Usage

Installation

Install the package by using the julia REPL and entering ] to enter the package manager. Then execute:

pkg> add https://github.com/janablechschmidt/MetaRange.jl.git

Alternatively use Pkg directly and enter:

using Pkg
Pkg.add(url = "https://github.com/janablechschmidt/MetaRange.jl.git")

Configuration

Configuration files for MetaRange are most conveniently supplied together in a folder. The folder should contain a configuration file and two sub-folders "environment/" and "species/". The configuration file can also define a path to environment or species files elsewhere.

configuration/
├── configuration.csv
├── environment/
│   ├── temperature.csv
│   ├── precipitation.csv
│   ├── parameter_1.csv
│   └── ...
└── species/
    ├── species_1.csv
    ├── species_2.csv
    └── ...

Configuration File

The configuration files are all formatted as space separated .csv files. This is the same minimal example as in examples/static/. More information on the configuration files can be found in the Parameters section.

Argument Value
experiment_name static
timesteps 50
temperature temperature.csv
precipitation precipitation.csv

# how are conflicts resolved if the same parameter is supplied in the configuration file and in the species file?

Environment Files

Environment files are formatted as space separated .csv files. The model needs a temperature file to calculate metabolic rates. MetaRange works with either a single .csv that is used for the whole simulation or a folder with several .csv files to simulate a change in the environment. In this case the folder should contain one file for each timestep.

Species Files

Several species files can be supplied to the model at the same time. Here is the example species file from examples/static/. More information on the species configuration files can be found in the Parameters section.

Argument Value
species_name example
mass 1.0
sd_mass 0.1
growrate 1.5
sd_growrate 0.1
max_dispersal_dist 3
max_dispersal_buffer 2
mean_dispersal_dist 1
allee -100.0
sd_allee 0.1
bevmort 0.2
sd_bevmort 0.35
carry 1500.0
sd_carry 50.0
upper_limit_temperature 300.0
lower_limit_temperature 285.0
optimum_temperature 292.5
response_temperature sqrt
upper_limit_precipitation 1900
lower_limit_precipitation 1100
optimum_precipitation 1500
response_precipitation sqrt
habitat_cutoff_suitability 0.01

Running the simulation

To run the simulation first load in your files by using read_input. Then run the simulation by using run_simulation!() on the object.

SD = read_input("./examples/static/configuration.csv")
run_simulation!(SD)

Output

Visualization

For direct visualization there are some functions that plot the simulation results. These can be found in the Visualization Functions section.

plot_abundances creates a line plot of the first species in the simulation over time.

img creates a heatmap of a chosen output at the specified time-step.

The function gif creates a gif of the chosen output heatmap over time:

Other visualization functions are img_complex and gif_complex.

Simulation Data Object

To directly check the results and to do more detailed analyses directly inspect the Simulation_Data object. In julia this is done by looking at the fields with the period character .. So to see the final population size of the first species you would use:

SD.species[1].abundances[:,:,end]