corLinkcommCentrality: Correlation of Community Centrality with Classic Centrality
In linkcomm: Tools for Generating, Visualizing, and Analysing Link Communities in Networks
Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
Examples
View source: R/linkcomm_misc.R
Description
This function calculates the correlation between the community centrality and classic centrality measures for a set of nodes in a network, and plots a scatterplot of the relationship together with a fitted straight line.
Usage
1
2
Arguments
x
An object of class linkcomm.
centrality
A character string naming the classic centrality measure. Can be one of "degree", "betweenness", "closeness", and "constraint". Defaults to "degree".
type
A character string naming the type of community centrality. Can be "commweight" or "commconn", defaults to "commweight".
method
A character string naming the correlation method. Can be one of "spearman", "pearson", or "kendall". Defaults to "spearman".
plot
Logical, whether to plot a scatterplot of the relationship, defaults to TRUE.
pch
An integer specifying the plot symbol (see par). Defaults to 20.
...
Additional arguments to be passed to plot.
Details
The correlation between community centrality and classic centrality measures, such as degree or betweenness, may reveal discrepancies, thereby indicating that community centrality scores provide a unique reflection of node importance.
Value
A correlation coefficient.
Author(s)
Alex T. Kalinka alex.t.kalinka@gmail.com
References
Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.
See Also
Examples
1
2
3
4
5
6
## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)
## Correlate community centrality with degree centrality.
corLinkcommCentrality(lc)
Example output
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: RColorBrewer
Welcome to linkcomm version 1.0-11
For a step-by-step guide to using linkcomm functions:
> vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
> demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
> citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))
Checking for loops and duplicate edges... 0.000%
Checking for loops and duplicate edges... 2.174%
Checking for loops and duplicate edges... 4.348%
Checking for loops and duplicate edges... 6.522%
Checking for loops and duplicate edges... 8.696%
Checking for loops and duplicate edges... 10.870%
Checking for loops and duplicate edges... 13.043%
Checking for loops and duplicate edges... 15.217%
Checking for loops and duplicate edges... 17.391%
Checking for loops and duplicate edges... 19.565%
Checking for loops and duplicate edges... 21.739%
Checking for loops and duplicate edges... 23.913%
Checking for loops and duplicate edges... 26.087%
Checking for loops and duplicate edges... 28.261%
Checking for loops and duplicate edges... 30.435%
Checking for loops and duplicate edges... 32.609%
Checking for loops and duplicate edges... 34.783%
Checking for loops and duplicate edges... 36.957%
Checking for loops and duplicate edges... 39.130%
Checking for loops and duplicate edges... 41.304%
Checking for loops and duplicate edges... 43.478%
Checking for loops and duplicate edges... 45.652%
Checking for loops and duplicate edges... 47.826%
Checking for loops and duplicate edges... 50.000%
Checking for loops and duplicate edges... 52.174%
Checking for loops and duplicate edges... 54.348%
Checking for loops and duplicate edges... 56.522%
Checking for loops and duplicate edges... 58.696%
Checking for loops and duplicate edges... 60.870%
Checking for loops and duplicate edges... 63.043%
Checking for loops and duplicate edges... 65.217%
Checking for loops and duplicate edges... 67.391%
Checking for loops and duplicate edges... 69.565%
Checking for loops and duplicate edges... 71.739%
Checking for loops and duplicate edges... 73.913%
Checking for loops and duplicate edges... 76.087%
Checking for loops and duplicate edges... 78.261%
Checking for loops and duplicate edges... 80.435%
Checking for loops and duplicate edges... 82.609%
Checking for loops and duplicate edges... 84.783%
Checking for loops and duplicate edges... 86.957%
Checking for loops and duplicate edges... 89.130%
Checking for loops and duplicate edges... 91.304%
Checking for loops and duplicate edges... 93.478%
Checking for loops and duplicate edges... 95.652%
Checking for loops and duplicate edges... 97.826%
Checking for loops and duplicate edges... 100.000%
