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soil/docs/soil_tutorial.rst
J. Fernando Sánchez bf481f0f88 v0.20.8 fix bugs
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Soil Tutorial
=============
Introduction
------------
This notebook is an introduction to the soil agent-based social network
simulation framework. In particular, we will focus on a specific use
case: studying the propagation of news in a social network.
The steps we will follow are:
- Modelling the behavior of agents
- Running the simulation using different configurations
- Analysing the results of each simulation
But before that, let’s import the soil module and networkx.
.. code:: ipython3
import soil
import networkx as nx
%load_ext autoreload
%autoreload 2
%matplotlib inline
# To display plots in the notebooed_
Basic concepts
--------------
There are three main elements in a soil simulation:
- The network topology. A simulation may use an existing NetworkX
topology, or generate one on the fly
- Agents. There are two types: 1) network agents, which are linked to a
node in the topology, and 2) environment agents, which are freely
assigned to the environment.
- The environment. It assigns agents to nodes in the network, and
stores the environment parameters (shared state for all agents).
Soil is based on ``simpy``, which is an event-based network simulation
library. Soil provides several abstractions over events to make
developing agents easier. This means you can use events (timeouts,
delays) in soil, but for the most part we will assume your models will
be step-based.
Modeling behaviour
------------------
Our first step will be to model how every person in the social network
reacts when it comes to news. We will follow a very simple model (a
finite state machine).
There are two types of people, those who have heard about a newsworthy
event (infected) or those who have not (neutral). A neutral person may
heard about the news either on the TV (with probability
**prob_tv_spread**) or through their friends. Once a person has heard
the news, they will spread it to their friends (with a probability
**prob_neighbor_spread**). Some users do not have a TV, so they only
rely on their friends.
The spreading probabilities will change over time due to different
factors. We will represent this variance using an environment agent.
Network Agents
~~~~~~~~~~~~~~
A basic network agent in Soil would typically inherit from
``soil.agents.NetworkAgent``, and define its behaviour in every step of
the simulation by implementing a ``run(self)`` method. The most
important attributes of the agent are:
- ``agent.state``, a dictionary with the state of the agent. This tate
will be saved in every step of the simulation. It can be accessed
from the agent as well:
.. code:: py
a = soil.agents.NetworkAgent(env=env)
agent.state['hours_of_sleep'] = 10
# is the same as
a['hours_of_sleep'] = 10
The state of the agent is stored in every step of the simulation:
``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``
- ``agent.env``, a reference to the environment. Most commonly used to
get access to the environment parameters and the topology: \```py
a.env.G.nodes() # Get all nodes ids in the topology
a.env[‘minimum_hours_of_sleep’]
\``\`
Since our model is a finite state machine, we will be basing it on
``soil.agents.FSM``.
Agents that inherit from ``soil.agents.FSM`` do not need to specify a
``step`` method. Instead, we describe each finite state with a function.
To change to another state, a function may return the new state, or the
``id`` of a state. If no state is returned, the state remains unchanged.
The current state of the agent can be checked with
``agent.state['id']``. That state id can be used to look for other
networks in that specific state
Our agent will have of two states, ``neutral`` (default) and
``infected``.
Here’s the code:
.. code:: ipython3
import random
class NewsSpread(soil.agents.FSM):
@soil.agents.default_state
@soil.agents.state
def neutral(self):
r = random.random()
if self['has_tv'] and r <= self.env['prob_tv_spread']:
return self.infected
return
@soil.agents.state
def infected(self):
prob_infect = self.env['prob_neighbor_spread']
for neighbor in self.get_neighboring_agents(state_id=self.neutral.id):
r = random.random()
if r < prob_infect:
neighbor.set_state(self.infected.id)
return
Environment agents
~~~~~~~~~~~~~~~~~~
Environment agents allow us to control the state of the environment. In
this case, we will use an environment agent to simulate a very viral
event.
When the event happens, the agent will modify the probability of
spreading the rumor.
