├── .gitattributes
├── .gitignore
├── DESCRIPTION.rst
├── LICENSE.txt
├── README.md
├── _config.yml
├── docs
├── Doxyfile
├── _config.yml
├── annotated.html
├── bc_s.png
├── bdwn.png
├── classes.html
├── classpathpy_1_1HigherOrderNetwork_1_1EmptySCCError.html
├── classpathpy_1_1HigherOrderNetwork_1_1EmptySCCError.png
├── classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork-members.html
├── classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html
├── classpathpy_1_1Log_1_1Log-members.html
├── classpathpy_1_1Log_1_1Log.html
├── classpathpy_1_1Log_1_1Severity-members.html
├── classpathpy_1_1Log_1_1Severity.html
├── classpathpy_1_1Log_1_1Severity.png
├── classpathpy_1_1MarkovSequence_1_1MarkovSequence-members.html
├── classpathpy_1_1MarkovSequence_1_1MarkovSequence.html
├── classpathpy_1_1MultiOrderModel_1_1MultiOrderModel-members.html
├── classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html
├── classpathpy_1_1Paths_1_1Paths-members.html
├── classpathpy_1_1Paths_1_1Paths.html
├── classpathpy_1_1TemporalNetwork_1_1TemporalNetwork-members.html
├── classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html
├── closed.png
├── dir_03abf54a0648869b4c214957834b2a86.html
├── doxygen.css
├── doxygen.png
├── dynsections.js
├── ftv2blank.png
├── ftv2cl.png
├── ftv2doc.png
├── ftv2folderclosed.png
├── ftv2folderopen.png
├── ftv2lastnode.png
├── ftv2link.png
├── ftv2mlastnode.png
├── ftv2mnode.png
├── ftv2mo.png
├── ftv2node.png
├── ftv2ns.png
├── ftv2plastnode.png
├── ftv2pnode.png
├── ftv2splitbar.png
├── ftv2vertline.png
├── functions.html
├── functions_func.html
├── functions_vars.html
├── hierarchy.html
├── index.html
├── jquery.js
├── nav_f.png
├── nav_g.png
├── nav_h.png
├── open.png
├── search
│ ├── all_0.html
│ ├── all_0.js
│ ├── all_1.html
│ ├── all_1.js
│ ├── all_10.html
│ ├── all_10.js
│ ├── all_11.html
│ ├── all_11.js
│ ├── all_12.html
│ ├── all_12.js
│ ├── all_13.html
│ ├── all_13.js
│ ├── all_2.html
│ ├── all_2.js
│ ├── all_3.html
│ ├── all_3.js
│ ├── all_4.html
│ ├── all_4.js
│ ├── all_5.html
│ ├── all_5.js
│ ├── all_6.html
│ ├── all_6.js
│ ├── all_7.html
│ ├── all_7.js
│ ├── all_8.html
│ ├── all_8.js
│ ├── all_9.html
│ ├── all_9.js
│ ├── all_a.html
│ ├── all_a.js
│ ├── all_b.html
│ ├── all_b.js
│ ├── all_c.html
│ ├── all_c.js
│ ├── all_d.html
│ ├── all_d.js
│ ├── all_e.html
│ ├── all_e.js
│ ├── all_f.html
│ ├── all_f.js
│ ├── classes_0.html
│ ├── classes_0.js
│ ├── classes_1.html
│ ├── classes_1.js
│ ├── classes_2.html
│ ├── classes_2.js
│ ├── classes_3.html
│ ├── classes_3.js
│ ├── classes_4.html
│ ├── classes_4.js
│ ├── classes_5.html
│ ├── classes_5.js
│ ├── classes_6.html
│ ├── classes_6.js
│ ├── close.png
│ ├── functions_0.html
│ ├── functions_0.js
│ ├── functions_1.html
│ ├── functions_1.js
│ ├── functions_2.html
│ ├── functions_2.js
│ ├── functions_3.html
│ ├── functions_3.js
│ ├── functions_4.html
│ ├── functions_4.js
│ ├── functions_5.html
│ ├── functions_5.js
│ ├── functions_6.html
│ ├── functions_6.js
│ ├── functions_7.html
│ ├── functions_7.js
│ ├── functions_8.html
│ ├── functions_8.js
│ ├── functions_9.html
│ ├── functions_9.js
│ ├── functions_a.html
│ ├── functions_a.js
│ ├── functions_b.html
│ ├── functions_b.js
│ ├── functions_c.html
│ ├── functions_c.js
│ ├── functions_d.html
│ ├── functions_d.js
│ ├── functions_e.html
│ ├── functions_e.js
│ ├── functions_f.html
│ ├── functions_f.js
│ ├── mag_sel.png
│ ├── nomatches.html
│ ├── search.css
│ ├── search.js
│ ├── search_l.png
│ ├── search_m.png
│ ├── search_r.png
│ ├── variables_0.html
│ ├── variables_0.js
│ ├── variables_1.html
│ ├── variables_1.js
│ ├── variables_2.html
│ ├── variables_2.js
│ ├── variables_3.html
│ ├── variables_3.js
│ ├── variables_4.html
│ ├── variables_4.js
│ ├── variables_5.html
│ ├── variables_5.js
│ ├── variables_6.html
│ ├── variables_6.js
│ ├── variables_7.html
│ ├── variables_7.js
│ ├── variables_8.html
│ ├── variables_8.js
│ ├── variables_9.html
│ ├── variables_9.js
│ ├── variables_a.html
│ ├── variables_a.js
│ ├── variables_b.html
│ └── variables_b.js
├── sync_off.png
├── sync_on.png
├── tab_a.png
├── tab_b.png
├── tab_h.png
├── tab_s.png
├── tabs.css
├── tutorial.html
└── tutorial.ipynb
├── multiorder.png
├── pathpy.pyproj
├── pathpy.sln
├── pathpy
├── HigherOrderNetwork.py
├── Log.py
├── MarkovSequence.py
├── MultiOrderModel.py
├── Paths.py
├── TemporalNetwork.py
└── __init__.py
├── pathpy_logo.png
├── setup.py
└── tests
├── README.md
├── conftest.py
├── test_Path.py
├── test_TemporalNetwork.py
├── test_data
├── edge_frequency.edge
├── example_int.tedges
├── example_timestamp.tedges
└── ngram_simple.ngram
└── test_estimation.py
/.gitattributes:
--------------------------------------------------------------------------------
1 | # Auto detect text files and perform LF normalization
2 | * text=auto
3 |
4 | # Custom for Visual Studio
5 | *.cs diff=csharp
6 |
7 | # Standard to msysgit
8 | *.doc diff=astextplain
9 | *.DOC diff=astextplain
10 | *.docx diff=astextplain
11 | *.DOCX diff=astextplain
12 | *.dot diff=astextplain
13 | *.DOT diff=astextplain
14 | *.pdf diff=astextplain
15 | *.PDF diff=astextplain
16 | *.rtf diff=astextplain
17 | *.RTF diff=astextplain
18 |
--------------------------------------------------------------------------------
/.gitignore:
--------------------------------------------------------------------------------
1 | # Byte-compiled / optimized / DLL files
2 | __pycache__/
3 | *.py[cod]
4 |
5 | # C extensions
6 | *.so
7 |
8 | # Distribution / packaging
9 | .Python
10 | env/
11 | build/
12 | develop-eggs/
13 | dist/
14 | downloads/
15 | eggs/
16 | lib/
17 | lib64/
18 | parts/
19 | sdist/
20 | var/
21 | *.egg-info/
22 | .installed.cfg
23 | *.egg
24 |
25 | # PyInstaller
26 | # Usually these files are written by a python script from a template
27 | # before PyInstaller builds the exe, so as to inject date/other infos into it.
28 | *.manifest
29 | *.spec
30 |
31 | # Installer logs
32 | pip-log.txt
33 | pip-delete-this-directory.txt
34 |
35 | # Unit test / coverage reports
36 | htmlcov/
37 | .tox/
38 | .coverage
39 | .cache
40 | nosetests.xml
41 | coverage.xml
42 |
43 | # Translations
44 | *.mo
45 | *.pot
46 |
47 | # Django stuff:
48 | *.log
49 |
50 | # PyBuilder
51 | target/
52 |
53 | # =========================
54 | # Operating System Files
55 | # =========================
56 |
57 | # OSX
58 | # =========================
59 |
60 | .DS_Store
61 | .AppleDouble
62 | .LSOverride
63 |
64 | # Thumbnails
65 | ._*
66 |
67 | # Files that might appear on external disk
68 | .Spotlight-V100
69 | .Trashes
70 |
71 | # Directories potentially created on remote AFP share
72 | .AppleDB
73 | .AppleDesktop
74 | Network Trash Folder
75 | Temporary Items
76 | .apdisk
77 |
78 | # Windows
79 | # =========================
80 |
81 | # Windows image file caches
82 | Thumbs.db
83 | ehthumbs.db
84 |
85 | # Folder config file
86 | Desktop.ini
87 |
88 | # Recycle Bin used on file shares
89 | $RECYCLE.BIN/
90 |
91 | # Windows Installer files
92 | *.cab
93 | *.msi
94 | *.msm
95 | *.msp
96 |
97 | # Windows shortcuts
98 | *.lnk
99 | pyTempNets.v12.suo
100 | *.png
101 | *.TMP
102 | pyTempNet.egg-info/requires.txt
103 | pyTempNet.egg-info/SOURCES.txt
104 | pyTempNet.egg-info/dependency_links.txt
105 | pyTempNet.egg-info/requires.txt
106 | *.suo
107 | pyTempNet.egg-info/top_level.txt
108 | pyTempNet.egg-info/requires.txt
109 | pyTempNet.egg-info/requires.txt
110 | pyTempNet.egg-info/dependency_links.txt
111 | pyTempNet.egg-info/SOURCES.txt
112 | .idea/
113 | .eggs/
114 | prof/*
115 |
--------------------------------------------------------------------------------
/DESCRIPTION.rst:
--------------------------------------------------------------------------------
1 | pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models.
--------------------------------------------------------------------------------
/README.md:
--------------------------------------------------------------------------------
1 |
2 |
3 | **Note**: This is the repository of an old version of pathpy. It will soon be replaced by [pathpy 3](https://github.com/pathpy/pathpy), which has a new [home on gitHub](https://github.com/pathpy/pathpy).
4 |
5 | # Introduction
6 |
7 | `pathpy` is an OpenSource python package for the modeling and analysis of pathways and temporal networks
8 | using **higher-order** and **multi-order** graphical models.
9 |
10 | The package is specifically tailored to analyze sequential data which capture multiple observations of short, independent paths
11 | observed in an underlying graph topology. Examples for such data include user click streams in information networks,
12 | biological pathways, or traces of information propagating in social media. Unifying the analysis of pathways and temporal networks,
13 | `pathpy` also supports the extraction of time-respecting paths from time-stamped network data. It extends (and will eventually supersede)
14 | the package [`pyTempnets`](https://github.com/IngoScholtes/pyTempNets).
15 |
16 | `pathpy` facilitates the analysis of temporal correlations in such sequential data. It uses a principled model selection
17 | technique to infer higher-order graphical representations that capture both topological and temporal
18 | characteristics of time-resolved relational data. It specifically allows to answer the question whether a (first-order) network
19 | abstraction of such data is justified, or whether higher-order network abstractions are needed.
20 |
21 | The theoretical foundation of this package, **higher-order network models**, has been developed in the following research works:
22 |
23 | 1. I Scholtes: [When is a network a network? Multi-Order Graphical Model Selection in Pathways and Temporal Networks](https://arxiv.org/abs/1702.05499), to appear in KDD'17, arXiv:1702.05499
24 | 2. I Scholtes, N Wider, A Garas: [Higher-Order Aggregate Networks in the Analysis of Temporal Networks: Path structures and centralities](http://dx.doi.org/10.1140/epjb/e2016-60663-0), The European Physical Journal B, 89:61, March 2016
25 | 3. I Scholtes, N Wider, R Pfitzner, A Garas, CJ Tessone, F Schweitzer: [Causality-driven slow-down and speed-up of diffusion in non-Markovian temporal networks](http://www.nature.com/ncomms/2014/140924/ncomms6024/full/ncomms6024.html), Nature Communications, 5, September 2014
26 | 4. R Pfitzner, I Scholtes, A Garas, CJ Tessone, F Schweitzer: [Betweenness preference: Quantifying correlations in the topological dynamics of temporal networks](http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.110.198701), Phys Rev Lett, 110(19), 198701, May 2013
27 |
28 | `pathpy` extends this approach towards **multi-layer graphical models** that capture temporal correlations in pathways at multiple length scales simultaneously. An illustrative example for
29 | a collection of pathways (left) and a multi-order graphical representation of these pathways is shown below. All mathematical details of the framework can be found in this [recent research paper](https://arxiv.org/abs/1702.05499).
30 |
31 | [](https://www.youtube.com/watch?v=CxJkVrD2ZlM)
32 |
33 |
34 |
35 | # Download and installation
36 |
37 | `pathpy` is pure python code. It has no platform-specific dependencies and should thus work on all platforms. It builds on `numpy` and `scipy`. The latest version of `pathpy` can be installed by typing:
38 |
39 | `> pip install git+git://github.com/IngoScholtes/pathpy.git`
40 |
41 | `pathpy` currently requires python 3.x. We are planning to make the next version backwards compatible with python 2.x.
