micom.elasticity
Contents
micom.elasticity
#
Calculate elasticity coefficients.
Functions to calculate elasticity coefficients for various community quantities.
Module Contents#
Functions#

Get the primal values for a set of variables. 

Get the elasticities for fluxes. 

Get the elasticity coefficients for a set of variables. 

Get the elasticity coefficients for a set of variables. 

Calculate elasticities for reactions. 
Attributes#
 micom.elasticity.elasticities_by_medium(com, reactions, fraction, growth_rate, progress)[source]#
Get the elasticity coefficients for a set of variables.
 Parameters
com (micom.Community) – The community for wrhich to calculate elasticities.
variables (list of optlang.Variable) – The variables for which to calculate the elasticities. All of these must have nonzero primal vaues in the previous solution.
 Returns
The long/tidy version of the elasticities. Contains columns variable, effector, and elasticity.
 Return type
pandas.Dataframe
 micom.elasticity.elasticities_by_abundance(com, reactions, fraction, growth_rate, progress)[source]#
Get the elasticity coefficients for a set of variables.
 Parameters
com (micom.Community) – The community for which to calculate elasticities.
variables (list of optlang.Variable) – The variables for which to calculate the elasticities. All of these must have nonzero primal vaues in the previous solution.
 Returns
The long/tidy version of the elasticities. Contains columns variable, effector, and elasticity.
 Return type
pandas.Dataframe
 micom.elasticity.elasticities(com, fraction=0.5, reactions=None, progress=True)[source]#
Calculate elasticities for reactions.
Calculates elasticity coefficients using the specified reactions as response and exchange bounds (diet) and taxa abundances as effectors/parameters. Will use an arbitrary flux distribution as base.
 Parameters
com (micom.Community) – The community for wrhich to calculate elasticities.
fraction (double) – The tradeoff to use for the cooperative tradeoff method. Fraction of maximal community growth to enforce.
reactions (iterable) – A list of reactions to get elasticities for. Elements can either be reactions from the model, strings specifying the ids of reactions or ints specifying the indices of reactions. Defaults to using all reactions.
progress (boolean) – Whether to shwo progress bars. Will show two, one for the diet optimizations and another one for the taxa abundances.
 Returns
A data frame with the following columns: “reaction”  the exchange reaction (response), “taxon”  the taxon the reaction is from, “effector”  the parameter that was changed, “direction”  whether the flux runs in the forward or reverse
direction,
”elasticity”  the elasticity coefficient, “type”  the type of effector either “exchange” for diet or “abundance” for taxa abundances.
 Return type
pandas.DataFrame