getTempEffectRealmMetab: getTempEffectRealmMetab method for the size based model

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

getTempEffectRealmMetab method for the size based model

Description

Calcuates the temperature effect on metabolism by realm, species, and size at each time step in the ocean_temp argument. Used by the project_therMizer method to perform simulations

getTempEffectRealmMetab method for therMizerParams object with constant temperature.

getTempEffectRealmMetab method for therMizerParams object with time-changing temp.

getTempEffectRealmMetab method for therMizerSim object.

Usage

getTempEffectRealmMetab(object, ocean_temp, ...)

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

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

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

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 (currently unused)
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.

Value

An array. If the ocean_temp argument has a time dimension, or a therMizerSim is passed in, the output array has four dimensions (time x realm x species x size). If the ocean_temp argument does not have a time dimension (i.e., it is a vector or a single numeric), the output array has three dimensions (realm x species x size).

Note

Here: Temperature effect results from exposure x ontogenetic migration x ocean temperature.

The ocean_temp argument is only used of a therMizerParams object is passed in. The ocean_temp argument can be a two dimensional 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.