.. code:: ipython3
NEIGHBOR_FACTOR = 0.9
TV_FACTOR = 0.5
class NewsEnvironmentAgent(soil.agents.NetworkAgent):
def step(self):
if self.now == self['event_time']:
self.env['prob_tv_spread'] = 1
self.env['prob_neighbor_spread'] = 1
elif self.now > self['event_time']:
self.env['prob_tv_spread'] = self.env['prob_tv_spread'] * TV_FACTOR
self.env['prob_neighbor_spread'] = self.env['prob_neighbor_spread'] * NEIGHBOR_FACTOR
Testing the agents
~~~~~~~~~~~~~~~~~~
Feel free to skip this section if this is your first time with soil.
Testing agents is not easy, and this is not a thorough testing process
for agents. Rather, this section is aimed to show you how to access
internal pats of soil so you can test your agents.
First of all, let’s check if our network agent has the states we would
expect:
.. code:: ipython3
NewsSpread.states
.. parsed-literal::
{'neutral': <function __main__.NewsSpread.neutral(self)>,
'infected': <function __main__.NewsSpread.infected(self)>}
Now, let’s run a simulation on a simple network. It is comprised of
three nodes:
.. code:: ipython3
G = nx.Graph()
G.add_edge(0, 1)
G.add_edge(0, 2)
G.add_edge(2, 3)
G.add_node(4)
pos = nx.spring_layout(G)
nx.draw_networkx(G, pos, node_color='red')
nx.draw_networkx(G, pos, nodelist=[0], node_color='blue')
.. image:: output_21_0.png
Let’s run a simple simulation that assigns a NewsSpread agent to all the
nodes in that network. Notice how node 0 is the only one with a TV.
.. code:: ipython3
import importlib
importlib.reload(soil.agents)
.. parsed-literal::
<module 'soil.agents' from '/mnt/data/home/j/git/lab.gsi/soil/soil/soil/agents/__init__.py'>
.. code:: ipython3
env_params = {
'prob_tv_spread': 0,
'prob_neighbor_spread': 0
}
MAX_TIME = 100
EVENT_TIME = 10
sim = soil.Simulation(topology=G,
num_trials=1,
max_time=MAX_TIME,
environment_agents=[{'agent_type': NewsEnvironmentAgent,
'state': {
'event_time': EVENT_TIME
}}],
network_agents=[{'agent_type': NewsSpread,
'weight': 1}],
states={0: {'has_tv': True}},
default_state={'has_tv': False},
environment_params=env_params)
env = sim.run_simulation(dry_run=True)[0]
Now we can access the results of the simulation and compare them to our
expected results
.. code:: ipython3
agents = list(env.network_agents)
# Until the event, all agents are neutral
for t in range(10):
for a in agents:
assert a['state_id', t] == a.neutral.id
# After the event, the node with a TV is infected, the rest are not
assert agents[0]['has_tv']
assert agents[0]['state_id', 11] == NewsSpread.infected.id
assert not agents[2]['has_tv']
assert agents[2]['state_id', 11] == NewsSpread.neutral.id
# At the end, the agents connected to the infected one will probably be infected, too.
assert agents[1]['state_id', MAX_TIME] == NewsSpread.infected.id
assert agents[2]['state_id', MAX_TIME] == NewsSpread.infected.id
# But the node with no friends should not be affected
assert agents[4]['state_id', MAX_TIME] == NewsSpread.neutral.id
Lastly, let’s see if the probabilities have decreased as expected:
.. code:: ipython3
assert abs(env.environment_params['prob_neighbor_spread'] - (NEIGHBOR_FACTOR**(MAX_TIME-1-10))) < 10e-4
assert abs(env.environment_params['prob_tv_spread'] - (TV_FACTOR**(MAX_TIME-1-10))) < 10e-6
Running the simulation
----------------------
To run a simulation, we need a configuration. Soil can load
configurations from python dictionaries as well as JSON and YAML files.
