2017-10-18 18:28:42 +00:00
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Soil Tutorial
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=============
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Introduction
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------------
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This notebook is an introduction to the soil agent-based social network
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simulation framework. In particular, we will focus on a specific use
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case: studying the propagation of news in a social network.
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The steps we will follow are:
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- Modelling the behavior of agents
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- Running the simulation using different configurations
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- Analysing the results of each simulation
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But before that, let’s import the soil module and networkx.
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2017-10-18 18:28:42 +00:00
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.. code:: ipython3
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import soil
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import networkx as nx
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%load_ext autoreload
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%autoreload 2
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%matplotlib inline
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# To display plots in the notebooed_
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Basic concepts
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--------------
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There are three main elements in a soil simulation:
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- The network topology. A simulation may use an existing NetworkX
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topology, or generate one on the fly
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- Agents. There are two types: 1) network agents, which are linked to a
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node in the topology, and 2) environment agents, which are freely
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assigned to the environment.
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- The environment. It assigns agents to nodes in the network, and
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stores the environment parameters (shared state for all agents).
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Soil is based on ``simpy``, which is an event-based network simulation
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library. Soil provides several abstractions over events to make
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developing agents easier. This means you can use events (timeouts,
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delays) in soil, but for the most part we will assume your models will
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be step-based.
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2017-10-18 18:28:42 +00:00
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Modeling behaviour
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------------------
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Our first step will be to model how every person in the social network
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reacts when it comes to news. We will follow a very simple model (a
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finite state machine).
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There are two types of people, those who have heard about a newsworthy
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event (infected) or those who have not (neutral). A neutral person may
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heard about the news either on the TV (with probability
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**prob_tv_spread**) or through their friends. Once a person has heard
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the news, they will spread it to their friends (with a probability
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**prob_neighbor_spread**). Some users do not have a TV, so they only
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rely on their friends.
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The spreading probabilities will change over time due to different
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factors. We will represent this variance using an environment agent.
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Network Agents
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~~~~~~~~~~~~~~
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A basic network agent in Soil would typically inherit from
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``soil.agents.NetworkAgent``, and define its behaviour in every step of
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the simulation by implementing a ``run(self)`` method. The most
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important attributes of the agent are:
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- ``agent.state``, a dictionary with the state of the agent. This tate
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will be saved in every step of the simulation. It can be accessed
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from the agent as well:
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.. code:: py
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a = soil.agents.NetworkAgent(env=env)
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agent.state['hours_of_sleep'] = 10
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# is the same as
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a['hours_of_sleep'] = 10
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The state of the agent is stored in every step of the simulation:
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``py print(a['hours_of_sleep', 10]) # hours of sleep before step #10 print(a[None, 0]) # whole state of the agent before step #0``
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- ``agent.env``, a reference to the environment. Most commonly used to
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get access to the environment parameters and the topology: \```py
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a.env.G.nodes() # Get all nodes ids in the topology
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a.env[‘minimum_hours_of_sleep’]
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\``\`
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Since our model is a finite state machine, we will be basing it on
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``soil.agents.FSM``.
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Agents that inherit from ``soil.agents.FSM`` do not need to specify a
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``step`` method. Instead, we describe each finite state with a function.
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To change to another state, a function may return the new state, or the
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``id`` of a state. If no state is returned, the state remains unchanged.
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The current state of the agent can be checked with
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``agent.state['id']``. That state id can be used to look for other
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networks in that specific state
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Our agent will have of two states, ``neutral`` (default) and
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``infected``.
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Here’s the code:
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.. code:: ipython3
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import random
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class NewsSpread(soil.agents.FSM):
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@soil.agents.default_state
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@soil.agents.state
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def neutral(self):
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r = random.random()
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if self['has_tv'] and r <= self.env['prob_tv_spread']:
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return self.infected
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return
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@soil.agents.state
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def infected(self):
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prob_infect = self.env['prob_neighbor_spread']
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for neighbor in self.get_neighboring_agents(state_id=self.neutral.id):
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r = random.random()
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if r < prob_infect:
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neighbor.set_state(self.infected.id)
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return
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Environment agents
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~~~~~~~~~~~~~~~~~~
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Environment agents allow us to control the state of the environment. In
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this case, we will use an environment agent to simulate a very viral
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event.
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When the event happens, the agent will modify the probability of
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spreading the rumor.
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.. code:: ipython3
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NEIGHBOR_FACTOR = 0.9
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TV_FACTOR = 0.5
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class NewsEnvironmentAgent(soil.agents.NetworkAgent):
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def step(self):
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if self.now == self['event_time']:
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self.env['prob_tv_spread'] = 1
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self.env['prob_neighbor_spread'] = 1
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elif self.now > self['event_time']:
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self.env['prob_tv_spread'] = self.env['prob_tv_spread'] * TV_FACTOR
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self.env['prob_neighbor_spread'] = self.env['prob_neighbor_spread'] * NEIGHBOR_FACTOR
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Testing the agents
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~~~~~~~~~~~~~~~~~~
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Feel free to skip this section if this is your first time with soil.
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Testing agents is not easy, and this is not a thorough testing process
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for agents. Rather, this section is aimed to show you how to access
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internal pats of soil so you can test your agents.
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First of all, let’s check if our network agent has the states we would
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expect:
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.. code:: ipython3
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NewsSpread.states
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.. parsed-literal::
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{'neutral': <function __main__.NewsSpread.neutral(self)>,
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'infected': <function __main__.NewsSpread.infected(self)>}
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Now, let’s run a simulation on a simple network. It is comprised of
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three nodes:
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.. code:: ipython3
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G = nx.Graph()
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G.add_edge(0, 1)
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G.add_edge(0, 2)
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G.add_edge(2, 3)
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G.add_node(4)
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pos = nx.spring_layout(G)
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nx.draw_networkx(G, pos, node_color='red')
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nx.draw_networkx(G, pos, nodelist=[0], node_color='blue')
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.. image:: output_21_0.png
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Let’s run a simple simulation that assigns a NewsSpread agent to all the
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nodes in that network. Notice how node 0 is the only one with a TV.
