fit_reaction_equation_MCMC_NNLS: Fit reaction equation using MCMC and NNLS

In shackett/simmer: Systematic Identification of Meaningful Metabolic Enzyme Regulation

Description

Run the MCMC-NNLS algorithm by continually updating kinetic parameters and evaluating their likelihood

Usage

fit_reaction_equation_MCMC_NNLS(markov_pars, kineticPars, kineticParPrior,
  rxnEquations, all_species, omic_data, kinetically_differing_isoenzymes)

Arguments

markov_pars	parameters for MCMC: a list containing 3 values: sample_freq, n_samples and burn_in
kineticPars	table summarizing which species all non-linear kinetic parameters correspond to
kineticParPrior	parameters for the proposal distribution of each kinetic parameter
rxnEquations	expressions for reaction equations
all_species	all_species table summarizing the types of all reaction species
omic_data	abundances and uncertainties of reaction species and flux: setup in format_omic_data
kinetically_differing_isoenzymes	True-False: does only one equation exist for the reaction (false) or are are reaction equations isoenzyme specific (true)

Value

write draws from the posterior distribution of non-linear kinetic parameters (markov_par_vals) and their log-likelihoods (lik_track) to the global environment

shackett/simmer documentation built on May 29, 2019, 8:06 p.m.