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Home Page: https://github.com/mauriceling/dose/wiki
License: GNU General Public License v3.0
Digital Organism Simulation Environment (DOSE)
Home Page: https://github.com/mauriceling/dose/wiki
License: GNU General Public License v3.0
Eg.
Change:
SIM_01.py
dose.step()
Into:
SIM_01.py
dose.step()
C:\Users\13035006\SkyDrive\GitHub\dose\examples>python 08_revive_simulation_03.py
Traceback (most recent call last):
File "08_revive_simulation_03.py", line 111, in <module>
dose.revive_simulation(rev_parameters, simulation_functions)
File "C:\Users\13035006\SkyDrive\GitHub\dose\dose\dose.py", line 568, in revive_simulation
simulation_core(sim_functions, rev_parameters, Populations, World)
File "C:\Users\13035006\SkyDrive\GitHub\dose\dose\simulation_calls.py", line 68, in simulation_core
pop_name, World)
File "C:\Users\13035006\SkyDrive\GitHub\dose\dose\simulation_calls.py", line 204, in interpret_chromosome
(x,y,z) = coordinates(location)
File "C:\Users\13035006\SkyDrive\GitHub\dose\dose\simulation_calls.py", line 89, in coordinates
x = location[0]
TypeError: 'NoneType' object has no attribute '__getitem__'
This simulation will have the most basic parameters and functions. Most parameters would be set to it's default value and most custom_functions would be passed (except for those that are required to be over-ridden).
Like "01_basic_functions_one_cell_deployment.py", this simulation shall also feature basic parameters and basic custom functions with the exception of having 2 populations and an even deployment scheme for the simulation's deployment scheme.
Deployment schemes 2-4 does not properly change the 'location' status of every deployed organism.
To aid in future data analyses, there should be a function to help the user extract a specific set of information from the database.
class simulation_functions():
def organism_movement(self, World, x, y, z): pass
def organism_location(self, World, x, y, z): pass
def ecoregulate(self, World): pass
def update_ecology(self, World, x, y, z): pass
def update_local(self, World, x, y, z): pass
def report(World): pass
def fitness(self, Populations, pop_name): pass
def mutation_scheme(self, organism): pass
def prepopulation_control(self, Populations, pop_name): pass
def mating(self, Populations, pop_name): pass
def postpopulation_control(self, Populations, pop_name): pass
def generation_events(self, Populations, pop_name): pass
def population_report(self, Populations, pop_name): pass
def deployment_scheme(Populations, pop_name, World): pass
New organisms created inside mating scheme shares the same status dictionary similar to issue #14.
Renaming entities into dose_functions/simulation_functions seem to restrict it as just a class of functions. It would be more suitable to initialize dose_world inside dose.py. Doing so would give a clear border between the simulation's world and the simulation functions.
This is to define a set of analytical functions to be placed in analytics.py
Returns a list of an entire generation's status. User is able to specify the starting time of the simulation, the name of the population, the generation to analyze and the status to be extracted.
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