For this demo, we will use a python dictionary:
.. code:: ipython3
config = {
'name': 'ExampleSimulation',
'max_time': 20,
'interval': 1,
'num_trials': 1,
'network_params': {
'generator': 'complete_graph',
'n': 500,
},
'network_agents': [
{
'agent_type': NewsSpread,
'weight': 1,
'state': {
'has_tv': False
}
},
{
'agent_type': NewsSpread,
'weight': 2,
'state': {
'has_tv': True
}
}
],
'environment_agents':[
{'agent_type': NewsEnvironmentAgent,
'state': {
'event_time': 10
}
}
],
'states': [ {'has_tv': True} ],
'environment_params':{
'prob_tv_spread': 0.01,
'prob_neighbor_spread': 0.5
}
}
Let’s run our simulation:
.. code:: ipython3
soil.simulation.run_from_config(config, dry_run=True)
In real life, you probably want to run several simulations, varying some
of the parameters so that you can compare and answer your research
questions.
For instance:
- Does the outcome depend on the structure of our network? We will use
different generation algorithms to compare them (Barabasi-Albert and
Erdos-Renyi)
- How does neighbor spreading probability affect my simulation? We will
try probability values in the range of [0, 0.4], in intervals of 0.1.
.. code:: ipython3
network_1 = {
'generator': 'erdos_renyi_graph',
'n': 500,
'p': 0.1
}
network_2 = {
'generator': 'barabasi_albert_graph',
'n': 500,
'm': 2
}
for net in [network_1, network_2]:
for i in range(5):
prob = i / 10
config['environment_params']['prob_neighbor_spread'] = prob
config['network_params'] = net
config['name'] = 'Spread_{}_prob_{}'.format(net['generator'], prob)
s = soil.simulation.run_from_config(config, exporters=['default', 'csv'])
The results are conveniently stored in sqlite (history of agent and
environment state) and the configuration is saved in a YAML file.
You can also export the results to GEXF format (dynamic network) and CSV
using .\ ``run_from_config(config, dump=['gexf', 'csv'])`` or the
command line flags ``--graph --csv``.
.. code:: ipython3
!tree soil_output
!du -xh soil_output/*
.. parsed-literal::
soil_output
├── Spread_barabasi_albert_graph_prob_0.0
│   ├── backup
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_12.57.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_14.06.30
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_14.19.33
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.dumped.yml@2023-03-23_14.30.56
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_12.57.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_14.06.31
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_14.19.33
│   │   ├── Spread_barabasi_albert_graph_prob_0.0.sqlite@2023-03-23_14.30.56
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_12.57.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_14.06.31
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_14.19.33
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.csv@2023-03-23_14.30.56
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_12.57.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.06.31
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.19.33
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.30.56
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_12.57.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.06.31
│   │   ├── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.19.33
│   │   └── Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.30.56
│   ├── 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
├── Spread_barabasi_albert_graph_prob_0.1
│   ├── backup
│   │   ├── Spread_barabasi_albert_graph_prob_0.1.dumped.yml@2023-03-23_12.57.35
│   │   ├── 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
│   │   ├── 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
│   │   ├── 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
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│   │   ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.06.31
│   │   ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.19.34
│   │   ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.30.56
│   │   ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.stats.csv@2023-03-23_12.57.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.06.31
│   │   ├── 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
│   ├── Spread_barabasi_albert_graph_prob_0.1.dumped.yml
│   ├── 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
├── Spread_barabasi_albert_graph_prob_0.2
│   ├── backup
│   │   ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_12.57.36
│   │   ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_14.06.31
│   │   ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_14.19.34
│   │   ├── Spread_barabasi_albert_graph_prob_0.2.dumped.yml@2023-03-23_14.30.56
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│   │   ├── 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
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│   │   └── 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
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│   ├── Spread_barabasi_albert_graph_prob_0.2_trial_0.sqlite
│   └── Spread_barabasi_albert_graph_prob_0.2_trial_0.stats.csv
├── Spread_barabasi_albert_graph_prob_0.3
│   ├── backup
│   │   ├── Spread_barabasi_albert_graph_prob_0.3.dumped.yml@2023-03-23_12.57.36
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│   │   ├── Spread_barabasi_albert_graph_prob_0.3_trial_0.stats.csv@2023-03-23_12.57.36
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│   │   └── Spread_barabasi_albert_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.30.57
│   ├── Spread_barabasi_albert_graph_prob_0.3.dumped.yml
│   ├── Spread_barabasi_albert_graph_prob_0.3.sqlite
│   ├── Spread_barabasi_albert_graph_prob_0.3_trial_0.csv
│   ├── Spread_barabasi_albert_graph_prob_0.3_trial_0.sqlite
