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S3 class for species x size rate arrays

Source: R/ArraySpeciesBySize-class.R
ArraySpeciesBySize.Rd

Many functions in mizer return two-dimensional arrays (species x size) holding rates like encounter rate, feeding level, growth rate, mortality etc. The ArraySpeciesBySize class wraps these arrays to provide convenient print(), summary(), plot(), and as.data.frame() methods.

Usage

ArraySpeciesBySize(
  x,
  value_name = NULL,
  units = NULL,
  type = NULL,
  params = NULL,
  representation = c("point", "average")
)

is.ArraySpeciesBySize(x)

Arguments

x

A matrix (species x size). For is.ArraySpeciesBySize(), any object to test.

value_name

A string giving the human-readable name for the value.

units

A string giving the units (e.g. "g/year", "1/year").

type

The kind of quantity the values are, see array_types: "value" (the default) for a rate or an amount, "density" for an amount per gram of body weight, "proportion" for a fraction. This is what tells plot() to multiply a density by the appropriate Jacobian when it is plotted against a length axis (size_axis = "l"), and to show a proportion against the whole of the interval from 0 to 1. The default, NULL, treats a value_name of "Number density" or units of "1/g" as a density, the way mizer recognised one before this attribute existed.

params

A MizerParams object. Used for species colours, linetypes, and size ranges in the plot() method.

representation

Either "point" (the default) for a quantity sampled at the grid nodes, or "average" for a finite-volume bin average. A bin-averaged quantity is drawn at the geometric bin centre rather than the left bin edge, but only when the model uses second-order bin-averaging (second_order_w[["bin_average"]]), so default plots are unchanged.

Value

An ArraySpeciesBySize object (inherits from matrix and array).

is.ArraySpeciesBySize() returns TRUE if x is an ArraySpeciesBySize object, FALSE otherwise.

Details

An ArraySpeciesBySize object behaves just like a regular matrix for arithmetic operations and subsetting. It carries a few lightweight attributes:

  • value_name – a human-readable name for the value (e.g. "Encounter rate").

  • units – the units of the rate (e.g. "g/year").

  • type – the kind of quantity the values are.

See also

print(), summary(), as.data.frame(), plot()

Examples

# \donttest{
enc <- getEncounter(NS_params)
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.
#> ℹ No `a` column so using a = 0.01 in w = a l^b, with w in g and l in cm.
#> ℹ No `b` column so using the isometric default b = 3 in w = a l^b.
is.ArraySpeciesBySize(enc)
#> [1] TRUE
summary(enc)
#> Encounter rate [g/year] 
#> 12 species x 100 sizes
#> 
#>  Species       Min        Mean         Max
#>    Sprat 0.2992076    37.92979    239.6706
#>  Sandeel 0.4528175    67.08030    434.6202
#>   N.pout 0.5019776   237.84164   2613.4140
#>  Herring 0.5752333   282.49597   2203.3821
#>      Dab 0.4916095   395.38383   4473.2748
#>  Whiting 0.4362525  2507.48128  28974.8976
#>     Sole 0.3646753   474.92455   5616.2042
#>  Gurnard 0.3122260   318.45335   3726.8753
#>   Plaice 0.2323659  1898.07284  24800.9828
#>  Haddock 0.5964130  3547.12149  49555.6495
#>      Cod 0.9658343 52646.61006 436916.9135
#>   Saithe 0.7709631 14646.02285 160506.0739
# }