The recommended way to change the resource dynamics parameters is to use
setResource(). The resource_params list contains values that are helpful
in setting up the actual size-dependent parameters with setResource(). If
you have specified a custom resource dynamics function that requires
additional parameters, then these should also be added to the
resource_params list.
Details
The resource_params list will at least contain the slots kappa, lambda,
w_pp_cutoff and n.
The resource parameter n is the exponent for the power-law form for the
replenishment rate \(r_R(w)\): $$r_R(w) = r_R\, w^{n-1}.$$
The resource parameter lambda (\(\lambda\)) is the exponent for the
power-law form for the carrying capacity \(c_R(w)\) and w_pp_cutoff is
its cutoff value: $$c_R(w) = c_R w^{-\lambda}$$ for all \(w\) less than
w_pp_cutoff and zero for larger sizes.
The resource parameter kappa (\(\kappa\)) is the coefficient \(c_R\) of
the carrying capacity in the power law above, so
$$c_R(w) = \kappa\, w^{-\lambda}$$
for all \(w\) less than w_pp_cutoff and zero for larger sizes. Changing
kappa therefore rescales the carrying capacity. It has a second role in that
the same expression also set the initial resource abundance when the model was
created: $$N_R(w) = \kappa\, w^{-\lambda}.$$
Unlike the carrying capacity, however, the initial resource abundance is
not updated when you subsequently change kappa (or call setResource()).
The resource parameters a and b give the allometric weight-length
relationship \(w = a l^b\) of the resource, with \(w\) in grams and
\(l\) in centimetres. They feed none of the rates; they exist so that the
resource can be shown on the length-based plots (size_axis = "l") alongside
the species. They default to the equivalent spherical diameter of an organism
with the density of water, \(a = \pi/6\) and \(b = 3\), which is the
convention plankton ecology uses for a composite of many taxa. This is a
different convention from the one the species use, so the resource and the
species each sit on the length axis at their own; see
resource_length_defaults.
Assigning to resource_params only rebuilds the size-dependent resource rate
and capacity arrays from these scalars (leaving any arrays you have set
manually untouched). Changing lambda also recalculates any q and gamma
species parameters that mizer calculated, and changing kappa recalculates
any calculated gamma; values you supplied explicitly are preserved. It
does not balance the resource, i.e. it does not adjust one of the rate or
capacity to keep the resource at the steady state where it replenishes at
the rate at which it is consumed. This mirrors the way the species
parameters feed the species rates. If you want to preserve the steady state
after changing a resource scalar, call setResource() with the appropriate
argument (which balances by default).