getTempEffectMetab: Get the total temperature effect on metabolism across all...

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

Get the total temperature effect on metabolism across all realms by time, species, and size.

Description

Calculates the temperature effect on metabolism across all realms by species and size at each time step in teh ocean_temp argument. The total temperature effect is just the sum of the temperature effects in each realm

getTempEffectMetab method for MizerParams object with constant temperature.

getTempEffectMetab method for therMizerParams object with time changing effort.

getTempEffectMetab method for therMizerSim object.

Usage

getTempEffectMetab(object, ocean_temp, ...)

## S4 method for signature 'therMizerParams,numeric'
getTempEffectMetab(object, ocean_temp, ...)

## S4 method for signature 'therMizerParams,matrix'
getTempEffectMetab(object, ocean_temp, ...)

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

Arguments

object	A therMizerParams object or a therMizerSim object
ocean_temp	The ocean temperature in each realm. Only needed if the object argument is of class therMizerParams. See notes below.
...	Other arguments passed to getTempEffect method.
time_range	Subset the returned temperature effects 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 has only 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 ocean_temp argument does not have a time dimension, the output array has two dimensions (species x size).

Note

Here: temperature effect is determined from exposure x ontogenetic_migration x ocean_temp.

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

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

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