src-exe/infomap-0.x/docs/index.md
In manlius/muxViz: MuxViz - Visualization and Analysis of Multilayer Networks
Infomap Software Package
Infomap is a network clustering algorithm based on the
Map equation.
Note: This is the page for the Infomap v1.0, which is currently in a beta testing phase. For the 0.x version and for more info, see www.mapequation.org/code.html.
Installation
Infomap can be downloaded here. Then do:
cd [path/to/Infomap]
unzip Infomap.zip
cd Infomap
make
Substitute [path/to/Infomap] to the folder where Infomap was downloaded, such as ~/Downloads.
Note that these download links currently points to the 0.x version of Infomap. For the v1 beta, please check below.
Using git
To download and install the v1 beta version, run
git clone git@github.com:mapequation/infomap.git
cd infomap
git checkout v1-beta
make
Run ./Infomap --help or visit options
for a list of available options.
Infomap can be used both as a standalone program and as a library.
See the examples folder for examples.
We also include a Jupyter notebook
with examples that can be viewed online.
Using Python:
Infomap v1 beta is available on the Python Package Index PyPi. To install, run
pip install infomap
To upgrade, run
pip install --upgrade infomap
Usage
Command line
In the Infomap path, run
./Infomap [options] network_data destination
The optional arguments can be put anywhere, see the Options section for the available options. The network_data should point to a valid network file (see Input section) and destination to a directory where the Infomap should write its output files.
Python binary
If the python infomap package is installed, a binary called infomap is available on the command line from any directory. In that case, you can run
infomap [options] network_data destination
Python interface
The python package can be imported with
import infomap
Simple example
import infomap
# Command line flags can be added as a string to Infomap
infomapSimple = infomap.Infomap("--two-level --directed")
# Access the default network to add links programmatically
network = myInfomap.network()
# Add weight as optional third argument
network.addLink(0, 1)
network.addLink(0, 2)
network.addLink(0, 3)
network.addLink(1, 0)
network.addLink(1, 2)
network.addLink(2, 1)
network.addLink(2, 0)
network.addLink(3, 0)
network.addLink(3, 4)
network.addLink(3, 5)
network.addLink(4, 3)
network.addLink(4, 5)
network.addLink(5, 4)
network.addLink(5, 3)
# Run the Infomap search algorithm to find optimal modules
myInfomap.run()
print("Found {} modules with codelength: {}".format(myInfomap.numTopModules(), myInfomap.codelength()))
print("Result")
print("\n#node module")
for node in myInfomap.iterTree():
if node.isLeaf():
print("{} {}".format(node.physicalId, node.moduleIndex()))
Python API
Infomap
Create an Infomap instance
"""
Create an Infomap instance.
Parameters
----------
flags : string
Optional flags, same as in the command line version, e.g. "--directed"
Returns
-------
Infomap
The Infomap instance
"""
myInfomap = infomap.Infomap(flags)
network()
"""
Access default underlying network.
Returns
-------
Network
The underlying network, configured as the infomap instance it belongs to
"""
network = myInfomap.network()
See Network for more information.
run()
"""
Run default search algorithm to find modules.
"""
myInfomap.run()
iterTree()
"""
Tree node iterator
Parameters
----------
moduleIndexLevel : int
The depth from the root on which to advance the moduleIndex accessed from the iterator for a tree with multiple levels
Set to 1 to have moduleIndex() return the coarsest level (top modules), set to 2 for second level modules, and -1 (default) for the finest level of modules (bottom level)
Returns
-------
InfomapIterator
The InfomapIterator instance, merged with the Node instance, see InfomapIterator and InfoNode
"""
myInfomap.iterTree(moduleIndexLevel = -1)
# Example
for node in myInfomap.iterTree():
print("{} {}".format(node.path(), node.physicalId))
See InfomapIterator for more information.
iterModules()
iterLeafModules()
iterLeafNodes()
iterTreePhysical()
iterLeafNodesPhysical()
Network
addNode()
"""
Add node.
Parameters
----------
id : unsigned int
Node id
name : string
Optional name
weight : float
Optional teleportation weight
"""
network.addNode(id)
network.addNode(id, name)
network.addNode(id, weight)
network.addNode(id, name, weight)
addLink()
"""
Add node.
Parameters
----------
source : unsigned int
Source node id
target : unsigned int
Target node id
weight : float
Optional link weight, default 1.0
"""
network.addLink(source, target)
network.addLink(source, target, weight)
InfomapIterator
path()
"""
The tree path for the iterator as a tuple of child node indices taken from the root to arrive at current node
Returns
-------
tuple
The current tree path
"""
node.path()
moduleIndex()
"""
Module index of the node collected by the iterator, default finest level (see `InfomapIterator`).
Returns
-------
unsigned int
The module index
"""
node.moduleIndex()
depth()
"""
The current depth from the start node in the iterator
Returns
-------
unsigned int
The current depth
"""
node.depth()
InfoNode
stateId
"""
The state node id, equals physicalId for ordinary networks
Returns
-------
unsigned int
The state node id
"""
node.stateId
physicalId
"""
The physical node id
Returns
-------
unsigned int
The id of the physical node
"""
node.physicalId
data
"""
The flow data of the node that defines:
node.data.flow
node.data.enterFlow
node.data.exitFlow
Returns
-------
FlowData
The flow data
"""
node.data
Authors:
Daniel Edler
Martin Rosvall
For contact information, see
http://www.mapequation.org/about.html
For a list of recent feature updates, see
CHANGES.txt in the source directory.
Terms of use:
The Infomap software is released under a dual licence.
To give everyone maximum freedom to make use of Infomap
and derivative works, we make the code open source under
the GNU Affero General Public License version 3 or any
later version (see LICENSE_AGPLv3.txt.)