Found and removed 4 loop(s)
Found and removed 2 duplicate edge(s)
Calculating edge similarities for 41 edges... 0.00%
Calculating edge similarities for 41 edges... 2.56%
Calculating edge similarities for 41 edges... 5.13%
Calculating edge similarities for 41 edges... 7.69%
Calculating edge similarities for 41 edges... 10.26%
Calculating edge similarities for 41 edges... 12.82%
Calculating edge similarities for 41 edges... 15.38%
Calculating edge similarities for 41 edges... 17.95%
Calculating edge similarities for 41 edges... 20.51%
Calculating edge similarities for 41 edges... 23.08%
Calculating edge similarities for 41 edges... 25.64%
Calculating edge similarities for 41 edges... 28.21%
Calculating edge similarities for 41 edges... 30.77%
Calculating edge similarities for 41 edges... 33.33%
Calculating edge similarities for 41 edges... 35.90%
Calculating edge similarities for 41 edges... 38.46%
Calculating edge similarities for 41 edges... 41.03%
Calculating edge similarities for 41 edges... 43.59%
Calculating edge similarities for 41 edges... 46.15%
Calculating edge similarities for 41 edges... 48.72%
Calculating edge similarities for 41 edges... 51.28%
Calculating edge similarities for 41 edges... 53.85%
Calculating edge similarities for 41 edges... 56.41%
Calculating edge similarities for 41 edges... 58.97%
Calculating edge similarities for 41 edges... 61.54%
Calculating edge similarities for 41 edges... 64.10%
Calculating edge similarities for 41 edges... 66.67%
Calculating edge similarities for 41 edges... 69.23%
Calculating edge similarities for 41 edges... 71.79%
Calculating edge similarities for 41 edges... 74.36%
Calculating edge similarities for 41 edges... 76.92%
Calculating edge similarities for 41 edges... 79.49%
Calculating edge similarities for 41 edges... 82.05%
Calculating edge similarities for 41 edges... 84.62%
Calculating edge similarities for 41 edges... 87.18%
Calculating edge similarities for 41 edges... 89.74%
Calculating edge similarities for 41 edges... 92.31%
Calculating edge similarities for 41 edges... 94.87%
Calculating edge similarities for 41 edges... 97.44%
Calculating edge similarities for 41 edges... 100.00%
Hierarchical clustering of edges...
Calculating link densities... 0.00%
Calculating link densities... 2.56%
Calculating link densities... 5.13%
Calculating link densities... 7.69%
Calculating link densities... 10.26%
Calculating link densities... 12.82%
Calculating link densities... 15.38%
Calculating link densities... 17.95%
Calculating link densities... 20.51%
Calculating link densities... 23.08%
Calculating link densities... 25.64%
Calculating link densities... 28.21%
Calculating link densities... 30.77%
Calculating link densities... 33.33%
Calculating link densities... 35.90%
Calculating link densities... 38.46%
Calculating link densities... 41.03%
Calculating link densities... 43.59%
Calculating link densities... 46.15%
Calculating link densities... 48.72%
Calculating link densities... 51.28%
Calculating link densities... 53.85%
Calculating link densities... 56.41%
Calculating link densities... 58.97%
Calculating link densities... 61.54%
Calculating link densities... 64.10%
Calculating link densities... 66.67%
Calculating link densities... 69.23%
Calculating link densities... 71.79%
Calculating link densities... 74.36%
Calculating link densities... 76.92%
Calculating link densities... 79.49%
Calculating link densities... 82.05%
Calculating link densities... 84.62%
Calculating link densities... 87.18%
Calculating link densities... 89.74%
Calculating link densities... 92.31%
Calculating link densities... 94.87%
Calculating link densities... 97.44%
Calculating link densities... 100.00%
Maximum partition density = 0.2601626
Finishing up...1/4... 12%
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Finishing up...4/4... 0.00%
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Finishing up...4/4... 19.05%
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Finishing up...4/4... 28.57%
Finishing up...4/4... 33.33%
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Finishing up...4/4... 47.62%
Finishing up...4/4... 52.38%
Finishing up...4/4... 57.14%
Finishing up...4/4... 61.90%
Finishing up...4/4... 66.67%
Finishing up...4/4... 71.43%
Finishing up...4/4... 76.19%
Finishing up...4/4... 80.95%
Finishing up...4/4... 85.71%
Finishing up...4/4... 90.48%
Finishing up...4/4... 95.24%
Finishing up...4/4... 100.00%
Plotting...