│   └── Spread_barabasi_albert_graph_prob_0.3_trial_0.stats.csv
├── Spread_barabasi_albert_graph_prob_0.4
│   ├── backup
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.dumped.yml@2023-03-23_12.57.36
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.dumped.yml@2023-03-23_14.06.32
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.dumped.yml@2023-03-23_14.19.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.dumped.yml@2023-03-23_14.30.57
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.sqlite@2023-03-23_12.57.36
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.sqlite@2023-03-23_14.06.32
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.sqlite@2023-03-23_14.19.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.4.sqlite@2023-03-23_14.30.57
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.csv@2023-03-23_12.57.36
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.csv@2023-03-23_14.06.32
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.csv@2023-03-23_14.19.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.csv@2023-03-23_14.30.57
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.sqlite@2023-03-23_12.57.36
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.06.32
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.19.35
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.30.57
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv@2023-03-23_12.57.36
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.06.32
│   │   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.19.35
│   │   └── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.30.57
│   ├── Spread_barabasi_albert_graph_prob_0.4.dumped.yml
│   ├── Spread_barabasi_albert_graph_prob_0.4.sqlite
│   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.csv
│   ├── Spread_barabasi_albert_graph_prob_0.4_trial_0.sqlite
│   └── Spread_barabasi_albert_graph_prob_0.4_trial_0.stats.csv
├── Spread_erdos_renyi_graph_prob_0.0
│   ├── backup
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml@2023-03-23_12.57.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml@2023-03-23_14.06.21
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml@2023-03-23_14.19.24
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml@2023-03-23_14.30.47
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_12.57.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_14.06.22
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_14.19.25
│   │   ├── Spread_erdos_renyi_graph_prob_0.0.sqlite@2023-03-23_14.30.47
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_12.57.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_14.06.22
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_14.19.25
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv@2023-03-23_14.30.47
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_12.57.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.06.22
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.19.25
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite@2023-03-23_14.30.47
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_12.57.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.06.22
│   │   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.19.25
│   │   └── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv@2023-03-23_14.30.47
│   ├── Spread_erdos_renyi_graph_prob_0.0.dumped.yml
│   ├── Spread_erdos_renyi_graph_prob_0.0.sqlite
│   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.csv
│   ├── Spread_erdos_renyi_graph_prob_0.0_trial_0.sqlite
│   └── Spread_erdos_renyi_graph_prob_0.0_trial_0.stats.csv
├── Spread_erdos_renyi_graph_prob_0.1
│   ├── backup
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_12.57.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_14.06.24
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_14.19.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml@2023-03-23_14.30.49
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_12.57.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_14.06.24
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_14.19.27
│   │   ├── Spread_erdos_renyi_graph_prob_0.1.sqlite@2023-03-23_14.30.49
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_12.57.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_14.06.24
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_14.19.27
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv@2023-03-23_14.30.49
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_12.57.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.06.24
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.19.27
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite@2023-03-23_14.30.49
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_12.57.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.06.24
│   │   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.19.27
│   │   └── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv@2023-03-23_14.30.49
│   ├── Spread_erdos_renyi_graph_prob_0.1.dumped.yml
│   ├── Spread_erdos_renyi_graph_prob_0.1.sqlite
│   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.csv
│   ├── Spread_erdos_renyi_graph_prob_0.1_trial_0.sqlite
│   └── Spread_erdos_renyi_graph_prob_0.1_trial_0.stats.csv
├── Spread_erdos_renyi_graph_prob_0.2
│   ├── backup
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_12.57.30
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_14.06.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_14.19.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml@2023-03-23_14.30.51
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_12.57.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_14.06.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_14.19.29