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.. code:: ipython3
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import importlib
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importlib.reload(soil.agents)
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.. parsed-literal::
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<module 'soil.agents' from '/mnt/data/home/j/git/lab.gsi/soil/soil/soil/agents/__init__.py'>
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2017-10-18 18:28:42 +00:00
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.. code:: ipython3
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env_params = {
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'prob_tv_spread': 0,
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'prob_neighbor_spread': 0
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}
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MAX_TIME = 100
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EVENT_TIME = 10
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sim = soil.Simulation(topology=G,
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num_trials=1,
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max_time=MAX_TIME,
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environment_agents=[{'agent_type': NewsEnvironmentAgent,
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'state': {
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'event_time': EVENT_TIME
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}}],
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network_agents=[{'agent_type': NewsSpread,
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'weight': 1}],
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states={0: {'has_tv': True}},
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default_state={'has_tv': False},
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environment_params=env_params)
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env = sim.run_simulation(dry_run=True)[0]
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Now we can access the results of the simulation and compare them to our
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expected results
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.. code:: ipython3
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agents = list(env.network_agents)
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# Until the event, all agents are neutral
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for t in range(10):
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for a in agents:
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assert a['state_id', t] == a.neutral.id
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# After the event, the node with a TV is infected, the rest are not
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assert agents[0]['has_tv']
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assert agents[0]['state_id', 11] == NewsSpread.infected.id
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assert not agents[2]['has_tv']
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assert agents[2]['state_id', 11] == NewsSpread.neutral.id
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# At the end, the agents connected to the infected one will probably be infected, too.
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assert agents[1]['state_id', MAX_TIME] == NewsSpread.infected.id
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assert agents[2]['state_id', MAX_TIME] == NewsSpread.infected.id
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# But the node with no friends should not be affected
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assert agents[4]['state_id', MAX_TIME] == NewsSpread.neutral.id
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Lastly, let’s see if the probabilities have decreased as expected:
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.. code:: ipython3
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assert abs(env.environment_params['prob_neighbor_spread'] - (NEIGHBOR_FACTOR**(MAX_TIME-1-10))) < 10e-4
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assert abs(env.environment_params['prob_tv_spread'] - (TV_FACTOR**(MAX_TIME-1-10))) < 10e-6
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Running the simulation
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----------------------
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To run a simulation, we need a configuration. Soil can load
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configurations from python dictionaries as well as JSON and YAML files.
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For this demo, we will use a python dictionary:
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.. code:: ipython3
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config = {
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'name': 'ExampleSimulation',
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'max_time': 20,
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'interval': 1,
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'num_trials': 1,
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'network_params': {
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'generator': 'complete_graph',
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'n': 500,
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},
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'network_agents': [
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{
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'agent_type': NewsSpread,
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'weight': 1,
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'state': {
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'has_tv': False
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}
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},
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{
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'agent_type': NewsSpread,
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'weight': 2,
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'state': {
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'has_tv': True
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}
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}
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],
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'environment_agents':[
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{'agent_type': NewsEnvironmentAgent,
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'state': {
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'event_time': 10
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}
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}
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],
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'states': [ {'has_tv': True} ],
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'environment_params':{
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'prob_tv_spread': 0.01,
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'prob_neighbor_spread': 0.5
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}
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}
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|
2023-03-23 13:49:09 +00:00
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Let’s run our simulation:
|
2017-10-18 18:28:42 +00:00
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.. code:: ipython3
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2023-03-23 13:49:09 +00:00
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soil.simulation.run_from_config(config, dry_run=True)
|
2017-10-18 18:28:42 +00:00
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In real life, you probably want to run several simulations, varying some
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of the parameters so that you can compare and answer your research
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questions.
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For instance:
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- Does the outcome depend on the structure of our network? We will use
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different generation algorithms to compare them (Barabasi-Albert and
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Erdos-Renyi)
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- How does neighbor spreading probability affect my simulation? We will
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try probability values in the range of [0, 0.4], in intervals of 0.1.
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.. code:: ipython3
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network_1 = {
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'generator': 'erdos_renyi_graph',
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'n': 500,
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'p': 0.1
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}
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network_2 = {
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'generator': 'barabasi_albert_graph',
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'n': 500,
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'm': 2
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}
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for net in [network_1, network_2]:
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for i in range(5):
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prob = i / 10
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config['environment_params']['prob_neighbor_spread'] = prob
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config['network_params'] = net
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|
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config['name'] = 'Spread_{}_prob_{}'.format(net['generator'], prob)
|
2023-03-23 13:49:09 +00:00
|
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|
|
s = soil.simulation.run_from_config(config, exporters=['default', 'csv'])
|
2017-10-18 18:28:42 +00:00
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|
2023-03-23 13:49:09 +00:00
|
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|
|
The results are conveniently stored in sqlite (history of agent and
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|
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environment state) and the configuration is saved in a YAML file.
|
2017-10-18 18:28:42 +00:00
|
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|
2023-03-23 13:49:09 +00:00
|
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You can also export the results to GEXF format (dynamic network) and CSV
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using .\ ``run_from_config(config, dump=['gexf', 'csv'])`` or the
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command line flags ``--graph --csv``.
