triversity v1.0

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Diversity Measures on Tripartite Graphs

Computing diversity measures on tripartite graphs. This package first implements a parametrized family of such diversity measures which apply on probability distributions. Sometimes called "True Diversity", this family contains famous measures such as the richness, the Shannon entropy, the Herfindahl-Hirschman index, and the Berger-Parker index. Second, the package allows to apply these measures on probability distributions resulting from random walks between the levels of tripartite graphs. By defining an initial distribution at a given level of the graph and a path to follow between the three levels, the probability of the walker's position within the final level is then computed, thus providing a particular instance of diversity to measure.

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triversity: Diversity Measures on Tripartite Graphs

triversity is an R package for the computation of diversity measures on tripartite graphs. First, it implements a parametrized family of such diversity measures which apply on probability distributions. Sometimes called "True Diversity", this family contains famous measures such as the Richness, the Shannon entropy, the Herfindahl-Hirschman index, and the Berger-Parker index. Second, the package allows to apply these measures on probability distributions resulting from random walks between the levels of tripartite graphs. By defining an initial distribution at a given level of the graph and a path to follow between the three levels, the probability of the walker's position within the final level is then computed, thus providing a particular instance of diversity to measure.

Clone

git clone https://github.com/Lamarche-Perrin/triversity

Authors

This package has been developed by researchers of the Complex Networks team, within the Computer Science Laboratory of Paris 6, for the AlgoDiv project, founded by the French National Agency of Research under grant ANR-15-CE38-0001.

List of main collaborators:

License

Copyright © 2017 Robin Lamarche-Perrin (Robin.Lamarche-Perrin@lip6.fr)
triversity is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. It is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

Functions in triversity

Name Description
get_transition_from_path Compute the transition matrix of a random walk following a path between the levels of a tripartite graph.
get_tripartite Build a properly-structured tripartite graph from raw data.
get_diversity_from_distribution Compute the diversity of a probability distribution.
get_diversity_from_path Compute the diversity associated to a random walk following a path between the levels of a tripartite graph.
get_conditional_diversity_from_transition Compute the conditional diversity of a transition matrix.
get_distribution_from_path Compute the probability distribution associated to a random walk following a path between the levels of a tripartite graph.
tripartite_example An example of dataframe encoding a small tripartite graph.
triversity Compute diversity measures on tripartite graphs.
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License GPL-3 | file LICENSE
Encoding UTF-8
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-10-11 14:54:28 UTC; lamarche
Repository CRAN
Date/Publication 2017-10-11 17:30:09 UTC
depends data.tree , Matrix , R (>= 3.2.3)
Contributors

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