For a non-copyleft license, please contact us.
manlius/muxViz documentation built on March 1, 2023, 10:28 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Infomap Software Package
Infomap is a network clustering algorithm based on the Map equation.
Note: This is the page for the Infomap v1.0, which is currently in a beta testing phase. For the 0.x version and for more info, see www.mapequation.org/code.html.
Installation
Infomap can be downloaded here. Then do:
cd [path/to/Infomap]
unzip Infomap.zip
cd Infomap
make
Substitute [path/to/Infomap] to the folder where Infomap was downloaded, such as ~/Downloads.
Note that these download links currently points to the 0.x version of Infomap. For the v1 beta, please check below.
Using git
To download and install the v1 beta version, run
git clone git@github.com:mapequation/infomap.git
cd infomap
git checkout v1-beta
make
Run ./Infomap --help or visit options
for a list of available options.
Infomap can be used both as a standalone program and as a library.
See the examples folder for examples.
We also include a Jupyter notebook with examples that can be viewed online.
Using Python:
Infomap v1 beta is available on the Python Package Index PyPi. To install, run
pip install infomap
To upgrade, run
pip install --upgrade infomap
Usage
Command line
In the Infomap path, run
./Infomap [options] network_data destination
The optional arguments can be put anywhere, see the Options section for the available options. The network_data should point to a valid network file (see Input section) and destination to a directory where the Infomap should write its output files.
Python binary
If the python infomap package is installed, a binary called infomap is available on the command line from any directory. In that case, you can run
infomap [options] network_data destination
Python interface
The python package can be imported with
import infomap
Simple example
import infomap
# Command line flags can be added as a string to Infomap
infomapSimple = infomap.Infomap("--two-level --directed")
# Access the default network to add links programmatically
network = myInfomap.network()
# Add weight as optional third argument
network.addLink(0, 1)
network.addLink(0, 2)
network.addLink(0, 3)
network.addLink(1, 0)
network.addLink(1, 2)
network.addLink(2, 1)
network.addLink(2, 0)
network.addLink(3, 0)
network.addLink(3, 4)
network.addLink(3, 5)
network.addLink(4, 3)
network.addLink(4, 5)
network.addLink(5, 4)
network.addLink(5, 3)
# Run the Infomap search algorithm to find optimal modules
myInfomap.run()
print("Found {} modules with codelength: {}".format(myInfomap.numTopModules(), myInfomap.codelength()))
print("Result")
print("\n#node module")
for node in myInfomap.iterTree():
if node.isLeaf():
print("{} {}".format(node.physicalId, node.moduleIndex()))
Python API
Infomap
Create an Infomap instance
"""
Create an Infomap instance.
Parameters
----------
flags : string
Optional flags, same as in the command line version, e.g. "--directed"
Returns
-------
Infomap
The Infomap instance
"""
myInfomap = infomap.Infomap(flags)
network()
"""
Access default underlying network.
Returns
-------
Network
The underlying network, configured as the infomap instance it belongs to
"""
network = myInfomap.network()
See Network for more information.
run()
"""
Run default search algorithm to find modules.
"""
myInfomap.run()
iterTree()
"""
Tree node iterator
Parameters
----------
moduleIndexLevel : int
The depth from the root on which to advance the moduleIndex accessed from the iterator for a tree with multiple levels
Set to 1 to have moduleIndex() return the coarsest level (top modules), set to 2 for second level modules, and -1 (default) for the finest level of modules (bottom level)
Returns
-------
InfomapIterator
The InfomapIterator instance, merged with the Node instance, see InfomapIterator and InfoNode
"""
myInfomap.iterTree(moduleIndexLevel = -1)
# Example
for node in myInfomap.iterTree():
print("{} {}".format(node.path(), node.physicalId))
See InfomapIterator for more information.
iterModules()
iterLeafModules()
iterLeafNodes()
iterTreePhysical()
iterLeafNodesPhysical()
Network
addNode()
"""
Add node.
Parameters
----------
id : unsigned int
Node id
name : string
Optional name
weight : float
Optional teleportation weight
"""
network.addNode(id)
network.addNode(id, name)
network.addNode(id, weight)
network.addNode(id, name, weight)
addLink()
"""
Add node.
Parameters
----------
source : unsigned int
Source node id
target : unsigned int
Target node id
weight : float
Optional link weight, default 1.0
"""
network.addLink(source, target)
network.addLink(source, target, weight)
InfomapIterator
path()
"""
The tree path for the iterator as a tuple of child node indices taken from the root to arrive at current node
Returns
-------
tuple
The current tree path
"""
node.path()
moduleIndex()
"""
Module index of the node collected by the iterator, default finest level (see `InfomapIterator`).
Returns
-------
unsigned int
The module index
"""
node.moduleIndex()
depth()
"""
The current depth from the start node in the iterator
Returns
-------
unsigned int
The current depth
"""
node.depth()
InfoNode
stateId
"""
The state node id, equals physicalId for ordinary networks
Returns
-------
unsigned int
The state node id
"""
node.stateId
physicalId
"""
The physical node id
Returns
-------
unsigned int
The id of the physical node
"""
node.physicalId
data
"""
The flow data of the node that defines:
node.data.flow
node.data.enterFlow
node.data.exitFlow
Returns
-------
FlowData
The flow data
"""
node.data
Authors:
Daniel Edler Martin Rosvall
For contact information, see http://www.mapequation.org/about.html
For a list of recent feature updates, see CHANGES.txt in the source directory.
Terms of use:
The Infomap software is released under a dual licence.
To give everyone maximum freedom to make use of Infomap and derivative works, we make the code open source under the GNU Affero General Public License version 3 or any later version (see LICENSE_AGPLv3.txt.)
For a non-copyleft license, please contact us.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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