|
2017-10-18 18:28:42 +00:00
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|
.. code:: ipython3
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|
|
!tree soil_output
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|
|
!du -xh soil_output/*
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.. parsed-literal::
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|
2023-03-23 13:49:09 +00:00
|
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|
[01;34msoil_output[00m
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├── [01;34mSpread_barabasi_albert_graph_prob_0.0[00m
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│ ├── [01;34mbackup[00m
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_12.57.35
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_14.06.30
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_14.19.33
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_14.30.56
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_12.57.35
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_14.06.31
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_14.19.33
|
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│ │ ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_14.30.56
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_12.57.35
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_14.06.31
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_14.19.33
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_14.30.56
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_12.57.35
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.06.31
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.19.33
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.30.56
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_12.57.35
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.06.31
|
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|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.19.33
|
|
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|
|
│ │ └── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.30.56
|
|
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|
|
│ ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.0.sqlite
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite
|
|
|
|
|
|
│ └── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv
|
|
|
|
|
|
├── [01;34mSpread_barabasi_albert_graph_prob_0.1[00m
|
|
|
|
|
|
│ ├── [01;34mbackup[00m
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.dumped.yml@2023-03-23_12.57.35
|
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|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.dumped.yml@2023-03-23_14.06.31
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.dumped.yml@2023-03-23_14.19.34
|
|
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|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.dumped.yml@2023-03-23_14.30.56
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.sqlite@2023-03-23_12.57.35
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.sqlite@2023-03-23_14.06.31
|
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|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.sqlite@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1.sqlite@2023-03-23_14.30.56
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.csv@2023-03-23_12.57.35
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.csv@2023-03-23_14.06.31
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.csv@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.csv@2023-03-23_14.30.56
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite@2023-03-23_12.57.35
|
|
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|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.06.31
|
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|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.19.34
|
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|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.30.56
|
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|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.stats.csv@2023-03-23_12.57.35
|
|
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|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.06.31
|
|
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|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ └── Spread_barabasi_albert_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.30.56
|
|
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|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.1.dumped.yml
|
|
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|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.1.sqlite
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.csv
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite
|
|
|
|
|
|
│ └── Spread_barabasi_albert_graph_prob_0.1_trial_0.stats.csv
|
|
|
|
|
|
├── [01;34mSpread_barabasi_albert_graph_prob_0.2[00m
|
|
|
|
|
|
│ ├── [01;34mbackup[00m
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_12.57.36
|
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|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_14.06.31
|
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|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_14.19.34
|
|
|
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|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_14.30.56
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.sqlite@2023-03-23_12.57.36
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.sqlite@2023-03-23_14.06.31
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.sqlite@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2.sqlite@2023-03-23_14.30.57
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.csv@2023-03-23_12.57.36
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.csv@2023-03-23_14.06.31
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.csv@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.csv@2023-03-23_14.30.57
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.sqlite@2023-03-23_12.57.36
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.06.31
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.30.57
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.stats.csv@2023-03-23_12.57.36
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.06.31
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ └── Spread_barabasi_albert_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.30.57
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.2.sqlite
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.csv
|
|
|
|
|
|
│ ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.sqlite
|
|
|
|
|
|
│ └── Spread_barabasi_albert_graph_prob_0.2_trial_0.stats.csv
|
|
|
|
|
|
├── [01;34mSpread_barabasi_albert_graph_prob_0.3[00m
|
|
|
|
|
|
│ ├── [01;34mbackup[00m
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.dumped.yml@2023-03-23_12.57.36
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.dumped.yml@2023-03-23_14.06.31
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.dumped.yml@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.dumped.yml@2023-03-23_14.30.57
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.sqlite@2023-03-23_12.57.36
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.sqlite@2023-03-23_14.06.32
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.sqlite@2023-03-23_14.19.34
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3.sqlite@2023-03-23_14.30.57
|
|
|
|
|
|
│ │ ├── Spread_barabasi_albert_graph_prob_0.3_trial_0.csv@2023-03-23_12.57.36
|
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│ │ ├── Spread_barabasi_albert_graph_prob_0.3_trial_0.csv@2023-03-23_14.19.34
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│ │ ├── Spread_barabasi_albert_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.19.34
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│ │ └── Spread_barabasi_albert_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.30.57
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│ │ ├── Spread_barabasi_albert_graph_prob_0.4.sqlite@2023-03-23_14.06.32
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│ │ ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.06.32
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│ │ ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.19.35
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│ │ └── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.30.57
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│ ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.csv
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│ ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.sqlite
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│ └── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv
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├── [01;34mSpread_erdos_renyi_graph_prob_0.0[00m
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml@2023-03-23_14.19.24
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml@2023-03-23_14.30.47
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_12.57.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_14.06.22
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_14.19.25
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_14.30.47
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_12.57.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_14.06.22
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_14.19.25
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_14.30.47
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_12.57.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.06.22
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.19.25
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.30.47
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_12.57.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.06.22
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│ │ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.19.25
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│ │ └── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.30.47
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│ ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml
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│ ├── Spread_erdos_renyi_graph_prob_0.0.sqlite
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│ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv
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│ ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite
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│ └── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv
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├── [01;34mSpread_erdos_renyi_graph_prob_0.1[00m
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│ ├── [01;34mbackup[00m
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_12.57.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_14.06.24
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_14.19.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_14.30.49
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_12.57.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_14.06.24
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_14.19.27
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_14.30.49
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_12.57.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_14.06.24
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_14.19.27
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_14.30.49
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_12.57.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.06.24
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.19.27
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.30.49
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_12.57.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.06.24
