macarthur

These scripts and notebooks are used to study the evolutionary trajectories in MacArthur resource-consumer systems.

Notebooks were used as a testing environment and not used for any simulations.

PARAMETERS

Name in Github	Symbol in report	Description
P_NORM	$p$	scaling in $L^p$ norm
K_SPECIES_MAX	$K_{init}$	maximum number of species at start simulation (in nonspeciating MA)
K_SPECIES_MAX	$K_{max}$	number of speciation events (in speciating MA)
D_DIMENSION	$d$	number of resources in system
GAMMA	$\gamma$	vector with resource influx rates
NOISE	n.a.	distribution of noise, constant "normal"
MEAN	n.a.	mean of evolutionary noise, constant at 0
SIGMA	$\eta$	standard deviation of noise
ABUNDANCE_SPAWN	n.a.	abundance of newly spawned species, constant 0.01
ABUNDANCE_DEATH	n.a.	abundance below which species is considered extinct, constant 0.001
DEATH_RATE	$\delta$	species death rate
ALPHA	$\alpha$	rate of reproduction, constant 0.005
BETA	$\beta$	rate of consumption, constant 0.01
DT_TIMESCALE	$h$	size of Euler step
MEAN_INTERARRIVAL_TIME	$\lambda$	average time between speciation events
SEED	n.a.	seed for random variables
WITH_RUNOUT	n.a.	if True, system will continue running after last speciation event
RUNOUT_SCALING	$\frac{\tau}{\lambda}$	amount of time the system will continue running after final speciation event, determined by the RUNOUT_SCALING multiplied with the MEAN_INTERARRIVAL_TIME
save_every	n.a.	Indicates interval between timepoints in results

FOLDERS

• 3D_strategy_evolution Contains scripts and figures used for showing the time evolution of systems with 3 resources. This folder contains additional figures corresponding to figures 3.2 and 3.3 in the report.

• figs_intro_withcode Contains scripts and figures used to support the introduction. This folder contains older versions of the figures.

• figs_presentation Contains scripts used to make figures to support the final presentation.

• notebooks Contains jupyter notebooks with the implementation of both nonspeciating and speciating MacArthur systems. These notebooks were used to test the implementation and are not used for any simulations.

• species_degree_specialisation Contains scripts and figures used for showing the time evolution of the species leven degree of specialisation.

  • Figures in nonspeciating_uniformdistribution correspond to figure 3.4, there are no additional figures.
  • Figures in nonspeciating_exponentialdistribution correspond to figure 3.5, there are no additional figures.
  • Figures in speciating_delta0.1 correspond to figures 3.6 and 3.7 in the report and contain additional figures with $\eta=0.1$ and $p = 2$.
  • Figures in speciating_delta0.01 correspond to figures 3.8 and 3.9 in the report and contain additional figures with $p=0.9$, $p=1$, $p=1.1$.

• system_degree_specialisation Contains scripts and figures used for showing the time evolution of the system level degree of specialisation.

  • Figures in not_weighted correspond to figures 3.10, 3.11, 3.12, and 3.13 in the report. This folder contains many additional figures, both for parameters and method of studying $S$.
  • Figures in weighted correspond to figures 3.14 and 3.15 in the report. This folder contains additional figures for different methods of studying $S$.