def __init__(self, no_agents, width, height, init_infected, perc_masked,
prob_trans_masked, prob_trans_unmasked, infection_period,
immunity_period):
self.no_agents = no_agents
self.grid = MultiGrid(width, height, True)
self.init_infected = init_infected
self.perc_masked = perc_masked
self.prob_trans_masked = prob_trans_masked
self.prob_trans_unmasked = prob_trans_unmasked
self.infection_period = infection_period
self.immunity_period = immunity_period
self.schedule = RandomActivation(self)
self.running = True
# Create agents
for i in range(self.no_agents):
a = Agent(i, self)
self.schedule.add(a)
# Add the agent to a random grid cell
x = self.random.randrange(self.grid.width)
y = self.random.randrange(self.grid.height)
self.grid.place_agent(a, (x, y))
# Collect count of susceptible, infected, and recovered agents
self.datacollector = DataCollector({
'Susceptible': 'susceptible',
'Infected': 'infected',
'Recovered & Immune': 'immune'
})
def __init__(self, no_people, total_area, no_agents, all_x, all_y,
infection_rate, first_infected, mobility, work_store,
home_store):
self.num_agents = no_agents
grid_size = round(
math.sqrt((self.num_agents / no_people) * total_area) * 100)
self.grid = MultiGrid(grid_size, grid_size, False)
self.schedule = RandomActivation(self)
self.running = True
for i in range(self.num_agents):
a = Agent(i, self, infection_rate, work_store, home_store,
mobility)
self.schedule.add(a)
self.grid.place_agent(a, (int(all_x[i]), int(all_y[i])))
if i == first_infected:
a.infected = 1
self.datacollector = DataCollector(
model_reporters={"Tot infections": compute_informed},
agent_reporters={
"Infected": "infected",
"R-Number": "rnumber"
})
def __init__(self, home_store):
self.num_agents = 1000
self.grid = MultiGrid(200, 200, True)
self.schedule = RandomActivation(self)
self.running = True
for i in range(self.num_agents):
a = Agent(i, self)
self.schedule.add(a)
while True:
#x = round(int(np.random.normal(self.grid.width/2, 10, 1)))
#y = round(int(np.random.normal(self.grid.height/2, 10, 1)))
x = self.random.randrange(self.grid.width)
y = self.random.randrange(self.grid.height)
if len(
self.grid.get_neighbors(
(x, y), moore=True, include_center=True,
radius=10)) <= 7:
self.grid.place_agent(a, (x, y))
home_store[i, :] = x, y
break
if i < 1:
a.infected = 1
self.datacollector = DataCollector(
model_reporters={"Tot informed": compute_informed},
agent_reporters={"Infected": "infected"})
def __init__(self, city_to_country, no_people, total_area, city_to_country_area, countryside):
self.num_agents = 2000
grid_size = round(math.sqrt((self.num_agents/no_people)*total_area)*100)
self.grid = MultiGrid(grid_size, grid_size, True)
self.schedule = RandomActivation(self)
self.running = True
centers = np.zeros((1, 2))
centers[0, :] = random.randrange(10, self.grid.width - 10), random.randrange(10, self.grid.height - 10)
x = np.zeros((1, round(int(city_to_country * self.num_agents))))
y = np.zeros((1, round(int(city_to_country * self.num_agents))))
x[0, :] = np.around(np.random.normal(centers[0, 0], 3, round(int(city_to_country * self.num_agents))))
y[0, :] = np.around(np.random.normal(centers[0, 1], 3, round(int(city_to_country * self.num_agents))))
count = 0
countryside_count = 0
while countryside_count < (countryside * self.num_agents):
countryside_count += counter(x)
runner = True
while runner:
new_center = (random.randrange(10, self.grid.width - 10), random.randrange(10, self.grid.height - 10))
if dist_check(new_center, centers):
centers = np.vstack((centers, new_center))
runner = False
new_x = np.around(np.random.normal(centers[count, 0], (1/(6*city_to_country_area*(math.sqrt(count+1))))
* self.grid.width, round(int(city_to_country * self.num_agents)
/ (count + 2))))
new_y = np.around(np.random.normal(centers[count, 1], (1/(6*city_to_country_area*(math.sqrt(count+1))))
* self.grid.height, round(int(city_to_country * self.num_agents)
/ (count + 2))))