42 |
43 | # Tutorial
44 |
45 | A [comprehensive educational tutorial](https://ingoscholtes.github.io/pathpy/tutorial.html) which shows how you can use `pathpy` to analyze data on pathways and temporal networks is [available online](https://ingoscholtes.github.io/pathpy/tutorial.html).
46 | Moreover, a tutorial which illustrates the abstraction of **higher-order networks** in the modeling of dynamical processes in temporal networks is [available here](https://www.sg.ethz.ch/team/people/ischoltes/research-insights/temporal-networks-demo/). The
47 | latter tutorial is based on the predecessor library [`pyTempNets`](https://github.com/IngoScholtes/pyTempNets). Most of its features have been ported to `pathpy`.
48 |
49 | # Documentation
50 |
51 | The code is fully documented via docstrings which are accessible through python's built-in help system. Just type `help(SYMBOL_NAME)` to see the documentation of a class or method. A [reference manual is available here](https://ingoscholtes.github.io/pathpy/hierarchy.html).
52 |
53 | # Releases and Versioning
54 |
55 | The first public beta release of pathpy (released February 17 2017) is [v1.0-beta](https://github.com/IngoScholtes/pathpy/releases/tag/v1.0-beta.1). Following versions are named MAJOR.MINOR.PATCH according to [semantic versioning](http://semver.org/). The date of each release is encoded in the PATCH version.
56 |
57 | # Acknowledgements
58 |
59 | The research behind this data analysis framework was funded by the Swiss State Secretariat for Education, Research and Innovation [(Grant C14.0036)](https://www.sg.ethz.ch/projects/seri-information-spaces/). The development of this package was generously supported by the [MTEC Foundation](http://www.mtec.ethz.ch/research/support/MTECFoundation.html) in the context of the project [The Influence of Interaction Patterns on Success in Socio-Technical Systems: From Theory to Practice](https://www.sg.ethz.ch/projects/mtec-interaction-patterns/).
60 |
61 | # Contributors
62 |
63 | [Ingo Scholtes](http://www.ingoscholtes.net) (project lead, development)
64 | [Luca Verginer](http://www.verginer.eu/about/) (development, testing)
65 |
66 | # Past Contributors
67 | Roman Cattaneo (development)
68 | Nicolas Wider (testing)
69 |
70 | # Copyright
71 |
72 | pathpy is licensed under the [GNU Affero General Public License](https://choosealicense.com/licenses/agpl-3.0/).
73 |
74 | (c) Copyright ETH Zürich, Chair of Systems Design, 2015-2018
75 |
--------------------------------------------------------------------------------
/_config.yml:
--------------------------------------------------------------------------------
1 | theme: jekyll-theme-minimal
--------------------------------------------------------------------------------
/docs/_config.yml:
--------------------------------------------------------------------------------
1 | theme: jekyll-theme-tactile
--------------------------------------------------------------------------------
/docs/bc_s.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/bc_s.png
--------------------------------------------------------------------------------
/docs/bdwn.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/bdwn.png
--------------------------------------------------------------------------------
/docs/classpathpy_1_1HigherOrderNetwork_1_1EmptySCCError.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 | pathpy: pathpy.HigherOrderNetwork.EmptySCCError Class Reference
8 |
9 |
10 |
11 |
12 |
13 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 | pathpy
26 | 1.0
27 |
28 | pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
39 |
61 |
69 |
70 |
75 |
76 |
77 |
78 |
81 |
82 |
83 |
87 |
88 |
92 |
93 |
95 |
96 |
97 |
98 |
99 |
100 |
101 |
102 |
This exception is thrown whenever a non-empty strongly
103 | connected component is needed, but we encounter an empty one
104 | The documentation for this class was generated from the following file:
105 | /mnt/c/Users/ingos/Desktop/pathpy/pathpy/HigherOrderNetwork.py
106 |
107 |
108 |
109 |
114 |
115 |
116 |
--------------------------------------------------------------------------------
/docs/classpathpy_1_1HigherOrderNetwork_1_1EmptySCCError.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/classpathpy_1_1HigherOrderNetwork_1_1EmptySCCError.png
--------------------------------------------------------------------------------
/docs/classpathpy_1_1Log_1_1Log-members.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 | pathpy: Member List
8 |
9 |
10 |
11 |
12 |
13 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 | pathpy
26 | 1.0
27 |
28 | pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
39 |
61 |
69 |
70 |
75 |
76 |
77 |
78 |
81 |
82 |
83 |
87 |
88 |
92 |
93 |
94 |
This is the complete list of members for pathpy.Log.Log , including all inherited members.
95 |
102 |
103 |
108 |
109 |
110 |
--------------------------------------------------------------------------------
/docs/classpathpy_1_1Log_1_1Severity-members.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 | pathpy: Member List
8 |
9 |
10 |
11 |
12 |
13 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 | pathpy
26 | 1.0
27 |
28 | pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
39 |
61 |
69 |
70 |
75 |
76 |
77 |
78 |
81 |
82 |
83 |
87 |
88 |
92 |
93 |
94 |
This is the complete list of members for pathpy.Log.Severity , including all inherited members.
95 |
102 |
103 |
108 |
109 |
110 |
--------------------------------------------------------------------------------
/docs/classpathpy_1_1Log_1_1Severity.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/classpathpy_1_1Log_1_1Severity.png
--------------------------------------------------------------------------------
/docs/closed.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/closed.png
--------------------------------------------------------------------------------
/docs/dir_03abf54a0648869b4c214957834b2a86.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 | pathpy: /mnt/c/Users/ingos/Desktop/pathpy/pathpy Directory Reference
8 |
9 |
10 |
11 |
12 |
13 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 | pathpy
26 | 1.0
27 |
28 | pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
39 |
61 |
62 |
67 |
68 |
69 |
70 |
73 |
74 |
75 |
79 |
80 |
84 |
85 |
86 |
88 | file __init__.py
89 |
90 | file HigherOrderNetwork.py
91 |
92 | file Log.py
93 |
94 | file MarkovSequence.py
95 |
96 | file MultiOrderModel.py
97 |
98 | file Paths.py
99 |
100 | file TemporalNetwork.py
101 |
102 | file test.py
103 |
104 |
105 |
106 |
107 |
112 |
113 |
114 |
--------------------------------------------------------------------------------
/docs/doxygen.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/doxygen.png
--------------------------------------------------------------------------------
/docs/dynsections.js:
--------------------------------------------------------------------------------
1 | function toggleVisibility(linkObj)
2 | {
3 | var base = $(linkObj).attr('id');
4 | var summary = $('#'+base+'-summary');
5 | var content = $('#'+base+'-content');
6 | var trigger = $('#'+base+'-trigger');
7 | var src=$(trigger).attr('src');
8 | if (content.is(':visible')===true) {
9 | content.hide();
10 | summary.show();
11 | $(linkObj).addClass('closed').removeClass('opened');
12 | $(trigger).attr('src',src.substring(0,src.length-8)+'closed.png');
13 | } else {
14 | content.show();
15 | summary.hide();
16 | $(linkObj).removeClass('closed').addClass('opened');
17 | $(trigger).attr('src',src.substring(0,src.length-10)+'open.png');
18 | }
19 | return false;
20 | }
21 |
22 | function updateStripes()
23 | {
24 | $('table.directory tr').
25 | removeClass('even').filter(':visible:even').addClass('even');
26 | }
27 | function toggleLevel(level)
28 | {
29 | $('table.directory tr').each(function(){
30 | var l = this.id.split('_').length-1;
31 | var i = $('#img'+this.id.substring(3));
32 | var a = $('#arr'+this.id.substring(3));
33 | if (l
2 |
3 |
4 |
5 |
6 |
7 | pathpy: Class Hierarchy
8 |
9 |
10 |
11 |
12 |
13 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 | pathpy
26 | 1.0
27 |
28 | pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
39 |
61 |
69 |
70 |
71 |
76 |
77 |
78 |
79 |
82 |
83 |
84 |
88 |
89 |
This inheritance list is sorted roughly, but not completely, alphabetically:
90 |
[detail level 1 2 ]
102 |
103 |
104 |
105 |
110 |
111 |
112 |
--------------------------------------------------------------------------------
/docs/index.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 | pathpy: Main Page
8 |
9 |
10 |
11 |
12 |
13 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 | pathpy
26 | 1.0
27 |
28 | pathpy is an OpenSource python package for the modeling and analysis of pathways and temporal networks using higher-order and multi-order graphical models
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
39 |
61 |
62 |
63 |
68 |
69 |
70 |
71 |
74 |
75 |
76 |
80 |
81 |
82 |
83 |
88 |
89 |
90 |
--------------------------------------------------------------------------------
/docs/nav_f.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/nav_f.png
--------------------------------------------------------------------------------
/docs/nav_g.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/nav_g.png
--------------------------------------------------------------------------------
/docs/nav_h.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/nav_h.png
--------------------------------------------------------------------------------
/docs/open.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/open.png
--------------------------------------------------------------------------------
/docs/search/all_0.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_0.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['_5f_5finit_5f_5f',['__init__',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a63d36720423ee8d6d88c5a06f4655c84',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.__init__()'],['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a670778608688e4926328cf2d851b7d6d',1,'pathpy.MarkovSequence.MarkovSequence.__init__()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#ac8dc89b42d8e51906ce15124da699409',1,'pathpy.MultiOrderModel.MultiOrderModel.__init__()'],['../classpathpy_1_1Paths_1_1Paths.html#a5e853dc424f2142bc53df219e33be29f',1,'pathpy.Paths.Paths.__init__()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a778b3b6f649c7057ac1f3f7dc3e43aff',1,'pathpy.TemporalNetwork.TemporalNetwork.__init__()']]],
4 | ['_5f_5fstr_5f_5f',['__str__',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a4aec883869195967a9209655905ace52',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.__str__()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#af69183cc68e6b8aae85cce91341dbf44',1,'pathpy.MultiOrderModel.MultiOrderModel.__str__()'],['../classpathpy_1_1Paths_1_1Paths.html#afdbe49d3727f7fd3022899cb3130c6db',1,'pathpy.Paths.Paths.__str__()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a0deb7b84090e2667840606ab0eeae509',1,'pathpy.TemporalNetwork.TemporalNetwork.__str__()']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/all_1.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_1.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['activities',['activities',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#ae9ea417aa751edb7e58bc1c23602b9b8',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
4 | ['activities_5fsets',['activities_sets',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a65a5f24cb5e6cf06960f8c93c6c8aa84',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
5 | ['add',['add',['../classpathpy_1_1Log_1_1Log.html#a7b948e9bbdcd1ab31bf6ee1a425195f7',1,'pathpy::Log::Log']]],
6 | ['addedge',['addEdge',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#aac7da90422a66a8123776b3d698b4615',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
7 | ['addpath',['addPath',['../classpathpy_1_1Paths_1_1Paths.html#a5af2d99bd84797a960e43bc78c57db5a',1,'pathpy::Paths::Paths']]],
8 | ['addpathtuple',['addPathTuple',['../classpathpy_1_1Paths_1_1Paths.html#ab1c50bfee7d28f3a180fc036000bc146',1,'pathpy::Paths::Paths']]]
9 | ];
10 |
--------------------------------------------------------------------------------
/docs/search/all_10.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_10.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['separator',['separator',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#af3e51491a2417e471eeb1404b44df204',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.separator()'],['../classpathpy_1_1Paths_1_1Paths.html#a0642d710d46cf929c00f22ed53510d92',1,'pathpy.Paths.Paths.separator()']]],
4 | ['sequence',['sequence',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#ac0cbbe436a3938f2ff94d313c72c4e67',1,'pathpy::MarkovSequence::MarkovSequence']]],
5 | ['setminseverity',['setMinSeverity',['../classpathpy_1_1Log_1_1Log.html#a9e0171144845116732949b87d348d27d',1,'pathpy::Log::Log']]],
6 | ['setoutputstream',['setOutputStream',['../classpathpy_1_1Log_1_1Log.html#a0e7ec3decada72adee6edcda4951e720',1,'pathpy::Log::Log']]],
7 | ['severity',['Severity',['../classpathpy_1_1Log_1_1Severity.html',1,'pathpy::Log']]],
8 | ['shuffleedges',['ShuffleEdges',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a50ea38c4325e1035966c4d2173599a1d',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
9 | ['sources',['sources',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a0716456e27f19af5522af30e071df0ff',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
10 | ['states',['states',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a77ca53bfcfb5458a8834b8b6392422ce',1,'pathpy::MarkovSequence::MarkovSequence']]],
11 | ['successors',['successors',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a522350b2e4a401732b64bb0acf1634ea',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
12 | ['summary',['summary',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ab35dd7f65e3bfeb280fcd38c1e7448f7',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.summary()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a58f11a90bea210c70f12eeac3af53d65',1,'pathpy.MultiOrderModel.MultiOrderModel.summary()'],['../classpathpy_1_1Paths_1_1Paths.html#ad519d020de268ea49898e7520be4ffcf',1,'pathpy.Paths.Paths.summary()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a39d2b3a872f2a19554ee505393a6f708',1,'pathpy.TemporalNetwork.TemporalNetwork.summary()']]]
13 | ];
14 |
--------------------------------------------------------------------------------
/docs/search/all_11.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_11.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['t',['T',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a93118aa6719067efdbe8b38ef85a578a',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
4 | ['targets',['targets',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#ae82b4df377620a626771cdcdcbb43b42',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
5 | ['tedges',['tedges',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a2ed001aa13e863e9ff6ab9ffc9ab998d',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
6 | ['temporalnetwork',['TemporalNetwork',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html',1,'pathpy::TemporalNetwork']]],
