In pwoodworth-jefcoats/Size-Based-Modeling: Mizer With The Effects Of Temperature Included

Load libraries

Mizer 2.0.1 updated at 23/05/2020 or later version is needed to use the background extension.

A. First and best option: download the most updated version of the package directly from GitHub using devtools::install_github("sizespectrum/mizer")

B. Second option: merge upstream master with your branch and upload code from local repository

rm(list=ls())

# option A
# devtools::install_github("sizespectrum/mizer") # run only once
library(mizer)

# option 2 
# library(Jmisc)
# path<-"/Users/nov017/R-projects/Mizer-trait/R"
# sourceAll(path)

Set up multispecies model

All parameters are made up

species_params = data.frame(species = c("pelagic", "benthic"), w_inf = c(100, 200), k_vb =c(0.2, 0.2), w_min = c(0.001, 0.001))

# available PP to species 
species_params$interaction_resource<-c(1,0.2)

# create the param object
# note: some def values are different from old mizer (e.g. kappa)
params<-newMultispeciesParams(species_params, no_w = 200, kappa = 0.001)
params@resource_params

# run projections:
sim<-project(params, t_max = 100, effort = 0)
plot(sim)

Add a second background spectrum to the Param object

To create a new component, the background resource spectrum, you need to use setComponent(). See extension.r in Mizer package for a detailed description of this function and its arguments

In brief, setComponent (params, component, initial_value, dynamics_fun, encounter_fun, mort_fun, component_params)

params = A MizerParams object
component = Name of the component
initial_value = Initial value of the component
dynamics_fun = Name of function to calculate value at the next time step
encounter_fun = Name of function to calculate contribution to encounter rate. Optional
mort_fun = Name of function to calculate contribution to the mortality rate. Optional
component_params = Named list of parameters needed by the component functions. Optional

How it works

We need to specify our own functions (dynamics, encounter and mortality) for each background resource component we'd like to add.

This can be done in 6 steps:

1. Specify the background dynamics function
   dynamics_fun = background_bb_semichemostat, which is the same as resource_semichemostat() in resource_dynamics.r, but uses newly defined rr_pp (here called rate) and cc_pp (here called capacity), and it includes the mortality function

background_bb_semichemostat <- function(params, n_other, rates, dt, ...) {

    # locate where (which params slot) the parameters needed for this function are stored 
    component <- "background_bb"
    c <- params@other_params[[component]] 

    # name of interaction parameter for this component in species_params
    interaction_component <- paste0("interaction_", component)
    interaction <- params@species_params[[interaction_component]]

    # Step 3: specify the background mortality function
    mort <- as.vector(interaction  %*% rates$pred_rate)

    # specify the background dynamics function. This is the same as resource_semichemostat() - see above
    tmp <- c$rate * c$capacity / (c$rate + mort) 
    return(tmp - (tmp - n_other[[component]]) * exp(-(c$rate + mort) * dt))
}

1. Specify the encounter function
   encounter_fun = background_bb_encounter, which is same as mizerEncounter() in project_methods.r, but now n_pp is the sum of the 2 background spectra

background_bb_encounter <- function(params, n, n_pp, n_other, ...) {
    mizerEncounter(params, n = n, n_pp = n_pp + n_other$background_bb, ...)
}

1. Specify the mortality function
   mort_fun = mort, which is the same as mizerResourceMort() in project_methods.r, but uses different interaction values (interaction_resource) and pred_rate. Mortality in this case is specified as part of background_bb_semichemostat(). For any other extensions you'd need something like:

# background_bb_mortality<-...mizerMortality()...

1. Set up parameters
   Calcualate rate and capacity used in background_bb_semichemostat() and given kappa, lambda etc. for the bb spectrum

kappa <- 0.001 
lambda <- 2.05 
r_pp <- 10
n <- 0.666 
w_pp_cutoff <- 10
rate <- r_pp * params@w_full^(n - 1)
capacity <- kappa * params@w_full^(-lambda)
capacity[params@w_full > w_pp_cutoff] <- 0
w_pp_min <- 1e-6 # set minimum size of new resource 
capacity[params@w_full > w_pp_cutoff] <- 0

# Set interaction species-background_bb - i.e. proportion available to each species.  
# this new species param column needs to be named as "interaction_" + component name
params@species_params$interaction_background_bb <- c(0,0.8)

1. Add components
   Add the background bb resource spectrum to the params object using setComponent()

params2 <- setComponent(params = params, component = "background_bb",
                        initial_value = params@initial_n_pp, 
                        dynamics_fun =  "background_bb_semichemostat",
                        component_params = list(rate = rate, 
                                                capacity = capacity))

1. Update the encounter function

params2 <- setRateFunction(params2, "Encounter", "background_bb_encounter")

1. Update the mortality function
   Mortality in this case is specified as part of background_bb_semichemostat() so you don't need to update this function. For any other extensions you'd need to run the line below:

# params2<-setRateFunction(params2, "Mortality", "background_bb_mortality")

Run project() using the newly defined Param object

Params now includes a pp and a bb background spectrum

sim2 <- project(params2, t_max = 100, effort = 0) 
plot(sim2)

# check the community 
# sim2@n_other[10,] # n background_bb at time step 10 

Plot community with additional resource

"to plot the results you will need to write your own plot function. You can of course use the built-in plot functions to get a ggplot2 object to which you then only need to add the extra stuff for your new components".

pwoodworth-jefcoats/Size-Based-Modeling documentation built on Sept. 15, 2023, 8:13 a.m.