Other packages > Find by keyword >

LoopDetectR  

Comprehensive Feedback Loop Detection in ODE Models
View on CRAN: Click here


Download and install LoopDetectR package within the R console
Install from CRAN:
install.packages("LoopDetectR")

Install from Github:
library("remotes")
install_github("cran/LoopDetectR")

Install by package version:
library("remotes")
install_version("LoopDetectR", "0.1.2")



Attach the package and use:
library("LoopDetectR")
Maintained by
Katharina Baum
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-07-20
Latest Update: 2020-07-20
Description:
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) . 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.
How to cite:
Katharina Baum (2020). LoopDetectR: Comprehensive Feedback Loop Detection in ODE Models. R package version 0.1.2, https://cran.r-project.org/web/packages/LoopDetectR. Accessed 06 Nov. 2024.
Previous versions and publish date:
No previous versions
Other packages that cited LoopDetectR R package
View LoopDetectR citation profile
Other R packages that LoopDetectR depends, imports, suggests or enhances
Complete documentation for LoopDetectR
Functions, R codes and Examples using the LoopDetectR R package
Some associated functions: compare_loop_list . find_edge . find_loops . find_loops_noscc . find_loops_vset . func_POSm4 . func_li08 . li08_solution . loop_summary . sort_loop_index . 
Some associated R codes: data.R . further_functions.R . loop_detection_functions.R .  Full LoopDetectR package functions and examples
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

maic  
Matching-Adjusted Indirect Comparison
A generalised workflow for generation of subject weights to be used in Matching-Adjusted Indirect C ...
Download / Learn more Package Citations See dependency  
mailR  
A Utility to Send Emails from R
Interface to Apache Commons Email to send emails from R. ...
Download / Learn more Package Citations See dependency  
ddp  
Desirable Dietary Pattern
The desirable Dietary Pattern (DDP)/ PPH score measures the variety of food consumption. The (weigh ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
memoise  
'Memoisation' of Functions
Cache the results of a function so that when you call it again with the same arguments it returns t ...
Download / Learn more Package Citations See dependency  
seriation  
Infrastructure for Ordering Objects Using Seriation
Infrastructure for ordering objects with an implementation of several seriation/sequencing/ordinati ...
Download / Learn more Package Citations See dependency  

23,092

R Packages

198,677

Dependencies

62,675

Author Associations

23,089

Publication Badges

© Copyright 2022 - present. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA