Population Model Matrix Elements for Anadromous Fish — pop_model_matrix_elements

Build population model matrix elements for anadromous fish.

Usage

pop_model_matrix_elements_anadromous(pop_mod_setup = NA, s0_calibrate = TRUE)

Arguments

pop_mod_setup: List. Object returned from population_model_setup_anadromous(). Use pop_model_matrix_elements() for objects returned from population_model_setup().
s0_calibrate: Logical. If TRUE (default) and an adult capacity k is set (with no Beverton-Holt flags), fry survival (s0) is re-calibrated so that lambda = 1. Set to FALSE to keep the raw s0 from the life cycles file - used by sensitivity analyses (e.g., pop_model_ltre) that must measure lambda responses on the un-calibrated matrix.

Value

a list object of symbolic objects.

Details

This is an intermediate setup function to run the population model. However, some of outputs are useful on their own, especially for eigen analyses. pop_model_matrix_elements() is run after pop_model_setup() or pop_model_setup_anadromous(), but pop_model_matrix_elements() must be run before Projection_DD(). Key outputs to explore include a density independent projection matrix, life histories, and a symbolic representation of the matrix math for density dependent and density independent components. population_model_setup() should be run with pop_model_matrix_elements() for non-anadromous species. population_model_setup_anadromous() should be run with pop_model_matrix_elements_anadromous() for anadromous species.

Examples

if (FALSE) { # \dontrun{

# Load the CEMPRA package.
library(CEMPRA)

filename_lc <- system.file("extdata", "life_cycles.csv", package = "CEMPRA")
life_cycles <- read.csv(filename_lc)

# Setup objects for population model
pop_mod_setup <- pop_model_setup(life_cycles = life_cycles)

# Build matrix elements for population model
pop_mod_mat <- pop_model_matrix_elements(pop_mod_setup = pop_mod_setup)
names(pop_mod_mat)

# A density independent projection matrix
pop_mod_mat$projection_matrix



} # }