In sizespectrum/mizerStarvation: Starvation mortality for mizer

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

mizerStarvation

This is an extension package for the mizer package (https://sizespectrum.org/mizer/) to implement starvation mortality.

Installation

You can install the development version of mizerStarvation from GitHub with

remotes::install_github("sizespectrum/mizerStarvation")

Example

This is an artificial example just to illustrate usage. We start with the North Sea model that comes with the mizer package.

library(mizerStarvation)
library(tidyverse)
library(ggplot2)
params <- NS_params
plotSpectra(params, power = 2)

We add starvation mortality

params <- setStarvation(NS_params, 10)

We decrease resource availability to create some starvation

capacity <- getResourceCapacity(params)
capacity[w_full(params) > 0.1] <- 0
params <- setResource(params, resource_capacity = capacity)
initialNResource(params)[w_full(params) > 0.1] <- 0

We can calculate the starvation mortality for each species as a function of size with getStarvMort():

starv_mort <- getStarvMort(params)

This returns a matrix. For plotting we turn this into a data frame with melt() and send it to ggplot:

ggplot(melt(starv_mort)) +
    geom_line(aes(x = w, y = value, colour = sp, linetype = sp), size = 1) +
    scale_x_log10() +
    xlab("Size [g]") +
    ylab("Starvation mortality [1/year]") +
    scale_colour_manual(values = params@linecolour) +
    scale_linetype_manual(values = params@linetype)

Of course now Saithe will go extinct, not only because of the starvation mortality but also because it stops growing before maturity.

sim <- project(params, t_max = 30)
plotBiomass(sim)

sizespectrum/mizerStarvation documentation built on Sept. 26, 2021, 11:05 a.m.