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│ │ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.19.27
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│ │ └── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.30.49
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│ ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml
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│ ├── Spread_erdos_renyi_graph_prob_0.1.sqlite
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│ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv
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│ ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite
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│ └── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv
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├── [01;34mSpread_erdos_renyi_graph_prob_0.2[00m
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│ ├── [01;34mbackup[00m
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_12.57.30
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_14.06.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_14.19.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_14.30.51
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_12.57.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_14.06.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_14.19.29
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_14.30.51
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_12.57.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_14.06.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_14.19.29
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_14.30.51
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_12.57.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.06.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.19.29
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.30.51
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_12.57.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.06.26
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│ │ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.19.29
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│ │ └── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.30.51
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│ ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml
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│ ├── Spread_erdos_renyi_graph_prob_0.2.sqlite
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│ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv
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│ ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite
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│ └── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv
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├── [01;34mSpread_erdos_renyi_graph_prob_0.3[00m
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│ ├── [01;34mbackup[00m
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_12.57.32
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_14.06.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_14.19.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_14.30.53
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_12.57.33
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_14.06.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_14.19.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_14.30.53
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_12.57.33
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_14.06.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_14.19.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_14.30.53
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_12.57.33
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_14.06.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_14.19.31
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_14.30.53
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_12.57.33
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.06.28
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│ │ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.19.31
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│ │ └── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.30.53
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│ ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml
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│ ├── Spread_erdos_renyi_graph_prob_0.3.sqlite
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|
│ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv
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|
│ ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite
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|
│ └── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv
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└── [01;34mSpread_erdos_renyi_graph_prob_0.4[00m
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├── [01;34mbackup[00m
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│ ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_12.57.34
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│ ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_14.06.30
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│ ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_14.19.33
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│ ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_14.30.55
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│ ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_12.57.35
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│ ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_14.06.30
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│ ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_14.19.33
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│ ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_14.30.56
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_12.57.35
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_14.06.30
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_14.19.33
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_14.30.56
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_12.57.35
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.06.30
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.19.33
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.30.56
|
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_12.57.35
|
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.06.30
|
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│ ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.19.33
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│ └── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.30.56
|
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├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml
|
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├── Spread_erdos_renyi_graph_prob_0.4.sqlite
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├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv
|
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|
├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite
|
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└── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv
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|
20 directories, 250 files
|
|
|
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|
|
1.3M soil_output/Spread_barabasi_albert_graph_prob_0.0/backup
|
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|
|
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|
1.7M soil_output/Spread_barabasi_albert_graph_prob_0.0
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1.3M soil_output/Spread_barabasi_albert_graph_prob_0.1/backup
|
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1.7M soil_output/Spread_barabasi_albert_graph_prob_0.1
|
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1.3M soil_output/Spread_barabasi_albert_graph_prob_0.2/backup
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1.6M soil_output/Spread_barabasi_albert_graph_prob_0.2
|
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1.3M soil_output/Spread_barabasi_albert_graph_prob_0.3/backup
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1.7M soil_output/Spread_barabasi_albert_graph_prob_0.3
|
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1.3M soil_output/Spread_barabasi_albert_graph_prob_0.4/backup
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1.7M soil_output/Spread_barabasi_albert_graph_prob_0.4
|
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|
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.0/backup
|
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|
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.0
|
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|
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.1/backup
|
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|
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.1
|
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|
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|
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.2/backup
|
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|
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.2
|
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|
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.3/backup
|
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|
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.3
|
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|
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.4/backup
|
|
|
|
|
|
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.4
|
2017-10-18 18:28:42 +00:00
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|
Analysing the results
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---------------------
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Loading data
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|
~~~~~~~~~~~~
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Once the simulations are over, we can use soil to analyse the results.
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|
Soil allows you to load results for specific trials, or for a set of
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|
trials if you specify a pattern. The specific methods are:
|
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- ``analysis.read_data(<directory pattern>)`` to load all the results
|
2023-03-23 13:49:09 +00:00
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|
from a directory. e.g. \ ``read_data('my_simulation/')``. For each
|
2017-10-18 18:28:42 +00:00
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trial it finds in each folder matching the pattern, it will return
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|
the dumped configuration for the simulation, the results of the
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trial, and the configuration itself. By default, it will try to load
|
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|
data from the sqlite database.
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- ``analysis.read_csv(<csv_file>)`` to load all the results from a CSV
|
2023-03-23 13:49:09 +00:00
|
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|
file.
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e.g. \ ``read_csv('my_simulation/my_simulation_trial0.environment.csv')``
|
2017-10-18 18:28:42 +00:00
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- ``analysis.read_sql(<sqlite_file>)`` to load all the results from a
|
2023-03-23 13:49:09 +00:00
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|
sqlite database .
