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] <-0params<- 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)