fit_cmp_net_edit: Greedy algorithm to test network improvements /refine rxn...

In borenstein-lab/mimosa2: Model-based Integration of Metabolite Observations and Species Abundances

Greedy algorithm to test network improvements /refine rxn network

Description

Greedy algorithm to test network improvements /refine rxn network

Usage

fit_cmp_net_edit(
  network,
  species,
  mets_melt,
  manual_agora = F,
  rsq_factor = 1.15,
  min_rsq = 0.1,
  min_rxns = 3,
  max_rxns_test = 40,
  rank_based = F,
  species_specific = T
)

Arguments

network	Edge list reaction table (including reversibility info)
species	Table of species abundances
mets_melt	Table of metabolite concentrations
manual_agora	Whether to leave in agora/bigg format
rsq_factor	Improvement in R squared needed to keep going
min_rsq	Minimum r squared needed to accept an improvement
min_rxns	Minimum number of reactions remaining to continue iterating
rank_based	Whether to use rank-based regression
species_specific	Whether to adjust rxns in a species-specific or whole-community manner
max_rxns	Maximum number of reactions to try

Value

A list of model fitting results as well as revised versions of the community metabolic network model and the updated CMP scores

Examples

get_best_rxn_subset(met1, species, met_data)

borenstein-lab/mimosa2 documentation built on Dec. 19, 2024, 12:44 a.m.