The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
Detect feedback loops (cycles, circuits) between species (nodes) in ordinary differential equation (ODE) models. Feedback loops are paths from a node to itself without visiting any other node twice, and they have important regulatory functions. Loops are reported with their order of participating nodes and their length, and whether the loop is a positive or a negative feedback loop. An upper limit of the number of feedback loops limits runtime (which scales with feedback loop count). Model parametrizations and values of the modelled variables are accounted for. Computation uses the characteristics of the Jacobian matrix as described e.g. in Thomas and Kaufman (2002) <doi:10.1016/s1631-0691(02)01452-x>. Input can be the Jacobian matrix of the ODE model or the ODE function definition; in the latter case, the Jacobian matrix is determined using 'numDeriv'. Graph-based algorithms from 'igraph' are employed for path detection.
Version: | 0.1.2 |
Depends: | R (≥ 4.0.0) |
Imports: | igraph, numDeriv |
Suggests: | deSolve, knitr, markdown, remotes, rmarkdown, utils |
Published: | 2020-07-20 |
DOI: | 10.32614/CRAN.package.LoopDetectR |
Author: | Katharina Baum |
Maintainer: | Katharina Baum <katharina.baum at hpi.de> |
License: | GPL-3 |
NeedsCompilation: | no |
CRAN checks: | LoopDetectR results |
Reference manual: | LoopDetectR.pdf |
Vignettes: |
LoopDetectR: Comprehensive Feedback Loop Detection in ODE models |
Package source: | LoopDetectR_0.1.2.tar.gz |
Windows binaries: | r-devel: LoopDetectR_0.1.2.zip, r-release: LoopDetectR_0.1.2.zip, r-oldrel: LoopDetectR_0.1.2.zip |
macOS binaries: | r-release (arm64): LoopDetectR_0.1.2.tgz, r-oldrel (arm64): LoopDetectR_0.1.2.tgz, r-release (x86_64): LoopDetectR_0.1.2.tgz, r-oldrel (x86_64): LoopDetectR_0.1.2.tgz |
Please use the canonical form https://CRAN.R-project.org/package=LoopDetectR to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.