Description Usage Arguments Details Value See Also Examples

View source: R/loop_detection_functions.R

Given the Jacobian matrix of an ODE system or the adjacency matrix of a graph, this function determines all loops in the system up to the maximal number supplied.

1 | ```
find_loops(jacobian, max_num_loops = 1e+05)
``` |

`jacobian` |
Square Jacobian matrix of an ODE system or the adjacency
matrix of a graph; captures interactions such that entry |

`max_num_loops` |
Positive numeric value indicating the maximal number
of loops that are reported. Default: |

The input matrix delivers the directed interactions in the ODE
system; if entry `(i,j)`

is non-zero it means that variable (or node) `i`

is
regulated by variable (node) `j`

. Johnson's algorithm for path detection
as well as Tarjan's algorithm for detecting strongly connected
components are used as implemented in the igraph package (functions:
`all_simple_paths`

, `components`

) .
If the maximal number of loops, max_num_loops, is reached, no warning is
issued. It is very probable that not all feedback loops of the system
have been found.
Running the function multiple times with re-ordered jacobian as input
can enable detection of alternative feedback loops while limiting the
runtime and output size of single runs.
If columns of the Jacobian are named,
the identification is given by the attribute `node_ids`

,
`attr(result,"node_ids")`

.

A data.frame with three columns: `loop`

, `length`

, `sign`

containing up to `max_num_loops`

loops of the systems defined
by matrix `jacobian`

. Each entry in the loop column is a list of
identifiers that correspond to the indices of the variable in the
Jacobian matrix and denote
in which order the variables form the loop.

`find_loops_noscc`

, `find_loops_vset`

1 2 3 4 |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.