7 | ['testnetworkassumption',['testNetworkAssumption',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#aaa9b2f2852c4ae513e5d42a96008c030',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
8 | ['time',['time',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a1f61dbedd4a4edde5176fec56fc1f0b3',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
9 | ['timing',['TIMING',['../classpathpy_1_1Log_1_1Severity.html#a0c184f8e48c1f5cb7f795d00c9205ed5',1,'pathpy::Log::Severity']]],
10 | ['totaledgeweight',['totalEdgeWeight',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a91626f933af603a73f8bb39249ab6c51',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
11 | ];
12 |
--------------------------------------------------------------------------------
/docs/search/all_12.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_12.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['vcount',['vcount',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a89ba7bbeb54449a87ba78eecc591fca4',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.vcount()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a727ebc2cc2eb2ad8c1ee23cdd5a25b6e',1,'pathpy.TemporalNetwork.TemporalNetwork.vcount()']]],
4 | ['visitationprobabilities',['VisitationProbabilities',['../classpathpy_1_1Paths_1_1Paths.html#a5c964af581ac3c48fbd2a3955f711bb2',1,'pathpy::Paths::Paths']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/all_13.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_13.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['warning',['WARNING',['../classpathpy_1_1Log_1_1Severity.html#ae4a13b6d9d1d2485bceb5843df6e3f40',1,'pathpy::Log::Severity']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/all_2.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_2.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['betweennesscentrality',['BetweennessCentrality',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#afcfdcfacef4f3beb7594a58600e833e4',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.BetweennessCentrality()'],['../classpathpy_1_1Paths_1_1Paths.html#add4dc55240d6ca92645f3709152d0545',1,'pathpy.Paths.Paths.BetweennessCentrality()']]],
4 | ['betweennesspreference',['BetweennessPreference',['../classpathpy_1_1Paths_1_1Paths.html#afc66998bbb85b5fd3e7b8cd049a2bfa1',1,'pathpy::Paths::Paths']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/all_3.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_3.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['closenesscentrality',['ClosenessCentrality',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a2f94ebbc8141be6f5194ec922e3b01a0',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.ClosenessCentrality()'],['../classpathpy_1_1Paths_1_1Paths.html#a45a27a4b5d8fe5aa368da221ab68502a',1,'pathpy.Paths.Paths.ClosenessCentrality()']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/all_4.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_4.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['debug',['DEBUG',['../classpathpy_1_1Log_1_1Severity.html#ad6d71133083c6972a8400a1e4b355381',1,'pathpy::Log::Severity']]],
4 | ['degrees',['degrees',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#acd9ab003f80216ed6beff9c513a7e876',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
5 | ['dof_5fngrams',['dof_ngrams',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a25d69b9cc9b7b328fbd201244e68ca95',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
6 | ['dof_5fpaths',['dof_paths',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a8a271893d9fb656f805e36335afca257',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
7 | ];
8 |
--------------------------------------------------------------------------------
/docs/search/all_5.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_5.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['ecount',['ecount',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ae425665357e88b0adf493854143a3f72',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.ecount()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a040f4101e98fb4507709976c2ef7452b',1,'pathpy.TemporalNetwork.TemporalNetwork.ecount()']]],
4 | ['edges',['edges',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a6eec968e72178ab2930f83928b3ca842',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
5 | ['emptysccerror',['EmptySCCError',['../classpathpy_1_1HigherOrderNetwork_1_1EmptySCCError.html',1,'pathpy::HigherOrderNetwork']]],
6 | ['error',['ERROR',['../classpathpy_1_1Log_1_1Severity.html#aa2e434a659bbb9f2e2c25e47fab1dc37',1,'pathpy::Log::Severity']]],
7 | ['estimateorder',['estimateOrder',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a0e794225267c8195f091f5ed452d34e6',1,'pathpy.MarkovSequence.MarkovSequence.estimateOrder()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a866b2b0b96f4bafa594b2a8d5a64efbf',1,'pathpy.MultiOrderModel.MultiOrderModel.estimateOrder()']]],
8 | ['evcent',['EvCent',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a57e8494220dd4a5b2a9a45de17f9d26a',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
9 | ['expandsubpaths',['expandSubPaths',['../classpathpy_1_1Paths_1_1Paths.html#a6e1941415a937fa9aa86b6b442f858e1',1,'pathpy::Paths::Paths']]]
10 | ];
11 |
--------------------------------------------------------------------------------
/docs/search/all_6.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_6.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['factorial',['factorial',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a7882e4dcbe9ec932e863e20d6b49a4ed',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
4 | ['filteredges',['filterEdges',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#aa1b765e6f119b214d78ba16de3b36cf4',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
5 | ['filterpaths',['filterPaths',['../classpathpy_1_1Paths_1_1Paths.html#a1c27b7c76d16437518f28734de2b86a5',1,'pathpy::Paths::Paths']]],
6 | ['fitmarkovmodel',['fitMarkovModel',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a422f6b70f888eaab6a6f942158355072',1,'pathpy::MarkovSequence::MarkovSequence']]],
7 | ['fromtemporalnetwork',['fromTemporalNetwork',['../classpathpy_1_1Paths_1_1Paths.html#a02f8ee9b6b4fa8c1e8012c9d21bfb76d',1,'pathpy::Paths::Paths']]]
8 | ];
9 |
--------------------------------------------------------------------------------
/docs/search/all_7.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_7.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['getadjacencymatrix',['getAdjacencyMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a8e10f45369dff5f7ccff3bcf7e6c5b33',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
4 | ['getaic',['getAIC',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#aba5377e966e3bfb9c4c736e782863484',1,'pathpy::MarkovSequence::MarkovSequence']]],
5 | ['getalgebraicconnectivity',['getAlgebraicConnectivity',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ae48d8ad635f7cf263897016d876c6fa2',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
6 | ['getbic',['getBIC',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a975922931ec471f436c4d340830a7ca3',1,'pathpy::MarkovSequence::MarkovSequence']]],
7 | ['getcontainedpaths',['getContainedPaths',['../classpathpy_1_1Paths_1_1Paths.html#af830708eaa318dd450193b8e6d7fb37a',1,'pathpy::Paths::Paths']]],
8 | ['getdegreesoffreedom',['getDegreesOfFreedom',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a219e12dca2b474515d74c65c4ad15c69',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
9 | ['getdistancematrix',['getDistanceMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a20092d5a4a182df408af6063a0887630',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.getDistanceMatrix()'],['../classpathpy_1_1Paths_1_1Paths.html#a5b6ad214815f9fbd687c457d53367f19',1,'pathpy.Paths.Paths.getDistanceMatrix()']]],
10 | ['getdistancematrixfirstorder',['getDistanceMatrixFirstOrder',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#abed4839be0864210c0b5aff9376fe307',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
11 | ['getdof',['getDoF',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a3a03ec6087add6dd0b54f7264b2e21c5',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
12 | ['geteigenvaluegap',['getEigenValueGap',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a556545310735cba27128afd37c59ed35',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
13 | ['getentropygrowthrateratio',['getEntropyGrowthRateRatio',['../classpathpy_1_1Paths_1_1Paths.html#a9bf65d20a97eb629a4d618a4e19160a7',1,'pathpy::Paths::Paths']]],
14 | ['getfiedlervectordense',['getFiedlerVectorDense',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#adea7800343373793dbd9688c77fb6191',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
15 | ['getfiedlervectorsparse',['getFiedlerVectorSparse',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#aa8f3ed627c16c15c877fc0316c88bdb3',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
16 | ['getintereventtimes',['getInterEventTimes',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a3e43ba8b22586d6f55b2ab28a65bf35b',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
17 | ['getinterpathtimes',['getInterPathTimes',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a7a385a1b17104011975aa9c0c3f2912a',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
18 | ['getlaplacianmatrix',['getLaplacianMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a69ea9c565b0d8bf7f1a2d0cb409f0e15',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
19 | ['getlayerlikelihood',['getLayerLikelihood',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#ab56ae5b47770b09178ae5aa49f695d17',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
20 | ['getleadingeigenvector',['getLeadingEigenvector',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a1b757112293f9093efc437ffb113df83',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
21 | ['getlikelihood',['getLikelihood',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#ab820bbcfb5569ef05e361aa478c521f6',1,'pathpy.MarkovSequence.MarkovSequence.getLikelihood()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#acceb5eabd7d1cb8a8856a485a29fc5f8',1,'pathpy.MultiOrderModel.MultiOrderModel.getLikelihood()']]],
22 | ['getnodenamemap',['getNodeNameMap',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#abd69fc6003eb13d11390466182a63357',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
23 | ['getnodes',['getNodes',['../classpathpy_1_1Paths_1_1Paths.html#a287a429de9a958ccc48658b9fb9f7665',1,'pathpy::Paths::Paths']]],
24 | ['getobservationlength',['getObservationLength',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a0ac006ac7818ef042fde95ea90deee80',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
25 | ['getsequence',['getSequence',['../classpathpy_1_1Paths_1_1Paths.html#ab457e7e3f439e193410be707a2cd39bd',1,'pathpy::Paths::Paths']]],
26 | ['getshortestpaths',['getShortestPaths',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a672cdad613e84eb0f528bbc02e7c6163',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.getShortestPaths()'],['../classpathpy_1_1Paths_1_1Paths.html#a99a295d0674ca4eb5ba6906b48893b26',1,'pathpy.Paths.Paths.getShortestPaths()']]],
27 | ['getslowdownfactor',['getSlowDownFactor',['../classpathpy_1_1Paths_1_1Paths.html#a60aa117d37a599f912122263bf9e3eea',1,'pathpy::Paths::Paths']]],
28 | ['gettemporalbetweenness',['GetTemporalBetweenness',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a948503bbe0104c9678778cdecfe8ceb7',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
29 | ['gettemporalbetweennessinstantaneous',['GetTemporalBetweennessInstantaneous',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#aa6a91612301e802d287f1fb58fe31961',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
30 | ['gettemporalcloseness',['GetTemporalCloseness',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a9dd08ea1ab218cb69b2fdd56cbcab61f',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
31 | ['gettemporalclosenessinstantaneous',['GetTemporalClosenessInstantaneous',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#ac73ea9fa5c13c1df5ac101d45473243d',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
32 | ['gettransitionmatrix',['getTransitionMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a20c4a62ca4706bdab81534332e3843fe',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
33 | ['getuniquepaths',['getUniquePaths',['../classpathpy_1_1Paths_1_1Paths.html#afc152a2783167b289326e528f0077951',1,'pathpy::Paths::Paths']]]
34 | ];
35 |
--------------------------------------------------------------------------------
/docs/search/all_8.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_8.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['higherordernetwork',['HigherOrderNetwork',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html',1,'pathpy::HigherOrderNetwork']]],
4 | ['higherordernodetopath',['HigherOrderNodeToPath',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a1963d0e4370e3818de3cf6886bba8594',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
5 | ['higherorderpathtofirstorder',['HigherOrderPathToFirstOrder',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ab71b78f1c9ffe7a06364841572f1fee2',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
6 | ];
7 |
--------------------------------------------------------------------------------
/docs/search/all_9.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_9.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['info',['INFO',['../classpathpy_1_1Log_1_1Severity.html#a12fb98e4cc0d9e68114e29e8f6758c22',1,'pathpy::Log::Severity']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/all_a.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_a.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['layers',['layers',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#abc678904e6dd23fc36bace35f8c8b651',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
4 | ['likelihoodratiotest',['likeliHoodRatioTest',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a0518e905c00b8c3a2df5cce509084fb8',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
5 | ['log',['Log',['../classpathpy_1_1Log_1_1Log.html',1,'pathpy::Log']]]
6 | ];
7 |
--------------------------------------------------------------------------------
/docs/search/all_b.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_b.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['markovsequence',['MarkovSequence',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html',1,'pathpy::MarkovSequence']]],
4 | ['maxorder',['maxOrder',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#ad77293d316dbc4264e07d33f15c43f55',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
5 | ['min_5fseverity',['min_severity',['../classpathpy_1_1Log_1_1Log.html#a327ac21443db1980997ddb0c8ef65313',1,'pathpy::Log::Log']]],
6 | ['multiordermodel',['MultiOrderModel',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html',1,'pathpy::MultiOrderModel']]]
7 | ];
8 |
--------------------------------------------------------------------------------
