LikelihoodProfiler.jl

LikelihoodProfiler is a Julia package for practical identifiability analysis and confidence intervals evaluation.
Author insysbio
Popularity
17 Stars
Updated Last
10 Months Ago
Started In
October 2018

LikelihoodProfiler

Documentation Build status Coverage Status GitHub release GitHub license DOI:10.1371/journal.pcbi.1008495

LikelihoodProfiler is a Julia language package for identifiability analysis and confidence intervals estimation.

See documentation.

Use cases

Notebooks with use cases can be found in a separate repository: https://github.com/insysbio/likelihoodprofiler-cases

Case Ref
PK model with saturation in elimination Binder
Local optim methods comparison Binder
TGF-β Signaling Pathway Model Binder
SIR Model. A simple model used as an exercise in identifiability analysis. Binder
Cancer Taxol Treatment Model Binder
STAT5 Dimerization Model Binder

Installation

julia> ]

(v1.7) pkg> add LikelihoodProfiler

Quick start

using LikelihoodProfiler

# testing profile function
f(x) = 5.0 + (x[1]-3.0)^2 + (x[1]-x[2]-1.0)^2 + 0*x[3]^2

# Calculate parameters intervals for first parameter component, x[1]
res_1 = get_interval(
  [3., 2., 2.1], # starting point
  1,             # parameter component to analyze
  f,             # profile function
  :LIN_EXTRAPOL; # method
  loss_crit = 9. # critical level of loss function
  )
#

# Plot parameter profile x[1]
using Plots
plotly()
plot(res_1)

Plot Linear

License

MIT Public license

How to cite

Borisov I, Metelkin E (2020) Confidence intervals by constrained optimization—An algorithm and software package for practical identifiability analysis in systems biology. PLoS Comput Biol 16(12): e1008495.

Ref: https://doi.org/10.1371/journal.pcbi.1008495

Used By Packages

No packages found.