while len(new_x) < round(int(city_to_country * self.num_agents)):
new_x = np.append(new_x, -1)
new_y = np.append(new_y, -1)
x = np.vstack((x, new_x))
y = np.vstack((y, new_y))
count += 1
new_x = np.delete(x.flatten(), np.where(x.flatten() == -1))
new_y = np.delete(y.flatten(), np.where(y.flatten() == -1))
x_countryside = np.around(np.random.uniform(0, self.grid.width-1, int(self.num_agents - len(new_x))))
y_countryside = np.around(np.random.uniform(0, self.grid.height-1, int(self.num_agents - len(new_y))))
all_x = np.concatenate((new_x, x_countryside))
all_y = np.concatenate((new_y, y_countryside))
for i in range(self.num_agents):
a = Agent(i, self)
self.schedule.add(a)
self.grid.place_agent(a, (int(all_x[i]), int(all_y[i])))
if i == 1:
a.infected = 1
self.datacollector = DataCollector(
model_reporters={"Tot informed": compute_informed},
agent_reporters={"Infected": "infected"})
def testGraphMovement3D(self):
ms, _grid = MeshSpace.read("test/meshes/sphere.msh")
nodes = ms.G.nodes
starting_node = 0
a = Agent(0, None)
ms.place_agent(a, starting_node)
possible_steps = ms.get_neighbors(a.pos, include_center=False)
self.assertEqual(possible_steps, [31, 43, 6])
new_position = random.choice(possible_steps)
ms.move_agent(a, new_position)
self.assertTrue(a.pos == new_position)
def __init__(self, N, width, height):
self.agents = N
self.grid = MultiGrid(width, height, True)
self.schedule = RandomActivation(self)
self.running = True
self.steps = 0
self.encounters = 0
self.mean_encounters = 0
# creating agents by iterating through n_agents
for i in range(self.agents):
# specify an agent as an object of class 'Agent' with unique_ID 'i'
agent = Agent(i, self)
# specify pitch measures for the agent as type 'float'
agent.iqr = float(iqr.iloc[i])
agent.speechrate = float(speechrate.iloc[i])
agent.mad = float(mad.iloc[i])
agent.pause = float(pause.iloc[i])
agent.diagnosis = float(diagnosis.iloc[i])
agent.symptom_severity = (agent.iqr + agent.mad +
(1 - agent.speechrate) + agent.pause) / 4
# add the agent to the model schedule
self.schedule.add(agent)
# adding the agent to a random grid cell
x = self.random.randrange(self.grid.width)
y = self.random.randrange(self.grid.height)
self.grid.place_agent(agent, (x, y))
# add data-collector to the agent
self.datacollector = DataCollector(
agent_reporters={
"interactions": "unique_interactions",
"interaction_time": "interaction_time",
"conversation_time": "conversation_time",
"change_IQR": "change_iqr",
"change_MAD": "change_mad",
"change_Speechrate": "change_speechrate",
"change_PauseFreq": "change_pause",
"abs_change_IQR": "abs_change_iqr",
"abs_change_MAD": "abs_change_mad",
"abs_change_Speechrate": "abs_change_speechrate",
"abs_change_PauseFreq": "abs_change_pause",
"activity": "activity",
"diagnosis": "diagnosis"
},
model_reporters={"Encounters": "encounters"})
def __init__(self, seed, collect_stepwise_data, N, x, y, z):
from mesa import Agent as Agent
self.N, self.x, self.y, self.z = N, x, y, z
self.schedule = RandomActivation(self)
self.schedule.add(Agent(2, self))
self.schedule.add(Agent(9, self))
from mesa.datacollection import DataCollector
self.datacollector = DataCollector(model_reporters={
'N': lambda m: m.N,
'X_1': lambda m: m.x,
'Y_2': lambda m: m.y,
'X_3': lambda m: m.z,
},
agent_reporters={
'id': lambda a: a.unique_id,
})
self.datacollector.collect(self)
self.step()
self.datacollector.collect(self)
self.step()
self.datacollector.collect(self)
self.running = True
def __init__(self, attributesFile, connectionsFile, xmax, ymax,
roleOrder): # coords of map edge
attributesDB = pd.read_csv(attributesFile, header=None)
connectionsDB = pd.read_csv(connectionsFile, header=None)
self.running = True
self.grid = MultiGrid(xmax, ymax, True) # bool = toroidal
self.schedule = Activation(self, roleOrder)
self.agents = []
# WALTHER DATA
# Create agents
for index, row in attributesDB.iterrows():
# From attributesDB: agent id, role, gender, current $, current rice, x coord and y coord
newAgent = Agent(