/docs/search/all_c.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_c.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['nodes',['nodes',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a6626777ff215fde5f7d92368a407c683',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.nodes()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a86e49baf6e63c58a3f993e2768097001',1,'pathpy.TemporalNetwork.TemporalNetwork.nodes()']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/all_d.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_d.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['observationcount',['ObservationCount',['../classpathpy_1_1Paths_1_1Paths.html#a4b4e13eb898dd55b9c1a381eaf22aea9',1,'pathpy::Paths::Paths']]],
4 | ['order',['order',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a6dea6fe6e34178adb395ad8e79403d5c',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
5 | ['ordered_5ftimes',['ordered_times',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a051e7d352da3d194387762134bd70992',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
6 | ['output_5fstream',['output_stream',['../classpathpy_1_1Log_1_1Log.html#a8f7664b2a5379f9e94402117e22ed058',1,'pathpy::Log::Log']]]
7 | ];
8 |
--------------------------------------------------------------------------------
/docs/search/all_e.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_e.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['p',['P',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#ac0d2ff028f2c2c88349555527e44a898',1,'pathpy::MarkovSequence::MarkovSequence']]],
4 | ['pagerank',['PageRank',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#abc76633f53a0747353e7ab0e15744d94',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
5 | ['paths',['Paths',['../classpathpy_1_1Paths_1_1Paths.html',1,'pathpy::Paths']]],
6 | ['paths',['paths',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ac4c8ee9f7775478793d88680d6f99fc8',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.paths()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#adf751f249355e9a26e8062050567cf54',1,'pathpy.MultiOrderModel.MultiOrderModel.paths()'],['../classpathpy_1_1Paths_1_1Paths.html#aacbff90d31fabf41c2413246aafc8275',1,'pathpy.Paths.Paths.paths()']]],
7 | ['pathtohigherordernodes',['pathToHigherOrderNodes',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a117fe621fb02d356f6591620f9340eaa',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
8 | ['projectpaths',['projectPaths',['../classpathpy_1_1Paths_1_1Paths.html#a160fb269d25c24adc4fbfdc3df71075c',1,'pathpy::Paths::Paths']]]
9 | ];
10 |
--------------------------------------------------------------------------------
/docs/search/all_f.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/all_f.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['readedges',['readEdges',['../classpathpy_1_1Paths_1_1Paths.html#adba5db911e0be900c03908f8b2ca511e',1,'pathpy::Paths::Paths']]],
4 | ['readfile',['readFile',['../classpathpy_1_1Paths_1_1Paths.html#a349974504cf0ef9fd1ff97a0249e649e',1,'pathpy.Paths.Paths.readFile()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a54bf4b554d7ca2a45a49cc76a0080cea',1,'pathpy.TemporalNetwork.TemporalNetwork.readFile()']]],
5 | ['reducetogcc',['reduceToGCC',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a4b71eed8268df33814725ae7832729e6',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
6 | ];
7 |
--------------------------------------------------------------------------------
/docs/search/classes_0.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/classes_0.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['emptysccerror',['EmptySCCError',['../classpathpy_1_1HigherOrderNetwork_1_1EmptySCCError.html',1,'pathpy::HigherOrderNetwork']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/classes_1.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/classes_1.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['higherordernetwork',['HigherOrderNetwork',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html',1,'pathpy::HigherOrderNetwork']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/classes_2.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/classes_2.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['log',['Log',['../classpathpy_1_1Log_1_1Log.html',1,'pathpy::Log']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/classes_3.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/classes_3.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['markovsequence',['MarkovSequence',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html',1,'pathpy::MarkovSequence']]],
4 | ['multiordermodel',['MultiOrderModel',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html',1,'pathpy::MultiOrderModel']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/classes_4.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/classes_4.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['paths',['Paths',['../classpathpy_1_1Paths_1_1Paths.html',1,'pathpy::Paths']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/classes_5.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/classes_5.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['severity',['Severity',['../classpathpy_1_1Log_1_1Severity.html',1,'pathpy::Log']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/classes_6.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/classes_6.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['temporalnetwork',['TemporalNetwork',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html',1,'pathpy::TemporalNetwork']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/close.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/search/close.png
--------------------------------------------------------------------------------
/docs/search/functions_0.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_0.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['_5f_5finit_5f_5f',['__init__',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a63d36720423ee8d6d88c5a06f4655c84',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.__init__()'],['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a670778608688e4926328cf2d851b7d6d',1,'pathpy.MarkovSequence.MarkovSequence.__init__()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#ac8dc89b42d8e51906ce15124da699409',1,'pathpy.MultiOrderModel.MultiOrderModel.__init__()'],['../classpathpy_1_1Paths_1_1Paths.html#a5e853dc424f2142bc53df219e33be29f',1,'pathpy.Paths.Paths.__init__()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a778b3b6f649c7057ac1f3f7dc3e43aff',1,'pathpy.TemporalNetwork.TemporalNetwork.__init__()']]],
4 | ['_5f_5fstr_5f_5f',['__str__',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a4aec883869195967a9209655905ace52',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.__str__()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#af69183cc68e6b8aae85cce91341dbf44',1,'pathpy.MultiOrderModel.MultiOrderModel.__str__()'],['../classpathpy_1_1Paths_1_1Paths.html#afdbe49d3727f7fd3022899cb3130c6db',1,'pathpy.Paths.Paths.__str__()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a0deb7b84090e2667840606ab0eeae509',1,'pathpy.TemporalNetwork.TemporalNetwork.__str__()']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/functions_1.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_1.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['add',['add',['../classpathpy_1_1Log_1_1Log.html#a7b948e9bbdcd1ab31bf6ee1a425195f7',1,'pathpy::Log::Log']]],
4 | ['addedge',['addEdge',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#aac7da90422a66a8123776b3d698b4615',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
5 | ['addpath',['addPath',['../classpathpy_1_1Paths_1_1Paths.html#a5af2d99bd84797a960e43bc78c57db5a',1,'pathpy::Paths::Paths']]],
6 | ['addpathtuple',['addPathTuple',['../classpathpy_1_1Paths_1_1Paths.html#ab1c50bfee7d28f3a180fc036000bc146',1,'pathpy::Paths::Paths']]]
7 | ];
8 |
--------------------------------------------------------------------------------
/docs/search/functions_2.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_2.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['betweennesscentrality',['BetweennessCentrality',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#afcfdcfacef4f3beb7594a58600e833e4',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.BetweennessCentrality()'],['../classpathpy_1_1Paths_1_1Paths.html#add4dc55240d6ca92645f3709152d0545',1,'pathpy.Paths.Paths.BetweennessCentrality()']]],
4 | ['betweennesspreference',['BetweennessPreference',['../classpathpy_1_1Paths_1_1Paths.html#afc66998bbb85b5fd3e7b8cd049a2bfa1',1,'pathpy::Paths::Paths']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/functions_3.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_3.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['closenesscentrality',['ClosenessCentrality',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a2f94ebbc8141be6f5194ec922e3b01a0',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.ClosenessCentrality()'],['../classpathpy_1_1Paths_1_1Paths.html#a45a27a4b5d8fe5aa368da221ab68502a',1,'pathpy.Paths.Paths.ClosenessCentrality()']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/functions_4.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_4.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['degrees',['degrees',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#acd9ab003f80216ed6beff9c513a7e876',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/functions_5.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_5.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['ecount',['ecount',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ae425665357e88b0adf493854143a3f72',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.ecount()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a040f4101e98fb4507709976c2ef7452b',1,'pathpy.TemporalNetwork.TemporalNetwork.ecount()']]],
4 | ['estimateorder',['estimateOrder',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a0e794225267c8195f091f5ed452d34e6',1,'pathpy.MarkovSequence.MarkovSequence.estimateOrder()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a866b2b0b96f4bafa594b2a8d5a64efbf',1,'pathpy.MultiOrderModel.MultiOrderModel.estimateOrder()']]],
5 | ['evcent',['EvCent',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a57e8494220dd4a5b2a9a45de17f9d26a',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
6 | ['expandsubpaths',['expandSubPaths',['../classpathpy_1_1Paths_1_1Paths.html#a6e1941415a937fa9aa86b6b442f858e1',1,'pathpy::Paths::Paths']]]
7 | ];
8 |
--------------------------------------------------------------------------------
/docs/search/functions_6.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_6.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['factorial',['factorial',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a7882e4dcbe9ec932e863e20d6b49a4ed',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
4 | ['filteredges',['filterEdges',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#aa1b765e6f119b214d78ba16de3b36cf4',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
5 | ['filterpaths',['filterPaths',['../classpathpy_1_1Paths_1_1Paths.html#a1c27b7c76d16437518f28734de2b86a5',1,'pathpy::Paths::Paths']]],
6 | ['fitmarkovmodel',['fitMarkovModel',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a422f6b70f888eaab6a6f942158355072',1,'pathpy::MarkovSequence::MarkovSequence']]],
7 | ['fromtemporalnetwork',['fromTemporalNetwork',['../classpathpy_1_1Paths_1_1Paths.html#a02f8ee9b6b4fa8c1e8012c9d21bfb76d',1,'pathpy::Paths::Paths']]]
8 | ];
9 |
--------------------------------------------------------------------------------
/docs/search/functions_7.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_7.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['getadjacencymatrix',['getAdjacencyMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a8e10f45369dff5f7ccff3bcf7e6c5b33',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
4 | ['getaic',['getAIC',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#aba5377e966e3bfb9c4c736e782863484',1,'pathpy::MarkovSequence::MarkovSequence']]],
5 | ['getalgebraicconnectivity',['getAlgebraicConnectivity',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ae48d8ad635f7cf263897016d876c6fa2',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
6 | ['getbic',['getBIC',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a975922931ec471f436c4d340830a7ca3',1,'pathpy::MarkovSequence::MarkovSequence']]],
7 | ['getcontainedpaths',['getContainedPaths',['../classpathpy_1_1Paths_1_1Paths.html#af830708eaa318dd450193b8e6d7fb37a',1,'pathpy::Paths::Paths']]],
8 | ['getdegreesoffreedom',['getDegreesOfFreedom',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a219e12dca2b474515d74c65c4ad15c69',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
9 | ['getdistancematrix',['getDistanceMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a20092d5a4a182df408af6063a0887630',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.getDistanceMatrix()'],['../classpathpy_1_1Paths_1_1Paths.html#a5b6ad214815f9fbd687c457d53367f19',1,'pathpy.Paths.Paths.getDistanceMatrix()']]],
10 | ['getdistancematrixfirstorder',['getDistanceMatrixFirstOrder',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#abed4839be0864210c0b5aff9376fe307',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
11 | ['getdof',['getDoF',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a3a03ec6087add6dd0b54f7264b2e21c5',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
12 | ['geteigenvaluegap',['getEigenValueGap',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a556545310735cba27128afd37c59ed35',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
13 | ['getentropygrowthrateratio',['getEntropyGrowthRateRatio',['../classpathpy_1_1Paths_1_1Paths.html#a9bf65d20a97eb629a4d618a4e19160a7',1,'pathpy::Paths::Paths']]],
14 | ['getfiedlervectordense',['getFiedlerVectorDense',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#adea7800343373793dbd9688c77fb6191',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
15 | ['getfiedlervectorsparse',['getFiedlerVectorSparse',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#aa8f3ed627c16c15c877fc0316c88bdb3',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
16 | ['getintereventtimes',['getInterEventTimes',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a3e43ba8b22586d6f55b2ab28a65bf35b',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
17 | ['getinterpathtimes',['getInterPathTimes',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a7a385a1b17104011975aa9c0c3f2912a',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
18 | ['getlaplacianmatrix',['getLaplacianMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a69ea9c565b0d8bf7f1a2d0cb409f0e15',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
19 | ['getlayerlikelihood',['getLayerLikelihood',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#ab56ae5b47770b09178ae5aa49f695d17',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
20 | ['getleadingeigenvector',['getLeadingEigenvector',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a1b757112293f9093efc437ffb113df83',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
