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Population Model Setup for Anadromous Species

Source: R/pop_model_setup_anadromous.R
pop_model_setup_anadromous.Rd

Generate symbolic objects for the population model and then generate parameter matrices for Pacific salmon.

Usage

pop_model_setup_anadromous(life_cycles = NA)

Arguments

life_cycles

Data frame. Raw life cycles.csv data frame.

Value

a list object of symbolic objects.

Details

This is an intermediate setup function to run the population, but some of its outputs are useful on their own, especially for eigen analyses from the projection matrix. pop_model_setup_anadromous() is run before pop_model_matrix_elements() and Projection_DD().

pop_model_setup_anadromous() is a customized version of pop_model_setup() for anadromous species (Salmon). Follow convention from Davison and Statterthwaite 2016 (Natural Resource Modelling Use of matrix model to predict life history schedules for semelparous population).

Transition Matrix:

  • Calculates stage-specific survivals and transition rates, survival probabilities, transition probabilities.

  • Initializes the survival/transition rates subject to a stage-specific density-dependence.

  • Checks for excessive compensation ratios.

Dataset for life-histories:

  • transition probabilities

  • egg-survival, age-0 survival, and then stage-specific survival probabilities

  • spawning events per year

  • eggs-per-spawner

  • number of spawning intervals

  • adult carrying capacity

  • sex ratio