│   │   ├── Spread_erdos_renyi_graph_prob_0.2.sqlite@2023-03-23_14.30.51
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_12.57.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_14.06.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_14.19.29
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv@2023-03-23_14.30.51
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_12.57.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.06.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.19.29
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite@2023-03-23_14.30.51
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_12.57.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.06.26
│   │   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.19.29
│   │   └── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv@2023-03-23_14.30.51
│   ├── Spread_erdos_renyi_graph_prob_0.2.dumped.yml
│   ├── Spread_erdos_renyi_graph_prob_0.2.sqlite
│   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.csv
│   ├── Spread_erdos_renyi_graph_prob_0.2_trial_0.sqlite
│   └── Spread_erdos_renyi_graph_prob_0.2_trial_0.stats.csv
├── Spread_erdos_renyi_graph_prob_0.3
│   ├── backup
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_12.57.32
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_14.06.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_14.19.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml@2023-03-23_14.30.53
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_12.57.33
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_14.06.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_14.19.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.3.sqlite@2023-03-23_14.30.53
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_12.57.33
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_14.06.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_14.19.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv@2023-03-23_14.30.53
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_12.57.33
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_14.06.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_14.19.31
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite@2023-03-23_14.30.53
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_12.57.33
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.06.28
│   │   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.19.31
│   │   └── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv@2023-03-23_14.30.53
│   ├── Spread_erdos_renyi_graph_prob_0.3.dumped.yml
│   ├── Spread_erdos_renyi_graph_prob_0.3.sqlite
│   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.csv
│   ├── Spread_erdos_renyi_graph_prob_0.3_trial_0.sqlite
│   └── Spread_erdos_renyi_graph_prob_0.3_trial_0.stats.csv
└── Spread_erdos_renyi_graph_prob_0.4
├── backup
│   ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_12.57.34
│   ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_14.06.30
│   ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_14.19.33
│   ├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml@2023-03-23_14.30.55
│   ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_12.57.35
│   ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_14.06.30
│   ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_14.19.33
│   ├── Spread_erdos_renyi_graph_prob_0.4.sqlite@2023-03-23_14.30.56
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_12.57.35
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_14.06.30
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_14.19.33
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv@2023-03-23_14.30.56
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_12.57.35
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.06.30
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.19.33
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite@2023-03-23_14.30.56
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_12.57.35
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.06.30
│   ├── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.19.33
│   └── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv@2023-03-23_14.30.56
├── Spread_erdos_renyi_graph_prob_0.4.dumped.yml
├── Spread_erdos_renyi_graph_prob_0.4.sqlite
├── Spread_erdos_renyi_graph_prob_0.4_trial_0.csv
├── Spread_erdos_renyi_graph_prob_0.4_trial_0.sqlite
└── Spread_erdos_renyi_graph_prob_0.4_trial_0.stats.csv
20 directories, 250 files
1.3M soil_output/Spread_barabasi_albert_graph_prob_0.0/backup
1.7M soil_output/Spread_barabasi_albert_graph_prob_0.0
1.3M soil_output/Spread_barabasi_albert_graph_prob_0.1/backup
1.7M soil_output/Spread_barabasi_albert_graph_prob_0.1
1.3M soil_output/Spread_barabasi_albert_graph_prob_0.2/backup
1.6M soil_output/Spread_barabasi_albert_graph_prob_0.2
1.3M soil_output/Spread_barabasi_albert_graph_prob_0.3/backup
1.7M soil_output/Spread_barabasi_albert_graph_prob_0.3
1.3M soil_output/Spread_barabasi_albert_graph_prob_0.4/backup
1.7M soil_output/Spread_barabasi_albert_graph_prob_0.4
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.0/backup
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.0
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.1/backup
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.1
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.2/backup
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.2
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.3/backup
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.3
2.7M soil_output/Spread_erdos_renyi_graph_prob_0.4/backup
3.4M soil_output/Spread_erdos_renyi_graph_prob_0.4
Analysing the results
---------------------
Loading data
~~~~~~~~~~~~
Once the simulations are over, we can use soil to analyse the results.