21 | ['getlikelihood',['getLikelihood',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#ab820bbcfb5569ef05e361aa478c521f6',1,'pathpy.MarkovSequence.MarkovSequence.getLikelihood()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#acceb5eabd7d1cb8a8856a485a29fc5f8',1,'pathpy.MultiOrderModel.MultiOrderModel.getLikelihood()']]],
22 | ['getnodenamemap',['getNodeNameMap',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#abd69fc6003eb13d11390466182a63357',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
23 | ['getnodes',['getNodes',['../classpathpy_1_1Paths_1_1Paths.html#a287a429de9a958ccc48658b9fb9f7665',1,'pathpy::Paths::Paths']]],
24 | ['getobservationlength',['getObservationLength',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a0ac006ac7818ef042fde95ea90deee80',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
25 | ['getsequence',['getSequence',['../classpathpy_1_1Paths_1_1Paths.html#ab457e7e3f439e193410be707a2cd39bd',1,'pathpy::Paths::Paths']]],
26 | ['getshortestpaths',['getShortestPaths',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a672cdad613e84eb0f528bbc02e7c6163',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.getShortestPaths()'],['../classpathpy_1_1Paths_1_1Paths.html#a99a295d0674ca4eb5ba6906b48893b26',1,'pathpy.Paths.Paths.getShortestPaths()']]],
27 | ['getslowdownfactor',['getSlowDownFactor',['../classpathpy_1_1Paths_1_1Paths.html#a60aa117d37a599f912122263bf9e3eea',1,'pathpy::Paths::Paths']]],
28 | ['gettemporalbetweenness',['GetTemporalBetweenness',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a948503bbe0104c9678778cdecfe8ceb7',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
29 | ['gettemporalbetweennessinstantaneous',['GetTemporalBetweennessInstantaneous',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#aa6a91612301e802d287f1fb58fe31961',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
30 | ['gettemporalcloseness',['GetTemporalCloseness',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a9dd08ea1ab218cb69b2fdd56cbcab61f',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
31 | ['gettemporalclosenessinstantaneous',['GetTemporalClosenessInstantaneous',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#ac73ea9fa5c13c1df5ac101d45473243d',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
32 | ['gettransitionmatrix',['getTransitionMatrix',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a20c4a62ca4706bdab81534332e3843fe',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
33 | ['getuniquepaths',['getUniquePaths',['../classpathpy_1_1Paths_1_1Paths.html#afc152a2783167b289326e528f0077951',1,'pathpy::Paths::Paths']]]
34 | ];
35 |
--------------------------------------------------------------------------------
/docs/search/functions_8.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_8.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['higherordernodetopath',['HigherOrderNodeToPath',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a1963d0e4370e3818de3cf6886bba8594',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
4 | ['higherorderpathtofirstorder',['HigherOrderPathToFirstOrder',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ab71b78f1c9ffe7a06364841572f1fee2',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/functions_9.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_9.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['likelihoodratiotest',['likeliHoodRatioTest',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a0518e905c00b8c3a2df5cce509084fb8',1,'pathpy::MultiOrderModel::MultiOrderModel']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/functions_a.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_a.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['observationcount',['ObservationCount',['../classpathpy_1_1Paths_1_1Paths.html#a4b4e13eb898dd55b9c1a381eaf22aea9',1,'pathpy::Paths::Paths']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/functions_b.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_b.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['pagerank',['PageRank',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#abc76633f53a0747353e7ab0e15744d94',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
4 | ['pathtohigherordernodes',['pathToHigherOrderNodes',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a117fe621fb02d356f6591620f9340eaa',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
5 | ['projectpaths',['projectPaths',['../classpathpy_1_1Paths_1_1Paths.html#a160fb269d25c24adc4fbfdc3df71075c',1,'pathpy::Paths::Paths']]]
6 | ];
7 |
--------------------------------------------------------------------------------
/docs/search/functions_c.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_c.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['readedges',['readEdges',['../classpathpy_1_1Paths_1_1Paths.html#adba5db911e0be900c03908f8b2ca511e',1,'pathpy::Paths::Paths']]],
4 | ['readfile',['readFile',['../classpathpy_1_1Paths_1_1Paths.html#a349974504cf0ef9fd1ff97a0249e649e',1,'pathpy.Paths.Paths.readFile()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a54bf4b554d7ca2a45a49cc76a0080cea',1,'pathpy.TemporalNetwork.TemporalNetwork.readFile()']]],
5 | ['reducetogcc',['reduceToGCC',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a4b71eed8268df33814725ae7832729e6',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
6 | ];
7 |
--------------------------------------------------------------------------------
/docs/search/functions_d.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_d.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['setminseverity',['setMinSeverity',['../classpathpy_1_1Log_1_1Log.html#a9e0171144845116732949b87d348d27d',1,'pathpy::Log::Log']]],
4 | ['setoutputstream',['setOutputStream',['../classpathpy_1_1Log_1_1Log.html#a0e7ec3decada72adee6edcda4951e720',1,'pathpy::Log::Log']]],
5 | ['shuffleedges',['ShuffleEdges',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a50ea38c4325e1035966c4d2173599a1d',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
6 | ['summary',['summary',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ab35dd7f65e3bfeb280fcd38c1e7448f7',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.summary()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a58f11a90bea210c70f12eeac3af53d65',1,'pathpy.MultiOrderModel.MultiOrderModel.summary()'],['../classpathpy_1_1Paths_1_1Paths.html#ad519d020de268ea49898e7520be4ffcf',1,'pathpy.Paths.Paths.summary()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a39d2b3a872f2a19554ee505393a6f708',1,'pathpy.TemporalNetwork.TemporalNetwork.summary()']]]
7 | ];
8 |
--------------------------------------------------------------------------------
/docs/search/functions_e.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_e.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['testnetworkassumption',['testNetworkAssumption',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#aaa9b2f2852c4ae513e5d42a96008c030',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
4 | ['totaledgeweight',['totalEdgeWeight',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a91626f933af603a73f8bb39249ab6c51',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/functions_f.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/functions_f.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['vcount',['vcount',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a89ba7bbeb54449a87ba78eecc591fca4',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.vcount()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a727ebc2cc2eb2ad8c1ee23cdd5a25b6e',1,'pathpy.TemporalNetwork.TemporalNetwork.vcount()']]],
4 | ['visitationprobabilities',['VisitationProbabilities',['../classpathpy_1_1Paths_1_1Paths.html#a5c964af581ac3c48fbd2a3955f711bb2',1,'pathpy::Paths::Paths']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/mag_sel.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/search/mag_sel.png
--------------------------------------------------------------------------------
/docs/search/nomatches.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
11 |
12 |
13 |
--------------------------------------------------------------------------------
/docs/search/search.css:
--------------------------------------------------------------------------------
1 | /*---------------- Search Box */
2 |
3 | #FSearchBox {
4 | float: left;
5 | }
6 |
7 | #MSearchBox {
8 | white-space : nowrap;
9 | position: absolute;
10 | float: none;
11 | display: inline;
12 | margin-top: 8px;
13 | right: 0px;
14 | width: 170px;
15 | z-index: 102;
16 | background-color: white;
17 | }
18 |
19 | #MSearchBox .left
20 | {
21 | display:block;
22 | position:absolute;
23 | left:10px;
24 | width:20px;
25 | height:19px;
26 | background:url('search_l.png') no-repeat;
27 | background-position:right;
28 | }
29 |
30 | #MSearchSelect {
31 | display:block;
32 | position:absolute;
33 | width:20px;
34 | height:19px;
35 | }
36 |
37 | .left #MSearchSelect {
38 | left:4px;
39 | }
40 |
41 | .right #MSearchSelect {
42 | right:5px;
43 | }
44 |
45 | #MSearchField {
46 | display:block;
47 | position:absolute;
48 | height:19px;
49 | background:url('search_m.png') repeat-x;
50 | border:none;
51 | width:111px;
52 | margin-left:20px;
53 | padding-left:4px;
54 | color: #909090;
55 | outline: none;
56 | font: 9pt Arial, Verdana, sans-serif;
57 | }
58 |
59 | #FSearchBox #MSearchField {
60 | margin-left:15px;
61 | }
62 |
63 | #MSearchBox .right {
64 | display:block;
65 | position:absolute;
66 | right:10px;
67 | top:0px;
68 | width:20px;
69 | height:19px;
70 | background:url('search_r.png') no-repeat;
71 | background-position:left;
72 | }
73 |
74 | #MSearchClose {
75 | display: none;
76 | position: absolute;
77 | top: 4px;
78 | background : none;
79 | border: none;
80 | margin: 0px 4px 0px 0px;
81 | padding: 0px 0px;
82 | outline: none;
83 | }
84 |
85 | .left #MSearchClose {
86 | left: 6px;
87 | }
88 |
89 | .right #MSearchClose {
90 | right: 2px;
91 | }
92 |
93 | .MSearchBoxActive #MSearchField {
94 | color: #000000;
95 | }
96 |
97 | /*---------------- Search filter selection */
98 |
99 | #MSearchSelectWindow {
100 | display: none;
101 | position: absolute;
102 | left: 0; top: 0;
103 | border: 1px solid #90A5CE;
104 | background-color: #F9FAFC;
105 | z-index: 1;
106 | padding-top: 4px;
107 | padding-bottom: 4px;
108 | -moz-border-radius: 4px;
109 | -webkit-border-top-left-radius: 4px;
110 | -webkit-border-top-right-radius: 4px;
111 | -webkit-border-bottom-left-radius: 4px;
112 | -webkit-border-bottom-right-radius: 4px;
113 | -webkit-box-shadow: 5px 5px 5px rgba(0, 0, 0, 0.15);
114 | }
115 |
116 | .SelectItem {
117 | font: 8pt Arial, Verdana, sans-serif;
118 | padding-left: 2px;
119 | padding-right: 12px;
120 | border: 0px;
121 | }
122 |
123 | span.SelectionMark {
124 | margin-right: 4px;
125 | font-family: monospace;
126 | outline-style: none;
127 | text-decoration: none;
128 | }
129 |
130 | a.SelectItem {
131 | display: block;
132 | outline-style: none;
133 | color: #000000;
134 | text-decoration: none;
135 | padding-left: 6px;
136 | padding-right: 12px;
137 | }
138 |
139 | a.SelectItem:focus,
140 | a.SelectItem:active {
141 | color: #000000;
142 | outline-style: none;
143 | text-decoration: none;
144 | }
145 |
146 | a.SelectItem:hover {
147 | color: #FFFFFF;
148 | background-color: #3D578C;
149 | outline-style: none;
150 | text-decoration: none;
151 | cursor: pointer;
152 | display: block;
153 | }
154 |
155 | /*---------------- Search results window */
156 |
157 | iframe#MSearchResults {
158 | width: 60ex;
159 | height: 15em;
160 | }
161 |
162 | #MSearchResultsWindow {
163 | display: none;
164 | position: absolute;
165 | left: 0; top: 0;
166 | border: 1px solid #000;
167 | background-color: #EEF1F7;
168 | }
169 |
170 | /* ----------------------------------- */
171 |
172 |
173 | #SRIndex {
174 | clear:both;
175 | padding-bottom: 15px;
176 | }
177 |
178 | .SREntry {
179 | font-size: 10pt;
180 | padding-left: 1ex;
181 | }
182 |
183 | .SRPage .SREntry {
184 | font-size: 8pt;
185 | padding: 1px 5px;
186 | }
187 |
188 | body.SRPage {
189 | margin: 5px 2px;
190 | }
191 |
192 | .SRChildren {
193 | padding-left: 3ex; padding-bottom: .5em
194 | }
195 |
196 | .SRPage .SRChildren {
197 | display: none;
198 | }
199 |
200 | .SRSymbol {
201 | font-weight: bold;
202 | color: #425E97;
203 | font-family: Arial, Verdana, sans-serif;
204 | text-decoration: none;
205 | outline: none;
206 | }
207 |
208 | a.SRScope {
209 | display: block;
210 | color: #425E97;
211 | font-family: Arial, Verdana, sans-serif;
212 | text-decoration: none;
213 | outline: none;
214 | }
215 |
216 | a.SRSymbol:focus, a.SRSymbol:active,
217 | a.SRScope:focus, a.SRScope:active {
218 | text-decoration: underline;
219 | }
220 |
221 | span.SRScope {
222 | padding-left: 4px;
223 | }
224 |
225 | .SRPage .SRStatus {
226 | padding: 2px 5px;
227 | font-size: 8pt;
228 | font-style: italic;
229 | }
230 |
231 | .SRResult {
232 | display: none;
233 | }
234 |
235 | DIV.searchresults {
236 | margin-left: 10px;
237 | margin-right: 10px;
238 | }
239 |
240 | /*---------------- External search page results */
241 |
242 | .searchresult {
243 | background-color: #F0F3F8;
244 | }
245 |
246 | .pages b {
247 | color: white;
248 | padding: 5px 5px 3px 5px;
249 | background-image: url("../tab_a.png");
250 | background-repeat: repeat-x;
251 | text-shadow: 0 1px 1px #000000;
252 | }
253 |
254 | .pages {
255 | line-height: 17px;
256 | margin-left: 4px;
257 | text-decoration: none;
258 | }
259 |
260 | .hl {
261 | font-weight: bold;
262 | }
263 |
264 | #searchresults {
265 | margin-bottom: 20px;
266 | }
267 |
268 | .searchpages {
269 | margin-top: 10px;
270 | }
271 |
272 |
--------------------------------------------------------------------------------
/docs/search/search_l.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/search/search_l.png
--------------------------------------------------------------------------------
/docs/search/search_m.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/search/search_m.png
--------------------------------------------------------------------------------
/docs/search/search_r.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/search/search_r.png
--------------------------------------------------------------------------------
/docs/search/variables_0.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_0.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['activities',['activities',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#ae9ea417aa751edb7e58bc1c23602b9b8',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
4 | ['activities_5fsets',['activities_sets',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a65a5f24cb5e6cf06960f8c93c6c8aa84',1,'pathpy::TemporalNetwork::TemporalNetwork']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/variables_1.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_1.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['debug',['DEBUG',['../classpathpy_1_1Log_1_1Severity.html#ad6d71133083c6972a8400a1e4b355381',1,'pathpy::Log::Severity']]],
4 | ['dof_5fngrams',['dof_ngrams',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a25d69b9cc9b7b328fbd201244e68ca95',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
