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S3 class for time x species x size arrays

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

Some functions in mizer return three-dimensional arrays (time x species x size) holding quantities like fishing mortality, feeding level, or predation mortality through time. The ArrayTimeBySpeciesBySize class wraps these arrays to provide convenient print(), summary(), plot(), animate(), and as.data.frame() methods.

Usage

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

Arguments

x

A 3D array (time x species x size).

value_name

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

units

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

params

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

representation

Either "point" (the default) for a quantity sampled at the grid nodes, or "average" for a finite-volume bin average, which is then drawn at the geometric bin centre when the model uses second-order bin-averaging (second_order_w[["bin_average"]]). See ArraySpeciesBySize().

Value

An ArrayTimeBySpeciesBySize object (inherits from array).

Details

An ArrayTimeBySpeciesBySize object behaves just like a regular array for arithmetic operations and subsetting. It carries these lightweight attributes:

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

  • units – the units of the value (e.g. "1/year").

  • params – the MizerParams object that the value was computed from.

See also

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

Examples

# \donttest{
fmort <- getFMort(NS_sim)
is.ArrayTimeBySpeciesBySize(fmort)
#> [1] TRUE
summary(fmort)
#> Fishing mortality [1/year] 
#> 44 times x 12 species x 100 sizes
#> 
#>  Species          Min       Mean       Max
#>    Sprat 0.0000000000 0.33743869 2.1827924
#>  Sandeel 0.0000000000 0.26816487 1.3102141
#>   N.pout 0.0000000000 0.30707882 2.1827924
#>  Herring 0.0077894362 0.32918211 1.9100547
#>      Dab 0.0017746971 0.04908083 0.1734253
#>  Whiting 0.0126246154 0.33123701 1.3975648
#>     Sole 0.0268320133 0.30068824 1.1274436
#>  Gurnard 0.0000000000 0.01269037 0.1307616
#>   Plaice 0.0089964121 0.24671481 0.8671267
#>  Haddock 0.0015854377 0.31410333 1.4275908
#>      Cod 0.0494762790 0.37063678 1.0721081
#>   Saithe 0.0009633361 0.15709914 1.2032865
plot(fmort, time = 2007)

# }