Package: LoopDetectR 0.1.2
LoopDetectR: Comprehensive Feedback Loop Detection in ODE Models
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.
Authors:
LoopDetectR_0.1.2.tar.gz
LoopDetectR_0.1.2.zip(r-4.5)LoopDetectR_0.1.2.zip(r-4.4)LoopDetectR_0.1.2.zip(r-4.3)
LoopDetectR_0.1.2.tgz(r-4.4-any)LoopDetectR_0.1.2.tgz(r-4.3-any)
LoopDetectR_0.1.2.tar.gz(r-4.5-noble)LoopDetectR_0.1.2.tar.gz(r-4.4-noble)
LoopDetectR_0.1.2.tgz(r-4.4-emscripten)LoopDetectR_0.1.2.tgz(r-4.3-emscripten)
LoopDetectR.pdf |LoopDetectR.html✨
LoopDetectR/json (API)
| # Install 'LoopDetectR' in R: |
| install.packages('LoopDetectR', repos = c('https://kathbaum.r-universe.dev', 'https://cloud.r-project.org')) |
- func_POSm4 - Example ODE function: chain model with positive regulation.
- func_li08 - Example ODE function: bacterial cell cycle.
- li08_solution - Solution for the cell cycle model related to func_li08
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 4 years agofrom:6018976168. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 25 2024 |
| R-4.5-win | OK | Aug 25 2024 |
| R-4.5-linux | OK | Aug 25 2024 |
| R-4.4-win | OK | Aug 25 2024 |
| R-4.4-mac | OK | Aug 25 2024 |
| R-4.3-win | OK | Aug 25 2024 |
| R-4.3-mac | OK | Aug 25 2024 |
Exports:compare_loop_listfind_edgefind_loopsfind_loops_nosccfind_loops_vsetloop_summarysort_loop_index
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixnumDerivpkgconfigrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compare two loop lists | compare_loop_list |
| Detecting loops with a certain edge | find_edge |
| Loop detection in a matrix | find_loops |
| Loop detection in a matrix | find_loops_noscc |
| Loop detection for an ODE model at multiple sets of variables | find_loops_vset |
| Example ODE function: bacterial cell cycle. | func_li08 |
| Example ODE function: chain model with positive regulation. | func_POSm4 |
| Solution for the cell cycle model related to func_li08 | li08_solution |
| Summary of a loop list | loop_summary |
| Sort loop indices | sort_loop_index |