5 | ['dof_5fpaths',['dof_paths',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a8a271893d9fb656f805e36335afca257',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
6 | ];
7 |
--------------------------------------------------------------------------------
/docs/search/variables_2.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_2.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['edges',['edges',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a6eec968e72178ab2930f83928b3ca842',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
4 | ['error',['ERROR',['../classpathpy_1_1Log_1_1Severity.html#aa2e434a659bbb9f2e2c25e47fab1dc37',1,'pathpy::Log::Severity']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/variables_3.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_3.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['info',['INFO',['../classpathpy_1_1Log_1_1Severity.html#a12fb98e4cc0d9e68114e29e8f6758c22',1,'pathpy::Log::Severity']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/variables_4.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_4.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['layers',['layers',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#abc678904e6dd23fc36bace35f8c8b651',1,'pathpy::MultiOrderModel::MultiOrderModel']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/variables_5.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_5.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['maxorder',['maxOrder',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#ad77293d316dbc4264e07d33f15c43f55',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
4 | ['min_5fseverity',['min_severity',['../classpathpy_1_1Log_1_1Log.html#a327ac21443db1980997ddb0c8ef65313',1,'pathpy::Log::Log']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/variables_6.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_6.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['nodes',['nodes',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a6626777ff215fde5f7d92368a407c683',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.nodes()'],['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a86e49baf6e63c58a3f993e2768097001',1,'pathpy.TemporalNetwork.TemporalNetwork.nodes()']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/search/variables_7.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_7.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['order',['order',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a6dea6fe6e34178adb395ad8e79403d5c',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]],
4 | ['ordered_5ftimes',['ordered_times',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a051e7d352da3d194387762134bd70992',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
5 | ['output_5fstream',['output_stream',['../classpathpy_1_1Log_1_1Log.html#a8f7664b2a5379f9e94402117e22ed058',1,'pathpy::Log::Log']]]
6 | ];
7 |
--------------------------------------------------------------------------------
/docs/search/variables_8.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_8.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['p',['P',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#ac0d2ff028f2c2c88349555527e44a898',1,'pathpy::MarkovSequence::MarkovSequence']]],
4 | ['paths',['paths',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#ac4c8ee9f7775478793d88680d6f99fc8',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.paths()'],['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#adf751f249355e9a26e8062050567cf54',1,'pathpy.MultiOrderModel.MultiOrderModel.paths()'],['../classpathpy_1_1Paths_1_1Paths.html#aacbff90d31fabf41c2413246aafc8275',1,'pathpy.Paths.Paths.paths()']]]
5 | ];
6 |
--------------------------------------------------------------------------------
/docs/search/variables_9.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_9.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['separator',['separator',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#af3e51491a2417e471eeb1404b44df204',1,'pathpy.HigherOrderNetwork.HigherOrderNetwork.separator()'],['../classpathpy_1_1Paths_1_1Paths.html#a0642d710d46cf929c00f22ed53510d92',1,'pathpy.Paths.Paths.separator()']]],
4 | ['sequence',['sequence',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#ac0cbbe436a3938f2ff94d313c72c4e67',1,'pathpy::MarkovSequence::MarkovSequence']]],
5 | ['sources',['sources',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a0716456e27f19af5522af30e071df0ff',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
6 | ['states',['states',['../classpathpy_1_1MarkovSequence_1_1MarkovSequence.html#a77ca53bfcfb5458a8834b8b6392422ce',1,'pathpy::MarkovSequence::MarkovSequence']]],
7 | ['successors',['successors',['../classpathpy_1_1HigherOrderNetwork_1_1HigherOrderNetwork.html#a522350b2e4a401732b64bb0acf1634ea',1,'pathpy::HigherOrderNetwork::HigherOrderNetwork']]]
8 | ];
9 |
--------------------------------------------------------------------------------
/docs/search/variables_a.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_a.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['t',['T',['../classpathpy_1_1MultiOrderModel_1_1MultiOrderModel.html#a93118aa6719067efdbe8b38ef85a578a',1,'pathpy::MultiOrderModel::MultiOrderModel']]],
4 | ['targets',['targets',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#ae82b4df377620a626771cdcdcbb43b42',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
5 | ['tedges',['tedges',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a2ed001aa13e863e9ff6ab9ffc9ab998d',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
6 | ['time',['time',['../classpathpy_1_1TemporalNetwork_1_1TemporalNetwork.html#a1f61dbedd4a4edde5176fec56fc1f0b3',1,'pathpy::TemporalNetwork::TemporalNetwork']]],
7 | ['timing',['TIMING',['../classpathpy_1_1Log_1_1Severity.html#a0c184f8e48c1f5cb7f795d00c9205ed5',1,'pathpy::Log::Severity']]]
8 | ];
9 |
--------------------------------------------------------------------------------
/docs/search/variables_b.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
Loading...
12 |
13 |
16 |
Searching...
17 |
No Matches
18 |
24 |
25 |
26 |
27 |
--------------------------------------------------------------------------------
/docs/search/variables_b.js:
--------------------------------------------------------------------------------
1 | var searchData=
2 | [
3 | ['warning',['WARNING',['../classpathpy_1_1Log_1_1Severity.html#ae4a13b6d9d1d2485bceb5843df6e3f40',1,'pathpy::Log::Severity']]]
4 | ];
5 |
--------------------------------------------------------------------------------
/docs/sync_off.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/sync_off.png
--------------------------------------------------------------------------------
/docs/sync_on.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/sync_on.png
--------------------------------------------------------------------------------
/docs/tab_a.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/tab_a.png
--------------------------------------------------------------------------------
/docs/tab_b.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/tab_b.png
--------------------------------------------------------------------------------
/docs/tab_h.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/tab_h.png
--------------------------------------------------------------------------------
/docs/tab_s.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/docs/tab_s.png
--------------------------------------------------------------------------------
/docs/tabs.css:
--------------------------------------------------------------------------------
1 | .tabs, .tabs2, .tabs3 {
2 | background-image: url('tab_b.png');
3 | width: 100%;
4 | z-index: 101;
5 | font-size: 13px;
6 | font-family: 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
7 | }
8 |
9 | .tabs2 {
10 | font-size: 10px;
11 | }
12 | .tabs3 {
13 | font-size: 9px;
14 | }
15 |
16 | .tablist {
17 | margin: 0;
18 | padding: 0;
19 | display: table;
20 | }
21 |
22 | .tablist li {
23 | float: left;
24 | display: table-cell;
25 | background-image: url('tab_b.png');
26 | line-height: 36px;
27 | list-style: none;
28 | }
29 |
30 | .tablist a {
31 | display: block;
32 | padding: 0 20px;
33 | font-weight: bold;
34 | background-image:url('tab_s.png');
35 | background-repeat:no-repeat;
36 | background-position:right;
37 | color: #283A5D;
38 | text-shadow: 0px 1px 1px rgba(255, 255, 255, 0.9);
39 | text-decoration: none;
40 | outline: none;
41 | }
42 |
43 | .tabs3 .tablist a {
44 | padding: 0 10px;
45 | }
46 |
47 | .tablist a:hover {
48 | background-image: url('tab_h.png');
49 | background-repeat:repeat-x;
50 | color: #fff;
51 | text-shadow: 0px 1px 1px rgba(0, 0, 0, 1.0);
52 | text-decoration: none;
53 | }
54 |
55 | .tablist li.current a {
56 | background-image: url('tab_a.png');
57 | background-repeat:repeat-x;
58 | color: #fff;
59 | text-shadow: 0px 1px 1px rgba(0, 0, 0, 1.0);
60 | }
61 |
--------------------------------------------------------------------------------
/multiorder.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/multiorder.png
--------------------------------------------------------------------------------
/pathpy.pyproj:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 | Debug
5 | 2.0
6 | {896991fc-0289-4bae-b680-88e19508c91f}
7 |
8 |
9 |
10 |
11 | .
12 | .
13 |
14 |
15 |
16 |
17 | 10.0
18 | $(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v$(VisualStudioVersion)
19 | pathpy
20 |
21 |
22 |
23 |
24 | $(MSBuildExtensionsPath32)\Microsoft\VisualStudio\v$(VisualStudioVersion)\Python Tools\Microsoft.PythonTools.targets
25 |
26 |
27 |
28 | Code
29 |
30 |
31 | Code
32 |
33 |
34 | Code
35 |
36 |
37 | Code
38 |
39 |
40 | Code
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
54 |
55 |
56 |
57 |
58 |
59 |
60 |
61 |
62 |
63 |
64 |
65 |
66 |
67 |
68 |
69 |
70 |
71 |
72 |
73 |
--------------------------------------------------------------------------------
/pathpy.sln:
--------------------------------------------------------------------------------
1 |
2 | Microsoft Visual Studio Solution File, Format Version 12.00
3 | # Visual Studio 14
4 | VisualStudioVersion = 14.0.25420.1
5 | MinimumVisualStudioVersion = 10.0.40219.1
6 | Project("{888888A0-9F3D-457C-B088-3A5042F75D52}") = "pathpy", "pathpy.pyproj", "{896991FC-0289-4BAE-B680-88E19508C91F}"
7 | EndProject
8 | Global
9 | GlobalSection(SolutionConfigurationPlatforms) = preSolution
10 | Debug|Any CPU = Debug|Any CPU
11 | Release|Any CPU = Release|Any CPU
12 | EndGlobalSection
13 | GlobalSection(ProjectConfigurationPlatforms) = postSolution
14 | {896991FC-0289-4BAE-B680-88E19508C91F}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
15 | {896991FC-0289-4BAE-B680-88E19508C91F}.Release|Any CPU.ActiveCfg = Release|Any CPU
16 | EndGlobalSection
17 | GlobalSection(SolutionProperties) = preSolution
18 | HideSolutionNode = FALSE
19 | EndGlobalSection
20 | EndGlobal
21 |
--------------------------------------------------------------------------------
/pathpy/Log.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | """
3 | pathpy is an OpenSource python package for the analysis of sequential data
4 | on pathways and temporal networks using higher- and multi order graphical models
5 |
6 | Copyright (C) 2016-2017 Ingo Scholtes, ETH Zürich
7 |
8 | This program is free software: you can redistribute it and/or modify
9 | it under the terms of the GNU Affero General Public License as published
10 | by the Free Software Foundation, either version 3 of the License, or
11 | (at your option) any later version.
12 |
13 | This program is distributed in the hope that it will be useful,
14 | but WITHOUT ANY WARRANTY; without even the implied warranty of
15 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
16 | GNU Affero General Public License for more details.
17 |
18 | You should have received a copy of the GNU Affero General Public License
19 | along with this program. If not, see .
20 |
21 | Contact the developer:
22 |
23 | E-mail: ischoltes@ethz.ch
24 | Web: http://www.ingoscholtes.net
25 | """
26 |
27 | import enum
28 | import time
29 | import io
30 | import sys
31 |
32 | class Severity(enum.IntEnum):
33 | """ An enumeration that can be used to indicate
34 | the severity of log messages, and which can be
35 | used tpo filter messages based on severities.
36 | """
37 |
38 | ## Error messages
39 | ERROR = 4
40 |
41 | ## Warning messages
42 | WARNING = 3
43 |
44 | ## Informational messages (default minimum level)
45 | INFO = 2
46 |
47 | ## Messages regarding timing and performance
48 | TIMING = 1
49 |
50 | ## Debug messages (really verbose)
51 | DEBUG = 0
52 |
53 |
54 | class Log:
55 | """ A simple logging class, that allows to select what messages should
56 | be recorded in the output, and where these message should be directed.
57 | """
58 |
59 | ## the output stream to which log entries will be written
60 | output_stream = sys.stdout
61 |
62 | ## The minimum severity level of messages to be logged
63 | min_severity = Severity.INFO
64 |
65 |
66 | @staticmethod
67 | def setMinSeverity(severity):
68 | """ Sets the minimum sveerity level a message
69 | needs to have in order to be recorded in the output stream.
70 | By default, any message which has a severity of at least
71 | Severity.INFO will be written to the output stream. All messages
72 | with lower priority will be surpressed.
73 | """
74 | Log.min_severity = severity
75 |
76 |
77 | @staticmethod
78 | def setOutputStream(stream):
79 | """ Sets the output stream to which all messages will be
80 | written. By default, this is sys.stdout, but it can be
81 | changed in order to redirect the log to a logfile.
82 | """
83 | output_stream = stream
84 |
85 |
86 | @staticmethod
87 | def add(msg, severity=Severity.INFO):
88 | """ Adds a message with the given severity to the log. This message will be written
89 | to the log output stream, which by default is sys.stdout. A newline character
90 | will be added to the message by default.
91 | """
92 | if severity >= Log.min_severity:
93 | ts = time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime())
94 | Log.output_stream.write(ts + ' [' + str(severity) + ']\t' + msg + '\n')
95 | Log.output_stream.flush()
96 |
--------------------------------------------------------------------------------
/pathpy/MarkovSequence.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | """
3 | pathpy is an OpenSource python package for the analysis of sequential data on pathways and temporal networks using higher- and multi order graphical models
4 |
5 | Copyright (C) 2016-2017 Ingo Scholtes, ETH Zürich
6 |
7 | This program is free software: you can redistribute it and/or modify
8 | it under the terms of the GNU Affero General Public License as published
9 | by the Free Software Foundation, either version 3 of the License, or
10 | (at your option) any later version.
11 |
12 | This program is distributed in the hope that it will be useful,
13 | but WITHOUT ANY WARRANTY; without even the implied warranty of
14 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
15 | GNU Affero General Public License for more details.
16 |
17 | You should have received a copy of the GNU Affero General Public License
18 | along with this program. If not, see .
