getFMort: Get the total fishing mortality from all fishing gears by...

In pwoodworth-jefcoats/Size-Based-Modeling: Mizer With The Effects Of Temperature Included

Get the total fishing mortality from all fishing gears by time, species and size.

Description

Calculates the fishing mortality from all gears by species and size at each time step in the effort argument. The total fishing mortality is just the sum of the fishing mortalities imposed by each gear.

getFMort method for therMizerParams object with constant effort.

getFMort method for therMizerParams object with time changing effort.

getFMort method for therMizerSim object.

Usage

getFMort(object, effort, ...)

## S4 method for signature 'therMizerParams,numeric'
getFMort(object, effort, ...)

## S4 method for signature 'therMizerParams,matrix'
getFMort(object, effort, ...)

## S4 method for signature 'therMizerSim,missing'
getFMort(object, effort,
  time_range = dimnames(object@effort)$time, drop = TRUE, ...)

Arguments

object	A therMizerParams object or a therMizerSim object
effort	The effort of each fishing gear. Only needed if the object argument is of class therMizerParams. See notes below.
...	Other arguments passed to getFMortGear method.
time_range	Subset the returned fishing mortalities by time. The time range is either a vector of values, a vector of min and max time, or a single value. Default is the whole time range. Only used if the object argument is of type therMizerSim.
drop	Only used when object is of type therMizerSim. Should dimensions of length 1 be dropped, e.g. if your community only has one species it might make presentation of results easier. Default is TRUE

Value

An array. If the effort argument has a time dimension, or object is of class therMizerSim, the output array has three dimensions (time x species x size). If the effort argument does not have a time dimension, the output array has two dimensions (species x size).

Note

Here: fishing mortality = catchability x selectivity x effort.

The effort argument is only used if a therMizerParams object is passed in. The effort argument can be a two dimensional array (time x gear), a vector of length equal to the number of gears (each gear has a different effort that is constant in time), or a single numeric value (each gear has the same effort that is constant in time). The order of gears in the effort argument must be the same the same as in the therMizerParams object.

If the object argument is of class therMizerSim then the effort slot of the therMizerSim object is used and the effort argument is not used.

See Also

getFMortGear, project_therMizer

Examples

## Not run: 
data(NS_species_params_gears)
data(inter)
params <- therMizerParams(NS_species_params_gears, inter)
# Get the total fishing mortality when effort is constant for all gears and time:
getFMort(params, effort = 1)
# Get the total fishing mortality when effort is different
# between the four gears but constant in time:
getFMort(params, effort = c(0.5,1,1.5,0.75))
# Get the total fishing mortality when effort is different
# between the four gears and changes with time:
effort <- array(NA, dim = c(20,4))
effort[,1] <- seq(from=0, to = 1, length=20)
effort[,2] <- seq(from=1, to = 0.5, length=20)
effort[,3] <- seq(from=1, to = 2, length=20)
effort[,4] <- seq(from=2, to = 1, length=20)
getFMort(params, effort=effort)
# Get the total fishing mortality using the effort already held in a therMizerSim
object.
sim <- project_therMizer(params, t_max = 20, effort = 0.5)
getFMort(sim)
getFMort(sim, time_range = c(10,20))

## End(Not run)

pwoodworth-jefcoats/Size-Based-Modeling documentation built on Sept. 15, 2023, 8:13 a.m.