Internal Documentation

** Connectance of a network**

Returns the connectance of a square matrix, defined as $S/L^2$.

Distance to a primary producer

This function measures, for every species, its shortest path to a primary producer using matrix exponentiation. A primary producer has a value of 1, a primary consumer a value of 2, and so forth.

Trophic rank

Based on the average distance of preys to primary producers. Specifically, the rank is defined as the average of the distance of preys to primary producers (recursively). Primary producers always have a trophic rank of 1.

Is the matrix correctly formatted?

A correct matrix has only 0 and 1, two dimensions, and is square.

This function returns nothing, but raises an AssertionError if one of the conditions is not met.

Derivatives

This function is the one wrapped by the various integration routines. Based on a timepoint t, an array of biomasses biomass, and a series of simulation parameters p, it will return dB/dt for every species.

Growth rate

TODO

Coefficient of variation

Corrected for the sample size.

Shannon's entropy

Corrected for the number of species, removes negative and null values, return NaN in case of problem.

Create default parameters

This function creates model parameters, based on a food web matrix A. See documentation for more information. Specifically, the default values of the keyword parameters are:

All of these values are passed as optional keyword arguments to the function.

A = [0 1 1; 0 0 0; 0 0 0]
p = model_parameters(A, Z=100.0, productivity=:system)

The productivity keyword can be either :species (each species has an independant carrying capacity equal to K), :system (the carrying capacity is K divided by the number of primary producers), or :competitive (the species compete with themselves at rate 1.0, and with one another at rate α).

It is possible for the user to specify a vector of species body-mass, called bodymass – please do pay attention to the fact that the default behavior is to assume that primary producers have a bodymass equal to unity, since all biological rates are expressed relatively. We do not perform any check on whether or not the user-supplied body-mass vector is correct (mostly because there is no way of defining correctness for vectors where body-mass of producers are not equal to unity). It is possible to turn off the scaling (scale_bodymass = false), in that case we strongly recommend setting scale_growth = true ( and possibly scale_metabolism = true and scale_maxcons = true).

The keyword vertebrates is an array of true or false for every species in the matrix. If the vector is of size 1 (e.g. [false]), all species will take this metabolic status. By default, all species are invertebrates.

A rewiring method can pe passed to specified if the foodweb should be rewired following extinctions events, and the method that should be used to perform the rewiring. This rewire_method keyword can be eighter :none (no rewiring), :ADBM (allometric diet breadth model as described in Petchey et al., 2008), :DS (rewiring mechanism used by Gilljam et al., 2015, based on diet similarity) or :DO (rewiring mechanism used by Staniczenko et al, 2010, based on diet overlap).

If rewire_methodis :ADBM or :DS, additional keywords can be passed. See the online documentation and the original references for more details.

Temperature dependence for metabolic rates and body masses can be implemented, please check the documentation for more information.

Check initial parameters

Are the simulation parameters present?

This function will make sure that all the required parameters are here, and that the arrays and matrices have matching dimensions.