row[0], self, row[1], row[2], row[3], row[4]
) # Gotta assume the IDs correspond to the row number because the OECD book says it's matrix-based
self.schedule.add(newAgent)
self.grid.place_agent(newAgent, (row[5], row[6]))
self.agents.append(newAgent)
# Add links
for index, row in connectionsDB.iterrows():
agent = next(
(x for x in self.agents if x.unique_id == row[0]), None
) # I'm gonna say for now you can't assume this list is ordered the way the agents are added even though that's pretty paranoid
print(agent)
for i in range(1, len(row)): # for column index aka other agent id
if row[i] == 1:
agent.pointsTo.append(
next(
(x for x in self.agents if x.unique_id == (i - 1)),
None))
agent.pointsToIDs.append(i - 1)
self.datacollector = DataCollector(
agent_reporters={
"unique_id": "unique_id",
"gender": "gender",
"role": "role",
"rice": "rice",
"capital": "capital",
"pointsTo": "pointsToIDs",
"soldTo": "soldTo"
})
def __init__(self, mobility):
self.num_agents = 1000
self.grid = MultiGrid(100, 100, True)
self.schedule = RandomActivation(self)
self.running = True
for i in range(self.num_agents):
a = Agent(i, mobility, self)
self.schedule.add(a)
x = self.random.randrange(self.grid.width)
y = self.random.randrange(self.grid.height)
self.grid.place_agent(a, (x, y))
if i < 1:
a.infected = 1
self.datacollector = DataCollector(
model_reporters={"Tot informed": compute_informed},
agent_reporters={"Infected": "infected"})
def __init__(self, height, width, a_density=0.1, r_=0.1, k_=0.1):
self.height = height
self.width = width
self.a_density = a_density
self.r_ = r_
self.k_ = k_
self.schedule = RandomActivation(self)
self.grid = SingleGrid(width, height, torus=False)
self.datacollector = DataCollector(
{"happy": "happy"}, # Model-level count of happy agents
# For testing purposes, agent's individual x and y
{
"x": lambda a: a.pos[0],
"y": lambda a: a.pos[1]
},
)
# Set up agents
# We use a grid iterator that returns
# the coordinates of a cell as well as
# its contents. (coord_iter)
#seed to always start agents in the same place
random.seed(9001)
#create food matrix
n = self.height
m = self.width
self.food_matrix = [[100] * m for i in range(n)]
#randomly place agents
for cell in self.grid.coord_iter():
x = cell[1]
y = cell[2]
a = random.random()
if a < self.a_density:
agent = Agent((x, y), self)
self.grid.place_agent(agent, (x, y))
self.schedule.add(agent)
self.running = True
self.datacollector.collect(self)
def __init__(self, width=5, height=5, threshold=0.5, population_density=0.8, population_breakdown=0.5):
'''
Initialize the model
Args:
width: Width of the grid containing agents.
height: Height of the grid containing agents.
threshold: Homophily threshold, the number, from 0-8, of nearest neighbours at which I am so unhappy that I move.
population_density: Proportion of cells occupied, from 0-1.
population_breakdown: Proportion of agents of type 1, from 0-1.
'''
self.running = True
self.height = height
self.width = width
self.threshold = threshold
self.population_density = population_density
self.population_breakdown = population_breakdown
self.no_happy_this_timestep = 0
self.schedule = RandomActivation(self)
self.grid = SingleGrid(width, height, torus=True)
self.datacollector = DataCollector(
{"happy": lambda m: m.no_happy_this_timestep},
{"x": lambda a: a.pos[0], "y": lambda a: a.pos[1]})
for cell in self.grid.coord_iter():
x = cell[1]
y = cell[2]
if random.random() < self.population_density:
if random.random() < self.population_breakdown:
agent_type = 1
else:
agent_type = 0
agent = Agent(self,(x, y), agent_type)
self.grid.position_agent(agent, (x, y))
self.schedule.add(agent)
def testGraphMovement2D(self):
ms, _grid = MeshSpace.read("test/meshes/plane.msh")
nodes = ms.G.nodes
starting_node = 0
ending_node = 10
a = Agent(0, None)
short_path = (nx.shortest_path(ms.G, starting_node, ending_node))
# check short path
self.assertEqual(short_path, [0, 19, 10])
