Package index • therMizer

Model setup

Functions for combining a standard mizer MizerParams object with therMizer’s temperature forcing, realm structure, and rate functions.

upgradeTherParams(): Upgrade a MizerParams object for therMizer
setVerticality(): Add realm-specific temperature structure to a therMizer model

Scaling parameters

Functions that compute the species-specific constants used to normalise the encounter/predation and metabolism temperature responses to the [0, 1] interval. These are called automatically by upgradeTherParams() but are also exported for direct use.

setEncounterPredScale(): Set the encounter and predation scaling constant
setMetabTher(): Set metabolism temperature scaling parameters

Temperature-scaled rate functions

Drop-in replacements for mizer’s built-in rate functions that incorporate temperature effects. Registered automatically by upgradeTherParams() and called internally by project().

therMizerEncounter(): Temperature-scaled encounter rate
therMizerPredRate(): Temperature-scaled predation mortality
therMizerEReproAndGrowth(): Temperature-scaled energy for growth and reproduction
plankton_forcing(): Resource forcing from n_pp_array

Diagnostics

Functions for inspecting the temperature scalars that therMizer applies at each time step.

scaled_temp_effect(): Calculate the encounter and predation temperature scalar

Visualisation

Plotting functions for exploring species’ thermal performance curves and the time-varying temperature scalars they experience.

plotTherPerformance(): Plot thermal performance curves
plotTherScalar(): Plot time-varying thermal scalars

Package

therMizer therMizer-package: therMizer: Extends the mizer package with temperature dynamics