdown, hexbin
SystemRequirements: GSL (>= 2.7)
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://icpm-kth.github.io/uqsa/
Config/roxygen2/version: 8.1.0
RoxygenNote: 7.3.3
Config/pak/sysreqs: libgsl0-dev
Repository: https://icpm-kth.r-universe.dev
Date/Publication: 2026-10-20 17:35:26 UTC
RemoteUrl: https://github.com/icpm-kth/uqsa
RemoteRef: HEAD
RemoteSha: b687349cf1fb4f323295728702c7bf6855848131
NeedsCompilation: yes
Packaged: 2026-10-20 19:33:44 UTC; root
Author: Alexandra Jauhiainen [aut],
  Olivia Eriksson [aut, ctb, cph],
  Federica Milinanni [aut],
  Andrei Kramer [cre]
Maintainer: Andrei Kramer <andreikr@kth.se>