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|
e.g. \ ``read_sql('my_simulation/my_simulation_trial0.db.sqlite')``
|
2017-10-18 18:28:42 +00:00
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|
2023-03-23 13:49:09 +00:00
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Let’s see it in action by loading the stored results into a pandas
|
2017-10-18 18:28:42 +00:00
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dataframe:
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|
.. code:: ipython3
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2023-03-23 13:49:09 +00:00
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from soil import analysis
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import pandas as pd
|
2017-10-18 18:28:42 +00:00
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.. code:: ipython3
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|
2023-03-23 13:49:09 +00:00
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df = analysis.read_csv('soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.csv')
|
2017-10-18 18:28:42 +00:00
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df
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.. raw:: html
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<div>
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<style scoped>
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.dataframe tbody tr th:only-of-type {
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vertical-align: middle;
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}
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.dataframe tbody tr th {
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vertical-align: top;
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2017-10-18 18:28:42 +00:00
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}
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2023-03-23 13:49:09 +00:00
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.dataframe thead tr th {
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2017-10-18 18:28:42 +00:00
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text-align: left;
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}
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2023-03-23 13:49:09 +00:00
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.dataframe thead tr:last-of-type th {
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text-align: right;
|
2017-10-18 18:28:42 +00:00
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}
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</style>
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<table border="1" class="dataframe">
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<thead>
|
2023-03-23 13:49:09 +00:00
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<tr>
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<th>key</th>
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<th>SEED</th>
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<th colspan="9" halign="left">alive</th>
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<th>...</th>
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<th colspan="10" halign="left">state_id</th>
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</tr>
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<tr>
|
2017-10-18 18:28:42 +00:00
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<th>agent_id</th>
|
2023-03-23 13:49:09 +00:00
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<th>env</th>
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<th>0</th>
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<th>1</th>
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<th>10</th>
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<th>100</th>
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<th>101</th>
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<th>102</th>
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<th>103</th>
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<th>104</th>
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<th>105</th>
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<th>...</th>
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<th>90</th>
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<th>91</th>
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<th>92</th>
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<th>93</th>
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<th>94</th>
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<th>95</th>
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<th>96</th>
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<th>97</th>
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<th>98</th>
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<th>99</th>
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</tr>
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<tr>
|
2017-10-18 18:28:42 +00:00
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<th>t_step</th>
|
2023-03-23 13:49:09 +00:00
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
|
2017-10-18 18:28:42 +00:00
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</tr>
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</thead>
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<tbody>
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<tr>
|
2023-03-23 13:49:09 +00:00
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<th>0.0</th>
|
|
|
|
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|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
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<td>True</td>
|
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<td>True</td>
|
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<td>True</td>
|
|
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<td>True</td>
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<td>True</td>
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<td>True</td>
|
|
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|
|
<td>True</td>
|
|
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|
<td>True</td>
|
|
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<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
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<td>neutral</td>
|
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<td>neutral</td>
|
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<td>neutral</td>
|
|
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<td>neutral</td>
|
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|
|
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<td>neutral</td>
|
|
|
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|
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<td>neutral</td>
|
|
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<td>neutral</td>
|
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<td>neutral</td>
|
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<td>neutral</td>
|
|
|
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<td>neutral</td>
|
|
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</tr>
|
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<tr>
|
2023-03-23 13:49:09 +00:00
|
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|
<th>1.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>2.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>3.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>4.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>5.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>...</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>6.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>7.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>8.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>9.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>10.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>11.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>12.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>13.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>14.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>15.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>16.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<tr>
|
|
|
|
|
|
<th>17.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>18.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>19.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
|
|
|
|
|
<p>20 rows × 2507 columns</p>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Soil can also process the data for us and split the results into
|
|
|
|
|
|
environment attributes and agent attributes:
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
|
|
|
|
|
env, agents = analysis.split_processed(df)
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
|
|
|
|
|
agents
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. raw:: html
|
|
|
|
|
|
|
|
|
|
|
|
<div>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<style scoped>
|
|
|
|
|
|
.dataframe tbody tr th:only-of-type {
|
|
|
|
|
|
vertical-align: middle;
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
.dataframe tbody tr th {
|
|
|
|
|
|
vertical-align: top;
|
2017-10-18 18:28:42 +00:00
|
|
|
|
}
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.dataframe thead tr th {
|
2017-10-18 18:28:42 +00:00
|
|
|
|
text-align: left;
|
|
|
|
|
|
}
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.dataframe thead tr:last-of-type th {
|
|
|
|
|
|
text-align: right;
|
2017-10-18 18:28:42 +00:00
|
|
|
|
}
|
|
|
|
|
|
</style>
|
|
|
|
|
|
<table border="1" class="dataframe">
|
|
|
|
|
|
<thead>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<tr>
|
|
|
|
|
|
<th>key</th>
|
|
|
|
|
|
<th colspan="10" halign="left">alive</th>
|
|
|
|
|
|
<th>...</th>
|
|
|
|
|
|
<th colspan="10" halign="left">state_id</th>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>agent_id</th>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>0</th>
|
|
|
|
|
|
<th>1</th>
|
|
|
|
|
|
<th>10</th>
|
|
|
|
|
|
<th>100</th>
|
|
|
|
|
|
<th>101</th>
|
|
|
|
|
|
<th>102</th>
|
|
|
|
|
|
<th>103</th>
|
|
|
|
|
|
<th>104</th>
|
|
|
|
|
|
<th>105</th>
|
|
|
|
|
|
<th>106</th>
|
|
|
|
|
|
<th>...</th>
|
|
|
|
|
|
<th>90</th>
|
|
|
|
|
|
<th>91</th>
|
|
|
|
|
|
<th>92</th>
|
|
|
|
|
|
<th>93</th>
|
|
|
|
|
|
<th>94</th>
|
|
|
|
|
|
<th>95</th>
|
|
|
|
|
|
<th>96</th>
|
|
|
|
|
|
<th>97</th>
|
|
|
|
|
|
<th>98</th>
|
|
|
|
|
|
<th>99</th>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>t_step</th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<th></th>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</thead>
|
|
|
|
|
|
<tbody>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>0.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>1.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>2.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>3.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>...</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>4.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>5.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>6.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>7.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>8.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>9.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>10.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>11.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>12.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>13.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>14.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<tr>
|
|
|
|
|
|
<th>15.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>16.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>17.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>18.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>19.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
|
|
|
|
|
<p>20 rows × 2504 columns</p>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
The index of the results are the simulation step. Hence, we can access
|
|
|
|
|
|
the state of the simulation at a given step (e.g., 13):
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
|
|
|
|
|
agents.loc[13, 'state_id']
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. parsed-literal::
|
|
|
|
|
|
|
|
|
|
|
|
agent_id
|
|
|
|
|
|
0 infected
|
|
|
|
|
|
1 infected
|
|
|
|
|
|
10 infected
|
|
|
|
|
|
100 infected
|
|
|
|
|
|
101 infected
|
|
|
|
|
|
...
