To compile the paper we use remake. The easiest way to install remake is via drat:
drat:::add("traitecoevo")
install.packages("remake")(install drat itself with install.packages("drat"))
Compilation requires a reasonably complete LaTeX installation (e.g. MacTeX).
We use the non-CRAN packages callr. This can be installed by remake:
remake::install_missing_packages()To compile everything, run
remake::make()parameters can be modified by changing the values in parameters.json
to run the simulation: change to the python directory and run the command
python simulation.py
in your terminal
Explanation of parameters in parameters.json
| parameter | explanation |
|---|---|
| random_seed | the seed for the random number generator |
| debug | if true detailed messages about what is happening ieach gen will be printed |
| generation_plot | if true interactive plots will be shown at the end of each gen\ |
| save_pngs | if true png's will be saved of the scatter plots |
| save_every | which generations will be saved to png |
| initial_plot | if true will display an interactive plot after the first gen |
| trait_bins | the number of bins in the trait histogram |
| final_plot | if true will display an interactive plot after the final gens |
| generations | how many generations to run the simulation for |
| ----------------- | --------------------------- |
| time_female_maturity | when do the females mature |
| time_step | the delta time for each |
| N | the initial number of nests |
| K | the initial number of individuals |
| rr_mean | the average reproductive power of a nest |
| rr_sd | the standard deviation of reproductive power of a nest |
| maturation_center | the point of inflection for the logistic male maturation function |
| maturation_width | the scale of the logistic male maturation function |
| growth_param_a | see ms.pdf eqn 3,4 |
| growth_param_b | see ms.pdf eqn 3,4 |
| initial_mass | the mass of the males at time 0 |
| mass_to_energy | a male with m mass gets this m * this value starting energy |
| metabolic_cost_search | the cost of searching for nests per timestep |
| metabolic_cost_occupy | the cost of occupying a nest per time step |
| display_1_cost | the cost of escalating to display 1 |
| fight_cost | the cost of escalating to a fight |
| aggression_max | the maximum value for aggression allowed |
| exploration_mean | the inital mean value for the distribution of exploration traits |
| exploration_sd | the inital standard deviation for the distribution |
| exploration_prob_scale | exploration = logistic.cdf (exploration trait / this) |
| mutation_rate | chance that a trait will mutate |
| mutation_sd | the standard deviation of a mutation, 0 mean |