Soil allows you to load results for specific trials, or for a set of
trials if you specify a pattern. The specific methods are:
- ``analysis.read_data(<directory pattern>)`` to load all the results
from a directory. e.g. \ ``read_data('my_simulation/')``. For each
trial it finds in each folder matching the pattern, it will return
the dumped configuration for the simulation, the results of the
trial, and the configuration itself. By default, it will try to load
data from the sqlite database.
- ``analysis.read_csv(<csv_file>)`` to load all the results from a CSV
file.
e.g. \ ``read_csv('my_simulation/my_simulation_trial0.environment.csv')``
- ``analysis.read_sql(<sqlite_file>)`` to load all the results from a
sqlite database .
e.g. \ ``read_sql('my_simulation/my_simulation_trial0.db.sqlite')``
Let’s see it in action by loading the stored results into a pandas
dataframe:
.. code:: ipython3
from soil import analysis
import pandas as pd
.. code:: ipython3
df = analysis.read_csv('soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.csv')
df
.. raw:: html
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
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>SEED</th>
<th colspan="9" halign="left">alive</th>
<th>...</th>
<th colspan="10" halign="left">state_id</th>
</tr>
<tr>
<th>agent_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>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>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>
<td>neutral</td>
</tr>
<tr>
<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>
<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>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>
<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>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>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>neutral</td>
<td>infected</td>
<td>infected</td>
<td>infected</td>
<td>infected</td>
</tr>
<tr>
<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>
<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>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>
<td>infected</td>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<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:
.. code:: ipython3
env, agents = analysis.split_processed(df)
.. code:: ipython3
agents
.. raw:: html
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
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 colspan="10" halign="left">alive</th>
<th>...</th>
<th colspan="10" halign="left">state_id</th>
</tr>
<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>
<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>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>
</tr>
<tr>
<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>
<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>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>
<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>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>
<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>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>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<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:
.. code:: ipython3
agents.swaplevel(axis=1)
.. raw:: html
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
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>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>
<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>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>
</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>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>
</tr>
<tr>
<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>
<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>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>
<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>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>
<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>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>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<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>
Plotting data
~~~~~~~~~~~~~
If you don’t want to work with pandas, you can also use some pre-defined
functions from soil to conveniently plot the results:
.. code:: ipython3
analysis.plot_all('soil_output/Spread_barabasi_albert_graph_prob_0.0/', analysis.get_count, 'state_id');
.. image:: output_55_0.png
.. code:: ipython3
analysis.plot_all('soil_output/Spread_barabasi_albert_graph_prob_0.3/', analysis.get_count, 'state_id');
.. image:: output_56_0.png
You can use wildcards in the results path:
.. code:: ipython3
analysis.plot_all('soil_output/Spread_barabasi*/', analysis.get_count, 'state_id');
.. image:: output_58_0.png
.. image:: output_58_1.png
.. image:: output_58_2.png
.. image:: output_58_3.png
.. image:: output_58_4.png
If we compare these results to those of the other graph model (a
fully-connected graph), we can see a stark difference:
.. code:: ipython3
analysis.plot_all('soil_output/Spread_erdos*', analysis.get_count, 'state_id');
.. image:: output_60_0.png
.. image:: output_60_1.png
.. image:: output_60_2.png
.. image:: output_60_3.png
.. image:: output_60_4.png
The previous cells were using the ``count_value`` function for
aggregation. There’s another function to plot numeral values:
.. code:: ipython3
analysis.plot_all('soil_output/Spread_erdos*', analysis.get_value, 'prob_tv_spread');
.. image:: output_62_0.png
.. image:: output_62_1.png
.. image:: output_62_2.png
.. image:: output_62_3.png
.. image:: output_62_4.png
Manually plotting with pandas
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Although the simplest way to visualize the results of a simulation is to
use the built-in methods in the analysis module, sometimes the setup is
more complicated and we need to explore the data a little further.