|
|
|
|
|
|
95 infected
|
|
|
|
|
|
96 infected
|
|
|
|
|
|
97 infected
|
|
|
|
|
|
98 infected
|
|
|
|
|
|
99 infected
|
|
|
|
|
|
Name: 13.0, Length: 500, dtype: object
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Or, we can perform more complex tasks such as showing the agents that
|
|
|
|
|
|
have changed their state between two simulation steps (2 and 1):
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
|
|
|
|
|
(agents.loc[2]['state_id'] != agents.loc[1]['state_id']).sum()
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. parsed-literal::
|
|
|
|
|
|
|
|
|
|
|
|
2
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
To focus on specific agents, we can swap the levels of the index:
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
agents.swaplevel(axis=1)
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. raw:: html
|
|
|
|
|
|
|
|
|
|
|
|
<div>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<style scoped>
|
|
|
|
|
|
.dataframe tbody tr th:only-of-type {
|
|
|
|
|
|
vertical-align: middle;
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
.dataframe tbody tr th {
|
|
|
|
|
|
vertical-align: top;
|
2017-10-18 18:28:42 +00:00
|
|
|
|
}
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.dataframe thead tr th {
|
2017-10-18 18:28:42 +00:00
|
|
|
|
text-align: left;
|
|
|
|
|
|
}
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.dataframe thead tr:last-of-type th {
|
|
|
|
|
|
text-align: right;
|
2017-10-18 18:28:42 +00:00
|
|
|
|
}
|
|
|
|
|
|
</style>
|
|
|
|
|
|
<table border="1" class="dataframe">
|
|
|
|
|
|
<thead>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>agent_id</th>
|
|
|
|
|
|
<th>0</th>
|
|
|
|
|
|
<th>1</th>
|
|
|
|
|
|
<th>10</th>
|
|
|
|
|
|
<th>100</th>
|
|
|
|
|
|
<th>101</th>
|
|
|
|
|
|
<th>102</th>
|
|
|
|
|
|
<th>103</th>
|
|
|
|
|
|
<th>104</th>
|
|
|
|
|
|
<th>105</th>
|
|
|
|
|
|
<th>106</th>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>...</th>
|
|
|
|
|
|
<th>90</th>
|
|
|
|
|
|
<th>91</th>
|
|
|
|
|
|
<th>92</th>
|
|
|
|
|
|
<th>93</th>
|
|
|
|
|
|
<th>94</th>
|
|
|
|
|
|
<th>95</th>
|
|
|
|
|
|
<th>96</th>
|
|
|
|
|
|
<th>97</th>
|
|
|
|
|
|
<th>98</th>
|
|
|
|
|
|
<th>99</th>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>key</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>alive</th>
|
|
|
|
|
|
<th>...</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
|
|
|
|
|
<th>state_id</th>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>t_step</th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
</thead>
|
|
|
|
|
|
<tbody>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>0.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>1.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>2.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>3.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>4.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>5.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>6.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>7.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>8.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>9.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>10.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>11.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>12.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>13.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>14.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>15.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>16.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>17.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>18.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>19.0</th>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<p>20 rows × 2504 columns</p>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</div>
|
|
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|
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|
|
|
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|
|
Plotting data
|
|
|
|
|
|
~~~~~~~~~~~~~
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
If you don’t want to work with pandas, you can also use some pre-defined
|
2017-10-18 18:28:42 +00:00
|
|
|
|
functions from soil to conveniently plot the results:
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
analysis.plot_all('soil_output/Spread_barabasi_albert_graph_prob_0.0/', analysis.get_count, 'state_id');
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_55_0.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
analysis.plot_all('soil_output/Spread_barabasi_albert_graph_prob_0.3/', analysis.get_count, 'state_id');
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_56_0.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
You can use wildcards in the results path:
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. code:: ipython3
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
analysis.plot_all('soil_output/Spread_barabasi*/', analysis.get_count, 'state_id');
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_58_0.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
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|
|
|
|
|
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|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_58_1.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
|
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|
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|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_58_2.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_58_3.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
|
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|
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|
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|
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|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_58_4.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
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|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
If we compare these results to those of the other graph model (a
|
|
|
|
|
|
fully-connected graph), we can see a stark difference:
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. code:: ipython3
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
analysis.plot_all('soil_output/Spread_erdos*', analysis.get_count, 'state_id');
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_60_0.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
2023-03-23 13:49:09 +00:00
|
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|
|
.. image:: output_60_1.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
2023-03-23 13:49:09 +00:00
|
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|
|
.. image:: output_60_2.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_60_3.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
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|
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|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_60_4.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
The previous cells were using the ``count_value`` function for
|
|
|
|
|
|
aggregation. There’s another function to plot numeral values:
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. code:: ipython3
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
analysis.plot_all('soil_output/Spread_erdos*', analysis.get_value, 'prob_tv_spread');
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_62_0.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
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|
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|
|
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_62_1.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
|
|
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|
|
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_62_2.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
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|
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|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_62_3.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
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|
.. image:: output_62_4.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
|
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|
|
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|
|
Manually plotting with pandas
|
|
|
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
|
|
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Although the simplest way to visualize the results of a simulation is to
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use the built-in methods in the analysis module, sometimes the setup is
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more complicated and we need to explore the data a little further.
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For that, we can use native pandas over the results.
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Soil provides some convenience methods to simplify common operations:
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- ``analysis.split_df`` to separate a history dataframe into
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environment and agent parameters.
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- ``analysis.get_count`` to get a dataframe with the value counts for
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different attributes during the simulation.
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- ``analysis.get_value`` to get the evolution of the value of an
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attribute during the simulation.
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And, as we saw earlier, ``analysis.process`` can turn a dataframe in
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canonical form into a dataframe with a column per attribute.
