Functions to fetch information about the size bins used in the model
w(params) w_full(params) dw(params) dw_full(params)
A MizerParams object
w() returns a vector with the sizes at the start of each size bin
of the consumer spectrum.
w_full() returns a vector with the sizes at the start of each size bin
of the resource spectrum, which typically starts at smaller sizes than
the consumer spectrum.
dw() returns a vector with the widths of the size bins of the
dw_full() returns a vector with the widths of the size bins of the
To represent the continuous size spectrum in the computer, the size
variable is discretized into a vector
w of discrete weights,
providing a grid of sizes spanning the range from the smallest egg size
to the largest asymptotic size. These grid values divide the full size
range into a finite number of size bins. The size bins should be chosen
small enough to avoid the discretisation errors from becoming too big.
You can fetch this vector with
w() and the vector of bin widths with
The weight grid is set up to be logarithmically spaced, so that
w[j]=w*10^(j*dx) for some fixed
dx. This means that the bin widths
increase with size:
dw[j] = w[j] * (10^dx - 1).
This grid is set up automatically when creating a MizerParams object.
Because the resource spectrum spans a larger range of sizes, these sizes
are discretized into a different vector of weights
w_full. This usually
starts at a much smaller size than
w, but also runs up to the same
largest size, so that the last entries of
w_full have to coincide with the
w. The logarithmic spacing for
w_full is the same as that for
w, so that again
w_full[j]=w_full*10^(j*dx). The function
gives the vector of sizes and
dw_full() gives the vector of bin widths.
You will need these vectors when converting number densities to numbers.
For example the size spectrum of a species is stored as a vector of
values that represent the density of fish in each size bin rather than
the number of fish. The number of fish in the size bin between
w[j+1]=w[j]+dw[j] is obtained as
w can be used for example to convert the number of individuals
in a size bin into the biomass in the size bin. The biomass in the
jth bin is
biomass[j] = N[j] * dw[j] * w[j].
Of course all these calculations with discrete sizes and size bins are
only giving approximations to the continuous values, and these approximations
get better the smaller the size bins are, i.e., the more size bins are
used. However using more size bins also slows down the calculations, so
there is a trade-off. This is why the functions setting up MizerParams
objects allow you to choose the number of size bins
str(w(NS_params))#> num [1:100] 0.001 0.00119 0.00142 0.0017 0.00203 ...str(dw(NS_params))#> num [1:100] 0.000193 0.000231 0.000275 0.000329 0.000392 ...str(w_full(NS_params))#> num [1:226] 2.12e-13 2.53e-13 3.02e-13 3.61e-13 4.30e-13 ...str(dw_full(NS_params))#> num [1:226] 4.10e-14 4.90e-14 5.84e-14 6.97e-14 8.32e-14 ...# Calculating the biomass of Cod in each bin in the North Sea model biomass <- initialN(NS_params)["Cod", ] * dw(NS_params) * w(NS_params) # Summing to get total biomass sum(biomass)#>  601591842546