ms.place_agent(a, starting_node)
track_move = 0
while a.pos != ending_node:
possible_steps = ms.get_neighbors(a.pos, include_center=False)
#check neighbors for pos 0 pos 1 and pos 2
if a.pos == short_path[0]:
self.assertEqual(possible_steps, [4, 19, 2])
elif a.pos == short_path[1]:
self.assertEqual(possible_steps, [14, 10, 0])
for neighbor in possible_steps:
if neighbor == short_path[track_move + 1]:
new_position = neighbor
break
#check we have found the new path
self.assertNotEqual(a.pos, new_position)
#new_position = random.choice(possible_steps)
ms.move_agent(a, new_position)
self.assertTrue(a.pos == new_position)
track_move += 1
#Check that we have arrived to our destination
self.assertTrue(a.pos == ending_node)
def __init__(self, city_to_country, no_people, total_area, city_to_country_area, countryside, no_agents, Nc_N, n):
self.num_agents = no_agents
grid_size = round(math.sqrt((self.num_agents / no_people) * total_area) * 100)
self.grid = MultiGrid(grid_size, grid_size, False)
self.schedule = RandomActivation(self)
self.running = True
centers = np.zeros((1, 2))
centers[0, :] = random.randrange(10, self.grid.width - 10), random.randrange(10, self.grid.height - 10)
x = np.zeros((1, round(int(city_to_country * self.num_agents))))
y = np.zeros((1, round(int(city_to_country * self.num_agents))))
x[0, :] = np.around(np.random.normal(centers[0, 0], 3, round(int(city_to_country * self.num_agents))))
y[0, :] = np.around(np.random.normal(centers[0, 1], 3, round(int(city_to_country * self.num_agents))))
count = 0
countryside_count = 0
while countryside_count < (countryside * self.num_agents):
countryside_count += counter(x)
runner = True
while runner:
new_center = (random.randrange(10, self.grid.width - 10), random.randrange(10, self.grid.height - 10))
if dist_check(new_center, centers):
centers = np.vstack((centers, new_center))
runner = False
new_x = np.around(
np.random.normal(centers[count, 0], (1 / (6 * city_to_country_area * (math.sqrt(count + 1))))
* self.grid.width, round(int(city_to_country * self.num_agents)
/ (count + 2))))
new_y = np.around(
np.random.normal(centers[count, 1], (1 / (6 * city_to_country_area * (math.sqrt(count + 1))))
* self.grid.height, round(int(city_to_country * self.num_agents)
/ (count + 2))))
while len(new_x) < round(int(city_to_country * self.num_agents)):
new_x = np.append(new_x, -1)
new_y = np.append(new_y, -1)
x = np.vstack((x, new_x))
y = np.vstack((y, new_y))
count += 1
label = city_labeler(x)
for i in range(len(label)):
city_label[i] = label[i]
new_x = np.delete(x.flatten(), np.where(x.flatten() == -1))
new_y = np.delete(y.flatten(), np.where(y.flatten() == -1))
x_countryside = np.around(np.random.uniform(0, self.grid.width - 1, int(self.num_agents - len(new_x))))
y_countryside = np.around(np.random.uniform(0, self.grid.height - 1, int(self.num_agents - len(new_y))))
all_x = np.concatenate((new_x, x_countryside))
all_y = np.concatenate((new_y, y_countryside))
for i in range(self.num_agents):
a = Agent(i, self)
self.schedule.add(a)
self.grid.place_agent(a, (int(all_x[i]), int(all_y[i])))
home_store1[i, :] = int(all_x[i]), int(all_y[i])
if i == 1:
a.infected = 1
#a.working = 1
flux_store = np.zeros((1, 3))
for i in range(round(len(centers) / 2)):
print(i)
#print(round(len(centers))/2)
n_cities = random.sample(range(1, round(len(centers) / 2)), n)
for j in range(len(n_cities)):
mi = np.count_nonzero(city_label == i+1)
nj = np.count_nonzero(city_label == n_cities[j])
radius = math.sqrt((centers[i, 0] - centers[n_cities[j], 0]) ** 2 +
(centers[i, 1] - centers[n_cities[j], 1]) ** 2)
sij = 0
for k in range(len(all_x)):
if (all_x[k] - centers[i, 0]) ** 2 + (all_y[k] - centers[i, 1]) ** 2 < radius ** 2:
sij += 1
sij = sij - mi - nj
if sij < 0:
sij = 0
try:
Tij = (mi * Nc_N * mi * nj) / ((mi + sij) * (mi + nj + sij))*10
except ZeroDivisionError:
Tij = 0
if Tij > 75:
Tij = 75
if Tij > 1 and (i != n_cities[j]):