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.. code:: ipython3
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2023-03-23 13:49:09 +00:00
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!ls soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0*
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2017-10-18 18:28:42 +00:00
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.. parsed-literal::
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2023-03-23 13:49:09 +00:00
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soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0.dumped.yml
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soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0.sqlite
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soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.csv
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soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite
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soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv
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2017-10-18 18:28:42 +00:00
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.. code:: ipython3
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2023-03-23 13:49:09 +00:00
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df = analysis.read_sql('soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite')
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df
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2017-10-18 18:28:42 +00:00
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.. raw:: html
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<div>
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2023-03-23 13:49:09 +00:00
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<style scoped>
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.dataframe tbody tr th:only-of-type {
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vertical-align: middle;
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}
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.dataframe tbody tr th {
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vertical-align: top;
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2017-10-18 18:28:42 +00:00
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}
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2023-03-23 13:49:09 +00:00
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.dataframe thead tr th {
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2017-10-18 18:28:42 +00:00
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text-align: left;
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}
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2023-03-23 13:49:09 +00:00
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.dataframe thead tr:last-of-type th {
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text-align: right;
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}
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</style>
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<table border="1" class="dataframe">
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<thead>
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2023-03-23 13:49:09 +00:00
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<tr>
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<th>key</th>
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<th>SEED</th>
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<th colspan="9" halign="left">alive</th>
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<th>...</th>
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<th colspan="10" halign="left">state_id</th>
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</tr>
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<tr>
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<th>dict_id</th>
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<th>env</th>
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<th>0</th>
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<th>1</th>
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<th>10</th>
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<th>100</th>
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<th>101</th>
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<th>102</th>
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<th>103</th>
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<th>104</th>
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<th>105</th>
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<th>...</th>
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<th>90</th>
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<th>91</th>
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<th>92</th>
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<th>93</th>
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<th>94</th>
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<th>95</th>
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<th>96</th>
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<th>97</th>
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<th>98</th>
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<th>99</th>
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2017-10-18 18:28:42 +00:00
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</tr>
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<tr>
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<th>t_step</th>
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2023-03-23 13:49:09 +00:00
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
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<th></th>
|
2017-10-18 18:28:42 +00:00
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<th></th>
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<th></th>
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<th></th>
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</tr>
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</thead>
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<tbody>
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<tr>
|
2023-03-23 13:49:09 +00:00
|
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<th>0.0</th>
|
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|
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|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
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|
<td>True</td>
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<td>True</td>
|
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|
|
<td>True</td>
|
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<td>True</td>
|
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<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
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|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
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|
<td>True</td>
|
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|
|
|
|
<td>True</td>
|
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|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
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|
<td>neutral</td>
|
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|
<td>neutral</td>
|
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|
<td>neutral</td>
|
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<td>neutral</td>
|
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<td>neutral</td>
|
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<td>neutral</td>
|
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<td>neutral</td>
|
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<td>neutral</td>
|
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<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
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<td>neutral</td>
|
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|
</tr>
|
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|
<tr>
|
2023-03-23 13:49:09 +00:00
|
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|
<th>1.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>2.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>3.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>4.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>5.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>6.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>7.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>8.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>9.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>10.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>neutral</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>neutral</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>11.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>neutral</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>12.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>...</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>13.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>14.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>15.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>16.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>17.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<th>18.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>...</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
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<td>infected</td>
|
|
|
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<td>infected</td>
|
|
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<td>infected</td>
|
|
|
|
|
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<td>infected</td>
|
|
|
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|
|
<td>infected</td>
|
|
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|
|
|
<td>infected</td>
|
|
|
|
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|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
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|
<td>infected</td>
|
|
|
|
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|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
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|
<tr>
|
2023-03-23 13:49:09 +00:00
|
|
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<th>19.0</th>
|
|
|
|
|
|
<td>Spread_barabasi_albert_graph_prob_0.0_trial_0</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
|
|
|
|
|
<td>True</td>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
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|
|
<td>infected</td>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
<td>infected</td>
|
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|
|
|
<td>infected</td>
|
|
|
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|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
<td>infected</td>
|
|
|
|
|
|
</tr>
|
|
|
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|
|
</tbody>
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|
</table>
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<p>20 rows × 3008 columns</p>
|
2017-10-18 18:28:42 +00:00
|
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|
</div>
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|
2023-03-23 13:49:09 +00:00
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|
Let’s look at the evolution of agent parameters in the simulation
|
2017-10-18 18:28:42 +00:00
|
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|
.. code:: ipython3
|
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|
2023-03-23 13:49:09 +00:00
|
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|
|
df.plot()
|
2017-10-18 18:28:42 +00:00
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.. parsed-literal::
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|
2023-03-23 13:49:09 +00:00
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|
<Axes: xlabel='t_step'>
|
2017-10-18 18:28:42 +00:00
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2023-03-23 13:49:09 +00:00
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.. image:: output_68_1.png
|
2017-10-18 18:28:42 +00:00
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|
2023-03-23 13:49:09 +00:00
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As we can see, ``event_time`` and ``interval`` are cluttering our
|
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|
results,
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|
2017-10-18 18:28:42 +00:00
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|
.. code:: ipython3
|
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|
2023-03-23 13:49:09 +00:00
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|
del df['interval']
|
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|
del df['event_time']
|
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df.plot()
|
2017-10-18 18:28:42 +00:00
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.. parsed-literal::
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|
2023-03-23 13:49:09 +00:00
|
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|
<Axes: xlabel='t_step'>
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.. image:: output_70_1.png
|
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|
The ``soil.analysis`` module also provides convenient functions to count
|
|
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|
|
|
the number of agents in a given state:
|
|
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|
.. code:: ipython3
|
2017-10-18 18:28:42 +00:00
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
analysis.get_count(agents, 'state_id').plot();
|
2017-10-18 18:28:42 +00:00
|
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|
2023-03-23 13:49:09 +00:00
|
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|
.. image:: output_72_0.png
|
2017-10-18 18:28:42 +00:00
|
|
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|
|
Dealing with bigger data
|
|
|
|
|
|
------------------------
|
|
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|
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|
|
.. code:: ipython3
|
|
|
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|
|
from soil import analysis
|
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|
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|
|
.. code:: ipython3
|
|
|
|
|
|
|
|
|
|
|
|
!du -xsh ../rabbits/soil_output/rabbits_example/
|
|
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|
|
|
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|
.. parsed-literal::
|
|
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|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
1.1M ../rabbits/soil_output/rabbits_example/
|
2017-10-18 18:28:42 +00:00
|
|
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|
|
If we tried to load the entire history, we would probably run out of
|
|
|
|
|
|
memory. Hence, it is recommended that you also specify the attributes
|
|
|
|
|
|
you are interested in.