For that, we can use native pandas over the results.
Soil provides some convenience methods to simplify common operations:
- ``analysis.split_df`` to separate a history dataframe into
environment and agent parameters.
- ``analysis.get_count`` to get a dataframe with the value counts for
different attributes during the simulation.
- ``analysis.get_value`` to get the evolution of the value of an
attribute during the simulation.
And, as we saw earlier, ``analysis.process`` can turn a dataframe in
canonical form into a dataframe with a column per attribute.
.. code:: ipython3
!ls soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0*
.. parsed-literal::
soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0.dumped.yml
soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0.sqlite
soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.csv
soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite
soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.stats.csv
.. code:: ipython3
df = analysis.read_sql('soil_output/Spread_barabasi_albert_graph_prob_0.0/Spread_barabasi_albert_graph_prob_0.0_trial_0.sqlite')
df
.. raw:: html
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
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>SEED</th>
<th colspan="9" halign="left">alive</th>
<th>...</th>
<th colspan="10" 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>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>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>
<td>neutral</td>
</tr>
<tr>
<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>
<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>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>
<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>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>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>infected</td>
<td>neutral</td>
<td>neutral</td>
</tr>
<tr>
<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>
<td>neutral</td>
<td>infected</td>
<td>infected</td>
<td>infected</td>
<td>infected</td>
</tr>
<tr>
<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>
<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>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>
<td>infected</td>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<tr>
<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>
<td>infected</td>
</tr>
<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 × 3008 columns</p>
</div>
Let’s look at the evolution of agent parameters in the simulation
.. code:: ipython3
df.plot()
.. parsed-literal::
<Axes: xlabel='t_step'>
.. image:: output_68_1.png
As we can see, ``event_time`` and ``interval`` are cluttering our
results,
.. code:: ipython3
del df['interval']
del df['event_time']
df.plot()
.. parsed-literal::
<Axes: xlabel='t_step'>
.. image:: output_70_1.png
The ``soil.analysis`` module also provides convenient functions to count
the number of agents in a given state:
.. code:: ipython3
analysis.get_count(agents, 'state_id').plot();
.. image:: output_72_0.png
Dealing with bigger data
------------------------
.. code:: ipython3
from soil import analysis
.. code:: ipython3
!du -xsh ../rabbits/soil_output/rabbits_example/
.. parsed-literal::
1.1M ../rabbits/soil_output/rabbits_example/
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
p = analysis.plot_all('../rabbits/soil_output/rabbits_example/', analysis.get_count, 'state_id')
.. image:: output_77_0.png
.. code:: ipython3
!ls ../rabbits/soil_output/rabbits_example
.. parsed-literal::
backup rabbits_example.sqlite
rabbits_example.dumped.yml rabbits_example_trial_0.sqlite
.. code:: ipython3
df = analysis.read_sql('../rabbits/soil_output/rabbits_example/rabbits_example_trial_0.sqlite', keys=['state_id', 'rabbits_alive'])
.. code:: ipython3
df
.. raw:: html
<div>
<style scoped>
.dataframe tbody tr th:only-of-type {
vertical-align: middle;
}
.dataframe tbody tr th {
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>
.. code:: ipython3
states = analysis.get_count(df, 'state_id')
states.plot();
.. image:: output_81_0.png
.. code:: ipython3
alive = analysis.get_value(df, 'rabbits_alive', aggfunc='sum').apply(pd.to_numeric)
alive.plot()
.. parsed-literal::
<Axes: xlabel='t_step'>
.. image:: output_82_1.png
.. code:: ipython3
h = pd.concat([alive, states]);
h.plot();
.. image:: output_83_0.png
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