19 |
20 | Contact the developer:
21 |
22 | E-mail: ischoltes@ethz.ch
23 | Web: http://www.ingoscholtes.net
24 | """
25 |
26 | import numpy as _np
27 | import collections as _co
28 | import bisect as _bs
29 | import itertools as _iter
30 |
31 | import scipy.sparse as _sparse
32 | import scipy.misc as _misc
33 | import scipy.sparse.linalg as _sla
34 | import scipy.linalg as _la
35 |
36 | from scipy.stats import chi2
37 |
38 | from pathpy.Log import Log
39 | from pathpy.Log import Severity
40 |
41 | _np.seterr(all='warn')
42 |
43 |
44 | class MarkovSequence:
45 | """ Instances of this class can be used to fit
46 | standard higher-order Markov models for
47 | sequences generated from concatenated paths """
48 |
49 | def __init__(self, sequence):
50 | """
51 | Generates a Markov model for a sequence, given
52 | as a single list of strings
53 | """
54 |
55 | ## The sequence to be modeled
56 | self.sequence = sequence
57 |
58 | ## The transition probabilities of higher-order Markov chains
59 | self.P = {}
60 |
61 | ## the set of states of higher-order Markov chains
62 | self.states = {}
63 | self.states[1] = set(sequence)
64 |
65 |
66 | def fitMarkovModel(self, k=1):
67 | """ Generates a k-th order Markov model
68 | for the underlying sequence
69 | """
70 |
71 | # TODO: Add support for k=0
72 |
73 | assert len(self.sequence)>0, "Error: Empty sequence"
74 |
75 | # MLE fit of transition probabilities
76 | self.P[k] = _co.defaultdict( lambda: _co.defaultdict( lambda: 0.0 ) )
77 |
78 | Log.add('Fitting Markov model with order k = ' + str(k))
79 |
80 | # Generate initial memory prefix
81 | mem = (())
82 | for s in self.sequence[:k]:
83 | mem += (s,)
84 |
85 | # count state transitions
86 | for s in self.sequence[k:]:
87 | self.P[k][mem][s] += 1.0
88 |
89 | # shift memory by one element
90 | mem = mem[1:] + (s,)
91 |
92 | # normalize transitions
93 | for m in self.P[k]:
94 | S = float(sum(self.P[k][m].values()))
95 | for s in self.P[k][m]:
96 | self.P[k][m][s] /= S
97 | Log.add('finished.')
98 |
99 |
100 | def getLikelihood(self, k=1, log=True):
101 | """
102 | Returns the likelihood of the sequence
103 | assuming a k-th order Markov model
104 | """
105 |
106 | if k not in self.P:
107 | self.fitMarkovModel(k)
108 |
109 | L = 0
110 |
111 | # Generate initial prefix
112 | mem = (())
113 | for s in self.sequence[:k]:
114 | mem += (s,)
115 |
116 | for s in self.sequence[k:]:
117 | L += _np.log(self.P[k][mem][s])
118 |
119 | # shift memory by one element
120 | mem = mem[1:] + (s,)
121 |
122 | if log:
123 | return L
124 | else:
125 | return _np.exp(L)
126 |
127 |
128 | def getBIC(self, k=1, m=1):
129 | """ Returns the Bayesian Information Criterion
130 | assuming a k-th order Markov model """
131 |
132 | if k not in self.P:
133 | self.fitMarkovModel(k)
134 |
135 | if m not in self.P:
136 | self.fitMarkovModel(m)
137 |
138 | L_k = self.getLikelihood(k, log=True)
139 | L_m = self.getLikelihood(m, log=True)
140 |
141 | s = len(self.states[1])
142 | n = len(self.sequence)-k
143 |
144 | # the transition matrix of a first-order model with s states has s**2 entries, subject to the
145 | # constraint that entries in each row must sum up to one (thus effectively reducing
146 | # the degrees of freedom by a factor of s, i.e. we have s**2-s**1. Generalizing this to order k,
147 | # we arrive at s**k * (s-1) = s**(k+1) - s**k derees of freedom
148 | bic = _np.log(n) * (s**k - s**m) * (s-1) - 2.0 * (L_k-L_m)
149 |
150 | return bic
151 |
152 |
153 | def getAIC(self, k=1, m=1):
154 | """ Returns the Aikake Information Criterion
155 | assuming a k-th order Markov model """
156 |
157 | if k not in self.P:
158 | self.fitMarkovModel(k)
159 |
160 | if m not in self.P:
161 | self.fitMarkovModel(m)
162 |
163 | L_k = self.getLikelihood(k, log=True)
164 | L_m = self.getLikelihood(m, log=True)
165 |
166 | s = len(self.states[1])
167 | n = len(self.sequence)
168 |
169 | aic = 2 * (s**k - s**m) * (s-1) - 2.0 * (L_k - L_m)
170 |
171 | return aic
172 |
173 |
174 | def estimateOrder(self, maxOrder, method='BIC'):
175 | """ Estimates the optimal order of a Markov model
176 | based on Likelihood, BIC or AIC """
177 |
178 | assert method == 'BIC' or method == 'AIC' or method == 'Likelihood', "Error: Expecting method 'AIC', 'BIC' or 'Likelihood'"
179 |
180 | values = []
181 | orders = []
182 |
183 | # We need k < m for the BIC and AIC calculation, which
184 | # is why we only test up to maxOrder - 1
185 | for k in range(1, maxOrder):
186 | if k not in self.P:
187 | self.fitMarkovModel(k)
188 |
189 | orders.append(k)
190 |
191 | if method == 'AIC':
192 | values.append(self.getAIC(k, maxOrder))
193 | elif method == 'BIC':
194 | values.append(self.getBIC(k, maxOrder))
195 | elif method == 'Likelihood':
196 | values.append(self.getLikelihood(k, log=True))
197 |
198 | if method == 'Likelihood':
199 | values.append(self.getLikelihood(maxOrder, log=True))
200 | orders.append(maxOrder)
201 |
202 | # return order at which likelihood is maximized
203 | return orders[_np.argmax(values)]
204 | else:
205 | # return order at which BIC/AIC are minimized
206 | return orders[_np.argmin(values)]
207 |
--------------------------------------------------------------------------------
/pathpy/__init__.py:
--------------------------------------------------------------------------------
1 | from .Log import *
2 | from .TemporalNetwork import *
3 | from .Paths import *
4 | from .HigherOrderNetwork import *
5 | from .MultiOrderModel import *
6 | from .MarkovSequence import *
7 |
8 | import pathpy.Log as Log
--------------------------------------------------------------------------------
/pathpy_logo.png:
--------------------------------------------------------------------------------
https://raw.githubusercontent.com/IngoScholtes/pathpy/857f97d1b5a7eec8466775adfed29c28f32f87aa/pathpy_logo.png
--------------------------------------------------------------------------------
/setup.py:
--------------------------------------------------------------------------------
1 | """A python package for the analysis of sequential data on pathways and temporal networks from the perspective of higher-order network models.
2 |
3 | See: https://packaging.python.org/en/latest/distributing.html
4 | """
5 |
6 | # Always prefer setuptools over distutils
7 | from setuptools import setup, find_packages
8 | # To use a consistent encoding
9 | from codecs import open
10 | from os import path
11 | import sys
12 |
13 | here = path.abspath(path.dirname(__file__))
14 |
15 | # Get the long description from the relevant file
16 | with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
17 | long_description = f.read()
18 |
19 | required = ['numpy', 'scipy']
20 |
21 | if (sys.version_info.major, sys.version_info.minor) < (3,4):
22 | required.append('enum34')
23 |
24 | setup(
25 | name='pathpy',
26 |
27 | # Versions should comply with PEP440. For a discussion on single-sourcing
28 | # the version across setup.py and the project code, see
29 | # https://packaging.python.org/en/latest/single_source_version.html
30 | version='1.1.170316',
31 |
32 | description='A python package for the analysis of sequential data on pathways and temporal networks from the perspective of higher-order network models.',
33 | long_description=long_description,
34 |
35 | # The project's main homepage.
36 | url='https://github.com/IngoScholtes/pathpy',
37 |
38 | # Author details
39 | author='Ingo Scholtes',
40 | author_email='ischoltes@ethz.ch',
41 |
42 | # Choose your license
43 | license='AGPL-3.0+',
44 |
45 | # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
46 | classifiers=[
47 | # How mature is this project? Common values are
48 | # 3 - Alpha
49 | # 4 - Beta
50 | # 5 - Production/Stable
51 | 'Development Status :: 4 - Beta',
52 |
53 | # Indicate who your project is intended for
54 | 'Intended Audience :: Science/Research',
55 | 'Topic :: Scientific/Engineering :: Information Analysis',
56 |
57 | # Pick your license as you wish (should match "license" above)
58 | 'License :: OSI Approved :: AGPL-3.0+ License',
59 |
60 | # Specify the Python versions you support here. In particular, ensure
61 | # that you indicate whether you support Python 2, Python 3 or both.
62 | 'Programming Language :: Python :: 3',
63 | 'Programming Language :: Python :: 3.2',
64 | 'Programming Language :: Python :: 3.3',
65 | 'Programming Language :: Python :: 3.4',
66 | 'Programming Language :: Python :: 3.5',
67 | ],
68 |
69 | # What does your project relate to?
70 | keywords='network analysis temporal networks pathways sequence modeling graph mining',
71 |
72 | # You can just specify the packages manually here if your project is
73 | # simple. Or you can use find_packages().
74 | packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
75 |
76 | # List run-time dependencies here. These will be installed by pip when
77 | # your project is installed. For an analysis of "install_requires" vs pip's
78 | # requirements files see:
79 | # https://packaging.python.org/en/latest/requirements.html
80 | install_requires=required,
81 |
82 | # If there are data files included in your packages that need to be
83 | # installed, specify them here. If using Python 2.6 or less, then these
84 | # have to be included in MANIFEST.in as well.
85 | package_data={
86 | }
87 | )
--------------------------------------------------------------------------------
/tests/README.md:
--------------------------------------------------------------------------------
1 | # Unit tests for pypath
2 |
3 | This directory contains the unit tests for methods and functions
4 | in pathpy.
5 | The testing framework [pytest](doc.pytest.org/)
6 | is required to run the tests.
7 |
8 | To run the test suite (without slow tests) run
9 | ```bash
10 | $ pytest tests
11 | ```
12 |
13 | ## Slow functions
14 |
15 | Slow functions can be decorated with `slow` to mark them
16 | as skippable if you require only a quick check.
17 | To run all tests add the flag `--runslow`:
18 | ```bash
19 | $ pytest --runslow
20 | ```
21 |
22 | ## Coverage report
23 |
24 | To compute a coverage report of the tests you need to install
25 | [coverage.py](https://coverage.readthedocs.io/en/coverage-4.3.4/)
26 | as well as its `pytest` integration
27 | [pytest-cov][1]
28 | ```bash
29 | $ pytest tests/ --runslow --cov=pathpy --cov-report html
30 | ```
31 | which will create an html coverage report in the same directory.
