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schochastics committed Dec 2, 2022
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35 changes: 35 additions & 0 deletions paper.bib
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Expand Up @@ -215,3 +215,38 @@ @misc{fmtk-ergmdsnair-22
publisher = {{arXiv}},
doi = {10.48550/arXiv.2205.13411}
}

@article{an-dcopsnpc-20,
title = {Detecting Coalitions by Optimally Partitioning Signed Networks of Political Collaboration},
author = {Aref, Samin and Neal, Zachary},
year = {2020},
journal = {Scientific Reports},
volume = {10},
number = {1},
pages = {1506},
publisher = {{Nature Publishing Group}},
issn = {2045-2322},
doi = {10.1038/s41598-020-58471-z}
}

@manual{s-omsmilp-22,
title = {ompr: Model and Solve Mixed Integer Linear Programs},
author = {Dirk Schumacher},
year = {2022},
note = {R package version 1.0.3},
url = {https://CRAN.R-project.org/package=ompr},
}

@article{n-brpenb-22,
doi = {10.1371/journal.pone.0269137},
author = {Neal, Zachary P.},
journal = {PLOS ONE},
publisher = {Public Library of Science},
title = {backbone: An {{R}} package to extract network backbones},
year = {2022},
month = {05},
volume = {17},
url = {https://doi.org/10.1371/journal.pone.0269137},
pages = {1-24},
number = {5}
}
19 changes: 12 additions & 7 deletions paper.md
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Expand Up @@ -42,8 +42,9 @@ social media [@klb-szmsnne-09]. General purpose packages for network analysis
such as `igraph` [@cn-ispcnr-06] and `sna` [@b-snas-08] implement all commonly
used network analytic methods but do not offer any functionality for signed
networks. `signnet` closes this gap and makes many tools for signed
network available in R. The package has already found its place in empirical research
[@csr-avacpbsn-22;@fmtk-ergmdsnair-22].
networks available in R. The package has already found its place in empirical research
[@csr-avacpbsn-22;@fmtk-ergmdsnair-22] and the R package `backbone` [@n-brpenb-22] uses the data
structure suggested by `signnet` for signed backbones of networks.

# Implementation details
The package is modeled with `igraph` compatibility in mind and follows its
Expand All @@ -60,6 +61,7 @@ This section highlights some of the main methods implemented in the package.
For more details for each subsection see the respective package vignette.

```R
install.packages("signnet"")
library(signnet)
data("tribes") # dataset included in signnet
```
Expand Down Expand Up @@ -93,8 +95,11 @@ frustration_exact(tribes)
```
The return value `partition` gives the optimal partition into the two node sets for
which the optimal frustration is achieved. Note that the problem is NP hard and
frustration can thus only be calculated for rather small signed networks.
which the optimal frustration is achieved. The implemented algorithm can deal with fairly large
networks, even though the problem is NP hard [@an-dcopsnpc-20].
To use `frustation_exact()`, the package `ompr` and its auxiliary packages need to be installed
separately [@s-omsmilp-22].
## Blockmodeling
In signed blockmodeling, the goal is to determine $k$ blocks of nodes such that
Expand Down Expand Up @@ -163,11 +168,11 @@ pn_index(g)
## Signed two-mode networks
A common analytic tool for two-mode networks is to project the network onto on
relevant mode. This is easily done using the adjacency matrix $𝐴$. $𝐴𝐴^𝑇$
yields the row projection and $𝐴^𝑇𝐴$ the column projection. The resulting
relevant mode. This is easily done using the adjacency matrix $A$. $AA^T$
yields the row projection and $A^TA$ the column projection. The resulting
networks will thus be weighted. Several methods exist to turn a weighted
projection into an unweighted network where only the most significant edges are
included [@dns-brpebbp-21]. Projecting signed networks is not as
included [@n-brpenb-22]. Projecting signed networks is not as
straightforward, because "nullification" of edges can occur. @s-pstn-21
introduces two methods to deal with this issue which are implemented in
`signnet`. The trick is to convert the signed network into an a special
Expand Down

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