path_integral_B {fitlandr}R Documentation

Bhattacharya method for path integration

Description

A method to construct potential landscapes using path integration. See references for details.

Usage

path_integral_B(
  f,
  lims,
  n_path_int = 20,
  stepsize = 0.01,
  tol = 0.01,
  numTimeSteps = 1400,
  ...
)

Arguments

f

The vector field function. It should return ⁠c(<dx/dt>, <dy/dt>)⁠

lims

The limits of the range for the estimation as ⁠c(<xl>, <xu>, <yl>, <yu>)⁠.

n_path_int

The number of equally spaced points in each axis, at which the path integrals is to be calculated.

stepsize

The time step used in each iteration.

tol

The tolerance to test convergence.

numTimeSteps

Number of time steps for integrating along each path (to ensure uniform arrays). Choose high-enough number for convergence with given stepsize.

...

Not in use.

Value

A list with the following elements:

References

Bhattacharya, S., Zhang, Q., & Andersen, M. E. (2011). A deterministic map of Waddington’s epigenetic landscape for cell fate specification. BMC Systems Biology, 5(1), 85. https://doi.org/10.1186/1752-0509-5-85. The functions in this file were translated from the Matlab code provided with the reference above, and its Python translation at https://dynamo-release.readthedocs.io/en/v0.95.2/_modules/dynamo/vectorfield/Bhattacharya.html


[Package fitlandr version 0.1.0 Index]