32 |
33 | [1]: https://pypi.python.org/pypi/pytest-cov
34 |
--------------------------------------------------------------------------------
/tests/conftest.py:
--------------------------------------------------------------------------------
1 | import pathpy as pp
2 | import pytest
3 | import numpy as np
4 | import os
5 |
6 | test_directory = os.path.dirname(os.path.abspath(__file__))
7 | test_data_dir = os.path.join(test_directory, 'test_data')
8 |
9 |
10 | def pytest_addoption(parser):
11 | parser.addoption("--runslow", action="store_true",
12 | help="run slow tests")
13 |
14 |
15 | def pytest_runtest_setup(item):
16 | if 'slow' in item.keywords and not item.config.getvalue("runslow"):
17 | pytest.skip("need --runslow option to run")
18 |
19 |
20 |
21 | @pytest.fixture()
22 | def test_data_directory():
23 | return test_data_dir
24 |
25 |
26 | @pytest.fixture()
27 | def path_from_ngram_file():
28 | """load the example file as pypath.Path"""
29 | ngram_file_path = os.path.join(test_data_dir, 'ngram_simple.ngram')
30 | path = pp.Paths.readFile(ngram_file_path, pathFrequency=True)
31 | return path
32 |
33 |
34 | @pytest.fixture()
35 | def path_from_edge_file():
36 | file_path = os.path.join(test_data_dir, 'edge_frequency.edge')
37 | path = pp.Paths.readEdges(file_path, weight=True)
38 |
39 | return path
40 |
41 |
42 | @pytest.fixture()
43 | def path_from_edge_file_undirected():
44 | file_path = os.path.join(test_data_dir, 'edge_frequency.edge')
45 | path = pp.Paths.readEdges(file_path, weight=True, undirected=True)
46 | return path
47 |
48 |
49 | def generate_random_path(size, rnd_seed):
50 | """Generate a Path with random path sequences"""
51 | import string
52 | node_set = string.ascii_lowercase
53 |
54 | def random_ngram(p_len, nodes):
55 | num_elements = len(nodes)
56 | sequence = np.random.choice(num_elements, p_len)
57 | path = [nodes[i] for i in sequence]
58 | return ','.join(path)
59 |
60 | np.random.seed(rnd_seed)
61 | paths = pp.Paths()
62 | for _ in range(size):
63 | frequency = np.random.randint(1, 4)
64 | path_length = np.random.randint(1, 10)
65 | path_to_add = random_ngram(path_length, node_set)
66 | paths.addPath(path_to_add, pathFrequency=frequency)
67 |
68 | return paths
69 |
70 |
71 | @pytest.fixture(scope='function')
72 | def random_paths():
73 | """Generate a Path with random path sequences"""
74 | return generate_random_path
75 |
76 |
77 | @pytest.fixture()
78 | def temporal_network_object():
79 | t = pp.TemporalNetwork()
80 | # Path of length two
81 | t.addEdge("c", "e", 1)
82 | t.addEdge("e", "f", 2)
83 |
84 | # Path of length two
85 | t.addEdge("a", "e", 3)
86 | t.addEdge("e", "g", 4)
87 |
88 | # Path of length two
89 | t.addEdge("c", "e", 5)
90 | t.addEdge("e", "f", 6)
91 |
92 | # Path of length two
93 | t.addEdge("a", "e", 7)
94 | t.addEdge("e", "g", 8)
95 |
96 | # Path of length two
97 | t.addEdge("c", "e", 9)
98 | t.addEdge("e", "f", 10)
99 |
100 | # The next two edges continue the previous path to ( c-> e-> f-> e -> b )
101 | t.addEdge("f", "e", 11)
102 | t.addEdge("e", "b", 12)
103 |
104 | # This is an isolated edge (i.e. path of length one)
105 | t.addEdge("e", "b", 13)
106 |
107 | # Path of length two
108 | t.addEdge("c", "e", 14)
109 | t.addEdge("e", "f", 15)
110 |
111 | # Path of length two
112 | t.addEdge("b", "e", 16)
113 | t.addEdge("e", "g", 17)
114 |
115 | # Path of length two
116 | t.addEdge("c", "e", 18)
117 | t.addEdge("e", "f", 19)
118 |
119 | # Path of length two
120 | t.addEdge("c", "e", 20)
121 | t.addEdge("e", "f", 21)
122 |
123 | return t
124 |
--------------------------------------------------------------------------------
/tests/test_Path.py:
--------------------------------------------------------------------------------
1 | # -*- coding: utf-8 -*-
2 | """
3 | Created on Fri Feb 20 11:59:22 2015
4 | @author: Ingo Scholtes
5 |
6 | (c) Copyright ETH Zurich, Chair of Systems Design, 2015-2017
7 | """
8 | import pathpy as pp
9 | import pytest
10 |
11 |
12 | slow = pytest.mark.slow
13 |
14 |
15 | def test_readfile_import(path_from_ngram_file):
16 | levels = list(path_from_ngram_file.paths.keys())
17 | max_level = max(levels)
18 | expected = 5
19 | assert max_level == expected, \
20 | "The nodes have not been imported correctly"
21 |
22 | assert path_from_ngram_file.getNodes() == {'a', 'b', 'c', 'd', 'e'}, \
23 | "Wrong node labels"
24 |
25 |
26 | def test_write_file(tmpdir, random_paths):
27 | dir_path = tmpdir.mkdir("sub").join("test.edges")
28 | p = random_paths(30, 50)
29 |
30 | expected_seq = ''.join(p.getSequence())
31 | expected_paths = sorted(expected_seq.split('|'))
32 |
33 | p.writeFile(dir_path.strpath)
34 | p2 = pp.Paths.readFile(dir_path.strpath, pathFrequency=True)
35 |
36 | read_back = ''.join(p2.getSequence())
37 | read_back_paths = sorted(read_back.split('|'))
38 |
39 | assert expected_paths == read_back_paths
40 |
41 |
42 | def test_read_edges_import(path_from_edge_file):
43 | """test if the Paths.readEdges functions works"""
44 | levels = list(path_from_edge_file.paths.keys())
45 | max_level = max(levels)
46 | expected_max = 1
47 | assert expected_max == max_level, \
48 | "The nodes have not been imported correctly"
49 |
50 | assert path_from_edge_file.getNodes() == {'1', '2', '3', '5'}, \
51 | "Nodes not imported correctly"
52 |
53 |
54 | def test_read_edges_undirected(path_from_edge_file_undirected):
55 | p = path_from_edge_file_undirected
56 | layers = list(p.paths.keys())
57 | max_layers = max(layers)
58 | expected_layers = 1
59 | assert max_layers == expected_layers, \
60 | "The nodes have not been imported correctly"
61 |
62 | assert p.getNodes() == {'1', '2', '3', '5'}, \
63 | "Nodes not imported correctly"
64 |
65 |
66 | def test_get_sequence(path_from_ngram_file):
67 | from collections import Counter
68 | """Test if the Paths.getSequence function works correctly"""
69 | sequence = path_from_ngram_file.getSequence()
70 | sequence = "".join(sequence)
71 | ct = Counter(sequence.split('|'))
72 | assert dict(ct) == {'': 1, 'abcdab': 2, 'dedab': 4}, \
73 | "Returned the wrong sequence"
74 |
75 |
76 | def test_get_unique_paths(random_paths):
77 | p = random_paths(90, 90)
78 | assert p.getUniquePaths() == 87, \
79 | "Wrong number of paths detected"
80 |
81 |
82 | def test_observation_count_file(path_from_ngram_file):
83 | assert path_from_ngram_file.ObservationCount() == 6, \
84 | "Wrong number of observations detected"
85 |
86 |
87 | def test_observation_count_large(random_paths):
88 | p = random_paths(90, 90)
89 | assert p.ObservationCount() == 193, \
90 | "Wrong number of observations detected"
91 |
92 |
93 | def test_path_summary(random_paths):
94 | p = random_paths(90, 90)
95 | print(p)
96 |
97 |
98 | def test_summary_multi_order_model(random_paths):
99 | p = random_paths(90, 90)
100 | multi = pp.MultiOrderModel(paths=p, maxOrder=3)
101 | print(multi)
102 |
103 |
104 | def test_get_shortest_paths(path_from_ngram_file):
105 | path_from_ngram_file.getShortestPaths()
106 | paths_dict = path_from_ngram_file.getShortestPaths()
107 | expected_paths = {('d', 'a'): {('d', 'a')},
108 | ('b', 'd'): {('b', 'c', 'd')},
109 | ('d', 'e'): {('d', 'e')},
110 | ('a', 'c'): {('a', 'b', 'c')},
111 | ('a', 'a'): {('a',)},
112 | ('e', 'a'): {('e', 'd', 'a')},
113 | ('e', 'b'): {('e', 'd', 'a', 'b')},
114 | ('e', 'e'): {('e',)},
115 | ('a', 'b'): {('a', 'b')},
116 | ('b', 'b'): {('b',)},
117 | ('c', 'd'): {('c', 'd')},
118 | ('d', 'b'): {('d', 'a', 'b')},
119 | ('c', 'a'): {('c', 'd', 'a')},
120 | ('b', 'a'): {('b', 'c', 'd', 'a')},
121 | ('c', 'b'): {('c', 'd', 'a', 'b')},
122 | ('e', 'd'): {('e', 'd')},
123 | ('a', 'd'): {('a', 'b', 'c', 'd')},
124 | ('d', 'd'): {('d',)},
125 | ('c', 'c'): {('c',)},
126 | ('b', 'c'): {('b', 'c')}
127 | }
128 | paths_to_check = dict()
129 | for k in paths_dict:
130 | for p in paths_dict[k]:
131 | paths_to_check[(k, p)] = paths_dict[k][p]
132 | assert paths_to_check == expected_paths
133 |
134 |
135 | def test_get_contained_paths():
136 | path_to_check = ('a', 'b', 'c', 'd', 'e', 'f', 'g')
137 | node_filter = ('a', 'b', 'd', 'f', 'g')
138 | cont_paths = pp.Paths.getContainedPaths(path_to_check, node_filter)
139 | expected = [('a', 'b'), ('d',), ('f', 'g')]
140 | assert cont_paths == expected
141 |
142 |
143 | def test_filter_paths(path_from_ngram_file):
144 | from collections import Counter
145 | p = path_from_ngram_file
146 | new_paths = p.filterPaths(node_filter=['a', 'b', 'c'])
147 | expected_sequence = {'': 1, 'ab': 6, 'abc': 2}
148 |
149 | new_sequence = ''.join(new_paths.getSequence())
150 | ct = Counter(new_sequence.split('|'))
151 | assert dict(ct) == expected_sequence
152 |
153 |
154 | def test_project_paths(path_from_ngram_file):
155 | from collections import Counter
156 | p = path_from_ngram_file
157 | mapping = {'a': 'x', 'b': 'x', 'c': 'y', 'd': 'y', 'e': 'y'}
158 | new_p = p.projectPaths(mapping=mapping)
159 | new_sequence = ''.join(new_p.getSequence())
160 | ct = Counter(new_sequence.split('|'))
161 | expected_sequence = {'': 1, 'xxyyxx': 2, 'yyyxx': 4}
162 | assert dict(ct) == expected_sequence
163 |
164 |
165 | def test_get_nodes(random_paths):
166 | p = random_paths(3, 9)
167 | rest = p.getNodes()
168 | expected = {'b', 'o', 'u', 'v', 'w', 'y'}
169 | assert rest == expected
170 |
--------------------------------------------------------------------------------
/tests/test_TemporalNetwork.py:
--------------------------------------------------------------------------------
1 | import pathpy as pp
2 | import os
3 | import numpy as np
4 |
5 |
6 | def test_read_temporal_file_int(test_data_directory,):
7 | file_path = os.path.join(test_data_directory, 'example_int.tedges')
8 | t = pp.TemporalNetwork.readFile(file_path)
9 | times = t.ordered_times
10 | expected_times = [0, 2, 4, 5, 6, 8]
11 | assert times == expected_times
12 |
13 | activities = sorted(list(t.activities.values()))
14 | expected_activities = [[], [], [], [], [0, 2, 5], [2], [4], [6], [8]]
15 | assert expected_activities == activities
16 |
17 |
18 | def test_read_temporal_file_time_stamp(test_data_directory,):
19 | file_path = os.path.join(test_data_directory, 'example_timestamp.tedges')
20 | t = pp.TemporalNetwork.readFile(file_path, timestampformat="%Y-%m-%d %H:%M")
21 | times = t.ordered_times
22 | time_diffs = [j-i for i, j in zip(times[:-1], times[1:])]
23 | expected_diffs = [10800, 15060, 264960]
24 | # TODO: The actual time number depends on local set by the user
25 | assert time_diffs == expected_diffs
26 |
27 |
28 | def test_filter_temporal_edges(temporal_network_object):
29 | t = temporal_network_object
30 |
31 | def filter_func(v, w, time):
32 | return time % 2 == 0
33 |
34 | filtered = t.filterEdges(filter_func)
35 | times = filtered.ordered_times
36 | expected = [2, 4, 6, 8, 10, 12, 14, 16, 18, 20]
37 | assert times == expected
38 |
39 |
40 | def test_get_interpath_times(temporal_network_object):
41 | t = temporal_network_object
42 | inter_time = dict(t.getInterPathTimes())
43 | expected = {'e': [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
44 | 'b': [4, 3], 'f': [9, 5, 1]
45 | }
46 | assert inter_time == expected
47 |
48 |
49 | def test_shuffle_edges(temporal_network_object):
50 | t = temporal_network_object
51 | np.random.seed(90)
52 | t1 = t.ShuffleEdges(with_replacement=True)
53 | times1 = len(t1.tedges)
54 | expected1 = len(t.tedges)
55 | assert times1 == expected1
56 | np.random.seed(90)
57 | t2 = t.ShuffleEdges(l=4, with_replacement=False)
58 | edges2 = len(t2.tedges)
59 | expected2 = 4
60 | assert edges2 == expected2
61 |
62 |
63 | def test_inter_event_times(temporal_network_object):
64 | time_diffs = temporal_network_object.getInterEventTimes()
65 | # all time differences are 1
66 | assert (time_diffs == 1).all()
67 |
68 |
69 | def test_inter_path_times(temporal_network_object):
70 | t = temporal_network_object
71 | path_times = dict(t.getInterPathTimes())
72 | expected = {'f': [9, 5, 1],
73 | 'e': [1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
74 | 'b': [4, 3]}
75 | assert path_times == expected
76 |
77 |
78 | def test_temporal_summary(temporal_network_object):
79 | print(temporal_network_object)
80 |
--------------------------------------------------------------------------------
/tests/test_data/edge_frequency.edge:
--------------------------------------------------------------------------------
1 | 1,2,45,3,3,3
2 | 1,3,2,23,2,2
3 | 1,5,5,12,5,2
4 | 3,5,2,11,45,2
5 | 5,3,4,12,2,2
6 | 5,2,1,12,4,1
7 |
--------------------------------------------------------------------------------
/tests/test_data/example_int.tedges:
--------------------------------------------------------------------------------
1 | source,target,time
2 | 1,2,0
3 | 1,2,2
4 | 1,3,5
5 | 3,2,6
6 | 2,1,8
7 | 4,5,2
8 | 5,3,4
--------------------------------------------------------------------------------
/tests/test_data/example_timestamp.tedges:
--------------------------------------------------------------------------------
1 | source,target,time
2 | 1,4,2000-03-04 12:45
3 | 2,4,2000-03-04 15:45
4 | 5,2,2000-03-04 19:56
5 | 8,2,2000-03-07 21:32
--------------------------------------------------------------------------------
/tests/test_data/ngram_simple.ngram:
--------------------------------------------------------------------------------
1 | a,b,c,d,a,b,2
2 | d,e,d,a,b,4
3 |
--------------------------------------------------------------------------------