General function to apply community detection algorithms available in
`igraph`

. Follows the `EGAnet`

approach of setting
singleton and disconnected nodes to missing (`NA`

)

## Usage

```
community.detection(
network,
algorithm = c("edge_betweenness", "fast_greedy", "fluid", "infomap", "label_prop",
"leading_eigen", "leiden", "louvain", "optimal", "spinglass", "walktrap"),
allow.singleton = FALSE,
membership.only = TRUE,
...
)
```

## Arguments

- network
Matrix or

`igraph`

network object- algorithm
Character or

`igraph`

`cluster_*`

function (length = 1). Available options:`"edge_betweenness"`

— See`cluster_edge_betweenness`

for more details`"fast_greedy"`

— See`cluster_fast_greedy`

for more details`"fluid"`

— See`cluster_fluid_communities`

for more details`"infomap"`

— See`cluster_infomap`

for more details`"label_prop"`

— See`cluster_label_prop`

for more details`"leading_eigen"`

— See`cluster_leading_eigen`

for more details`"leiden"`

— See`cluster_leiden`

for more details.*Note*: The Leiden algorithm will default to the modularity objective function (`objective_function = "modularity"`

). Set`objective_function = "CPM"`

to use the Constant Potts Model instead (see examples)`"louvain"`

— See`cluster_louvain`

for more details`"optimal"`

— See`cluster_optimal`

for more details`"spinglass"`

— See`cluster_spinglass`

for more details`"walktrap"`

— See`cluster_walktrap`

for more details

- allow.singleton
Boolean (length = 1). Whether singleton or single node communities should be allowed. Defaults to

`FALSE`

. When`FALSE`

, singleton communities will be set to missing (`NA`

); otherwise, when`TRUE`

, singleton communities will be allowed- membership.only
Boolean (length = 1). Whether the memberships only should be output. Defaults to

`TRUE`

. Set to`FALSE`

to obtain all output for the community detection algorithm- ...
Additional arguments to be passed on to

`igraph`

's community detection functions (see`algorithm`

for link to arguments of each algorithm)

## References

Csardi, G., & Nepusz, T. (2006).
The igraph software package for complex network research.
*InterJournal, Complex Systems*, 1695.

## Author

Hudson Golino <hfg9s at virginia.edu> and Alexander P. Christensen <alexpaulchristensen@gmail.com>

## Examples

```
# Load data
wmt <- wmt2[,7:24]
# Estimate network
network <- EBICglasso.qgraph(data = wmt)
# Compute Edge Betweenness
community.detection(network, algorithm = "edge_betweenness")
#> Warning: At vendor/cigraph/src/community/edge_betweenness.c:497 : Membership vector will be selected based on the highest modularity score.
#> Algorithm: Edge Betweenness
#>
#> Number of communities: 4
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 NA 2 2 2 2 3 1 4 3 2 1
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 4 2 1 2 3
# Compute Fast Greedy
community.detection(network, algorithm = "fast_greedy")
#> Algorithm: Fast-greedy
#>
#> Number of communities: 3
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 3 3 2 2 3
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 3 2 3 2 2
# Compute Fluid
community.detection(
network, algorithm = "fluid",
no.of.communities = 2 # needs to be set
)
#> Algorithm: Fluid
#>
#> Number of communities: 2
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 2 1 2 2 2
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 2 2 2 2 2
# Compute Infomap
community.detection(network, algorithm = "infomap")
#> Algorithm: Infomap
#>
#> Number of communities: 1
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 1 1 1 1 1 1 1 1
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 1 1 1 1 1
# Compute Label Propagation
community.detection(network, algorithm = "label_prop")
#> Algorithm: Label Propagation
#>
#> Number of communities: 1
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 1 1 1 1 1 1 1 1
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 1 1 1 1 1
# Compute Leading Eigenvector
community.detection(network, algorithm = "leading_eigen")
#> Algorithm: Leading Eigenvector
#>
#> Number of communities: 3
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 3 1 2 2 3
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 3 3 3 2 2
# Compute Leiden (with modularity)
community.detection(
network, algorithm = "leiden",
objective_function = "modularity"
)
#> Algorithm: Leiden with Modularity
#>
#> Number of communities: 3
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 3 3 2 2 3
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 3 2 3 2 2
# Compute Leiden (with CPM)
community.detection(
network, algorithm = "leiden",
objective_function = "CPM",
resolution_parameter = 0.05 # "edge density"
)
#> Algorithm: Leiden with Constant Potts Model
#>
#> Number of communities: 4
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 3 3 2 2 3
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 3 2 3 4 4
# Compute Louvain
community.detection(network, algorithm = "louvain")
#> Algorithm: Louvain
#>
#> Number of communities: 3
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 3 3 2 2 3
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 3 2 3 2 2
# Compute Optimal (identifies maximum modularity solution)
community.detection(network, algorithm = "optimal")
#> Algorithm: Optimal
#>
#> Number of communities: 3
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 3 3 2 2 3
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 3 2 3 2 2
# Compute Spinglass
community.detection(network, algorithm = "spinglass")
#> Algorithm: Spinglass
#>
#> Number of communities: 3
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 3 3 2 2 3
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 3 2 3 2 2
# Compute Walktrap
community.detection(network, algorithm = "walktrap")
#> Algorithm: Walktrap
#>
#> Number of communities: 2
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 2 2 2 2 2
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 2 2 2 2 2
# Example with {igraph} network
community.detection(
convert2igraph(network), algorithm = "walktrap"
)
#> Algorithm: Walktrap
#>
#> Number of communities: 2
#>
#> wmt1 wmt2 wmt3 wmt4 wmt5 wmt6 wmt7 wmt8 wmt9 wmt10 wmt11 wmt12 wmt13
#> 1 1 1 1 1 2 2 2 2 2 2 2 2
#> wmt14 wmt15 wmt16 wmt17 wmt18
#> 2 2 2 2 2
```