flux_store = np.vstack((flux_store, (Tij, i+1, n_cities[j])))
work_place = np.zeros(self.num_agents)
work_store1 = np.zeros((num, 2))
flux_store = np.delete(flux_store, 0, 0)
for i in np.unique(flux_store[:, 1]):
place = np.where(flux_store[:, 1] == i)[0]
place1 = np.where(city_label == i)[0]
for j in place1:
for k in place:
if random.uniform(0, 100) < flux_store[k, 0]:
work_place[j] = flux_store[k, 2]
for i in range(len(work_store1)):
if work_place[i] != 0:
n = int(work_place[i])
work_store1[i, :] = centers[n, 0], centers[n, 1]
global work_store, home_store
work_store = np.int64(work_store1)
home_store = np.int64(home_store1)
self.datacollector = DataCollector(
model_reporters={"Tot informed": compute_informed},
agent_reporters={"Infected": "infected"})
def __init__(self, no_people, total_area, no_agents, Nc_N, n, all_x, all_y,
centers, infection_rate, city_label, first_infected,
mobility_data):
self.num_agents = no_agents
grid_size = round(
math.sqrt((self.num_agents / no_people) * total_area) * 100)
self.grid = MultiGrid(grid_size, grid_size, False)
self.schedule = RandomActivation(self)
self.running = True
flux_store = np.zeros((1, 3))
home_store1 = np.zeros((self.num_agents, 2))
for i in range(round(len(centers) / 2)):
print(i, datetime.datetime.now() - begin_time)
n_cities = random.sample(range(1, round(len(centers) / 2)), n)
for j in range(len(n_cities)):
mi = np.count_nonzero(city_label == i + 1)
nj = np.count_nonzero(city_label == n_cities[j])
radius = math.sqrt(
(centers[i, 0] - centers[n_cities[j], 0])**2 +
(centers[i, 1] - centers[n_cities[j], 1])**2)
sij = 0
for k in range(len(all_x)):
if (all_x[k] - centers[i, 0])**2 + (
all_y[k] - centers[i, 1])**2 < radius**2:
sij += 1
sij = sij - mi - nj
if sij < 0:
sij = 0
try:
Tij = (mi * Nc_N * mi * nj) / ((mi + sij) *
(mi + nj + sij)) * 10
except ZeroDivisionError:
Tij = 0
if Tij > 75:
Tij = 75
if Tij > 1 and (i != n_cities[j]):
flux_store = np.vstack(
(flux_store, (Tij, i + 1, n_cities[j])))
work_place = np.zeros(self.num_agents)
work_store1 = np.zeros((num, 2))
flux_store = np.delete(flux_store, 0, 0)
for i in np.unique(flux_store[:, 1]):
place = np.where(flux_store[:, 1] == i)[0]
place1 = np.where(city_label == i)[0]
for j in place1:
for k in place:
if random.uniform(0, 100) < flux_store[k, 0]:
work_place[j] = flux_store[k, 2]
for i in range(len(work_store1)):
if work_place[i] != 0:
n = int(work_place[i])
work_store1[i, :] = centers[n, 0], centers[n, 1]
for i in range(self.num_agents):
home_store1[i, :] = int(all_x[i]), int(all_y[i])
work_store = np.int64(work_store1)
home_store = np.int64(home_store1)
for i in range(self.num_agents):
if mobility_data:
a = Agent(i, self, infection_rate, work_store, home_store)
self.schedule.add(a)
self.grid.place_agent(a, (int(all_x[i]), int(all_y[i])))
else:
a = Agent1(i, self, infection_rate, work_store, home_store)
self.schedule.add(a)
self.grid.place_agent(a, (int(all_x[i]), int(all_y[i])))
if i == first_infected:
a.infected = 1
self.datacollector = DataCollector(
model_reporters={"Tot infections": compute_informed},
agent_reporters={
"Infected": "infected",
"R-Number": "rnumber"
})
model using Mesa in Python.
'''
'''
Import libraries and packages
'''
from mesa import Model, Agent
from mesa.time import RandomActivation
from mesa.space import SingleGrid
from mesa.datacollection import DataCollector
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
'''
Agent (human) class with attributes and a step function
defining what actions to perform during each step
'''
class Human(Agent):
def __init__(self, unique_id, model, sex, attract, relationship_status, current_dating_partners, focal):
'''
Create a new agent.
Args:
sex: agent's sex (female or male)
attract: agent's attractiveness (between 1 and 10)
relationship_status: agent's marital status (single or union)
current_dating_partners: list of id's of agent's current dating current_dating_partners
focal: agent's probability to start a union
'''