Package index
Model setup
Functions for combining a standard mizer MizerParams object with therMizer’s temperature forcing and realm structure. The result is a therMizer object, whose temperature-scaled encounter, predation and metabolism rates mizer dispatches to automatically during project().
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upgradeTherParams() - Upgrade a
MizerParamsobject 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.
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setEncounterPredScale() - Set the encounter and predation scaling constant
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setMetabTher() - Set metabolism temperature scaling parameters
Resource forcing
The resource dynamics function that reads the time-varying plankton spectrum stored in the model. upgradeTherParams() installs it automatically when it is given an n_pp_array.
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plankton_forcing() - Resource forcing from
n_pp_array
Diagnostics
Functions for inspecting the temperature scalars that therMizer applies at each time step.
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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.
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plotTherPerformance() - Plot thermal performance curves
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plotTherScalar() - Plot time-varying thermal scalars
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therMizertherMizer-package - therMizer: Extends the mizer package with temperature dynamics