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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,
  params = NULL,
  representation = c("point", "average")
)

Arguments

x

A matrix (species x size).

value_name

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

units

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

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).

Details

An ArraySpeciesBySize object behaves just like a regular matrix for arithmetic operations and subsetting. It carries two 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").

See also

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

Examples

# \donttest{
enc <- getEncounter(NS_params)
is.ArraySpeciesBySize(enc)
#> [1] TRUE
summary(enc)
#> Encounter rate [g/year] 
#> 12 species x 100 sizes
#> 
#>  Species       Min      Mean       Max
#>    Sprat 0.2992076  2929.178  39573.31
#>  Sandeel 0.4528175  3768.983  45507.81
#>   N.pout 0.5019776 16840.828 147886.62
#>  Herring 0.5752333  6241.503  80375.40
#>      Dab 0.4916095 24004.843 266704.99
#>  Whiting 0.4362525 17348.364 137539.48
#>     Sole 0.3646753 12087.308 148784.12
#>  Gurnard 0.3122260 11327.057 135351.68
#>   Plaice 0.2323659 11800.440 113242.16
#>  Haddock 0.5964130 24932.923 334719.58
#>      Cod 0.9658343 52646.610 436916.91
#>   Saithe 0.7709631 16377.321 187775.81
# }