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
p = analysis.plot_all('../rabbits/soil_output/rabbits_example/', analysis.get_count, 'state_id')
|
2017-10-18 18:28:42 +00:00
|
|
|
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|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_77_0.png
|
|
|
|
|
|
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
|
|
|
|
|
!ls ../rabbits/soil_output/rabbits_example
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. parsed-literal::
|
|
|
|
|
|
|
|
|
|
|
|
backup rabbits_example.sqlite
|
|
|
|
|
|
rabbits_example.dumped.yml rabbits_example_trial_0.sqlite
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
df = analysis.read_sql('../rabbits/soil_output/rabbits_example/rabbits_example_trial_0.sqlite', keys=['state_id', 'rabbits_alive'])
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
df
|
2017-10-18 18:28:42 +00:00
|
|
|
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|
|
|
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|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. raw:: html
|
|
|
|
|
|
|
|
|
|
|
|
<div>
|
|
|
|
|
|
<style scoped>
|
|
|
|
|
|
.dataframe tbody tr th:only-of-type {
|
|
|
|
|
|
vertical-align: middle;
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
.dataframe tbody tr th {
|
|
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|
|
|
vertical-align: top;
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
.dataframe thead tr th {
|
|
|
|
|
|
text-align: left;
|
|
|
|
|
|
}
|
|
|
|
|
|
|
|
|
|
|
|
.dataframe thead tr:last-of-type th {
|
|
|
|
|
|
text-align: right;
|
|
|
|
|
|
}
|
|
|
|
|
|
</style>
|
|
|
|
|
|
<table border="1" class="dataframe">
|
|
|
|
|
|
<thead>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>key</th>
|
|
|
|
|
|
<th>rabbits_alive</th>
|
|
|
|
|
|
<th colspan="20" halign="left">state_id</th>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>dict_id</th>
|
|
|
|
|
|
<th>env</th>
|
|
|
|
|
|
<th>0</th>
|
|
|
|
|
|
<th>1</th>
|
|
|
|
|
|
<th>10</th>
|
|
|
|
|
|
<th>100</th>
|
|
|
|
|
|
<th>101</th>
|
|
|
|
|
|
<th>102</th>
|
|
|
|
|
|
<th>103</th>
|
|
|
|
|
|
<th>104</th>
|
|
|
|
|
|
<th>105</th>
|
|
|
|
|
|
<th>...</th>
|
|
|
|
|
|
<th>90</th>
|
|
|
|
|
|
<th>91</th>
|
|
|
|
|
|
<th>92</th>
|
|
|
|
|
|
<th>93</th>
|
|
|
|
|
|
<th>94</th>
|
|
|
|
|
|
<th>95</th>
|
|
|
|
|
|
<th>96</th>
|
|
|
|
|
|
<th>97</th>
|
|
|
|
|
|
<th>98</th>
|
|
|
|
|
|
<th>99</th>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>t_step</th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
<th></th>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</thead>
|
|
|
|
|
|
<tbody>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>0.0</th>
|
|
|
|
|
|
<td>0</td>
|
|
|
|
|
|
<td>newborn</td>
|
|
|
|
|
|
<td>newborn</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>2.0</th>
|
|
|
|
|
|
<td>0</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>16.0</th>
|
|
|
|
|
|
<td>0</td>
|
|
|
|
|
|
<td>pregnant</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>49.0</th>
|
|
|
|
|
|
<td>8</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>51.0</th>
|
|
|
|
|
|
<td>8</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
<td>nan</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>...</th>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>739.0</th>
|
|
|
|
|
|
<td>15</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>742.0</th>
|
|
|
|
|
|
<td>14</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>743.0</th>
|
|
|
|
|
|
<td>12</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>744.0</th>
|
|
|
|
|
|
<td>10</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
<tr>
|
|
|
|
|
|
<th>751.0</th>
|
|
|
|
|
|
<td>9</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>...</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>fertile</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
<td>dead</td>
|
|
|
|
|
|
</tr>
|
|
|
|
|
|
</tbody>
|
|
|
|
|
|
</table>
|
|
|
|
|
|
<p>326 rows × 349 columns</p>
|
|
|
|
|
|
</div>
|
|
|
|
|
|
|
|
|
|
|
|
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. code:: ipython3
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
states = analysis.get_count(df, 'state_id')
|
|
|
|
|
|
states.plot();
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_81_0.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
alive = analysis.get_value(df, 'rabbits_alive', aggfunc='sum').apply(pd.to_numeric)
|
2017-10-18 18:28:42 +00:00
|
|
|
|
alive.plot()
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. parsed-literal::
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
<Axes: xlabel='t_step'>
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_82_1.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
.. code:: ipython3
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
h = pd.concat([alive, states]);
|
2017-10-18 18:28:42 +00:00
|
|
|
|
h.plot();
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
2023-03-23 13:49:09 +00:00
|
|
|
|
.. image:: output_83_0.png
|
2017-10-18 18:28:42 +00:00
|
|
|
|
|
