set_multispecies_model: Deprecated obsolete function for setting up multispecies parameters

Description

This function has been deprecated in favour of the function newMultispeciesParams() that sets better default values.

This wrapper keeps the legacy defaults and also fills in several columns in species_params if they are missing, using the same rules as older mizer versions.

Usage

set_multispecies_model(
  species_params,
  interaction = matrix(1, nrow = nrow(species_params), ncol = nrow(species_params)),
  min_w_pp = 1e-10,
  min_w = 0.001,
  max_w = NULL,
  no_w = 100,
  n = 2/3,
  q = 0.8,
  f0 = 0.6,
  kappa = 1e+11,
  lambda = 2 + q - n,
  r_pp = 10,
  ...
)

Value

A MizerParams object

Arguments

species_params: A data frame of species-specific parameter values.
interaction: Optional interaction matrix of the species (predator species x prey species). By default all entries are 1. See "Setting interaction matrix" section below.
min_w_pp: The smallest size of the resource spectrum. By default this is set to the smallest value at which any of the consumers can feed.
min_w: Sets the size of the eggs of all species for which this is not given in the w_min column of the species_params dataframe.
max_w: The largest size of the consumer spectrum. By default this is set to the largest w_max specified in the species_params data frame.
no_w: The number of size bins in the consumer spectrum.
n: The allometric growth exponent. This can be overruled for individual species by including a n column in the species_params.
q: Allometric exponent of search volume
f0: Expected average feeding level. Used to set gamma, the coefficient in the search rate. Ignored if gamma is given explicitly.
kappa: The coefficient of the initial resource abundance power-law.
lambda: Used to set power-law exponent for resource capacity if the resource_capacity argument is given as a single number.
r_pp: . Use resource_rate argument instead.
...: Further arguments passed to newMultispeciesParams().

Details

If species_params contains a w_inf column then it is copied to w_max. If max_w is not supplied then it is set to 1.1 * max(species_params$w_max). The supplied min_w_pp is shifted up by one grid step before being passed to newMultispeciesParams() to compensate for the fact that newer mizer versions extend the full size grid below min_w_pp.

Missing legacy columns in species_params are filled as follows: gear = species, k = 0, alpha = 0.6, erepro = 1, sel_func = "knife_edge", knife_edge_size = w_mat if needed, catchability = 1, ks = h * 0.2, and m = 1. If h is missing it is calculated from k_vb, alpha, f0 and w_max. If gamma is missing it is calculated from f0, h, beta, sigma, lambda and kappa.