Colouring dendrogram... 1%
Colouring dendrogram... 2%
Colouring dendrogram... 3%
Colouring dendrogram... 4%
Colouring dendrogram... 6%
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Colouring dendrogram... 70%
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Colouring dendrogram... 74%
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Colouring dendrogram... 76%
Colouring dendrogram... 77%
Colouring dendrogram... 79%
Colouring dendrogram... 80%
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Colouring dendrogram... 82%
Colouring dendrogram... 83%
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Colouring dendrogram... 86%
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Colouring dendrogram... 88%
Colouring dendrogram... 90%
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Completed... 3%
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[1] 0.7306163
linkcomm documentation built on Feb. 4, 2021, 5:05 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/linkcomm_misc.R
Description
This function calculates the correlation between the community centrality and classic centrality measures for a set of nodes in a network, and plots a scatterplot of the relationship together with a fitted straight line.
Usage
1 2 |
Arguments
x |
An object of class |
centrality |
A character string naming the classic centrality measure. Can be one of |
type |
A character string naming the type of community centrality. Can be |
method |
A character string naming the correlation method. Can be one of |
plot |
Logical, whether to plot a scatterplot of the relationship, defaults to TRUE. |
pch |
An integer specifying the plot symbol (see |
... |
Additional arguments to be passed to |
Details
The correlation between community centrality and classic centrality measures, such as degree or betweenness, may reveal discrepancies, thereby indicating that community centrality scores provide a unique reflection of node importance.
Value
A correlation coefficient.
Author(s)
Alex T. Kalinka alex.t.kalinka@gmail.com
References
Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.
See Also
Examples
1 2 3 4 5 6 | ## Generate graph and extract link communities.
g <- swiss[,3:4]
lc <- getLinkCommunities(g)
## Correlate community centrality with degree centrality.
corLinkcommCentrality(lc)
|
Example output
Loading required package: igraph
Attaching package: 'igraph'
The following objects are masked from 'package:stats':
decompose, spectrum
The following object is masked from 'package:base':
union
Loading required package: RColorBrewer
Welcome to linkcomm version 1.0-11
For a step-by-step guide to using linkcomm functions:
> vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
> demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
> citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))
Checking for loops and duplicate edges... 0.000%
Checking for loops and duplicate edges... 2.174%
Checking for loops and duplicate edges... 4.348%
Checking for loops and duplicate edges... 6.522%
Checking for loops and duplicate edges... 8.696%
Checking for loops and duplicate edges... 10.870%
Checking for loops and duplicate edges... 13.043%
Checking for loops and duplicate edges... 15.217%
Checking for loops and duplicate edges... 17.391%
Checking for loops and duplicate edges... 19.565%
Checking for loops and duplicate edges... 21.739%
Checking for loops and duplicate edges... 23.913%
Checking for loops and duplicate edges... 26.087%
Checking for loops and duplicate edges... 28.261%
Checking for loops and duplicate edges... 30.435%
Checking for loops and duplicate edges... 32.609%
Checking for loops and duplicate edges... 34.783%
Checking for loops and duplicate edges... 36.957%
Checking for loops and duplicate edges... 39.130%
Checking for loops and duplicate edges... 41.304%
Checking for loops and duplicate edges... 43.478%
Checking for loops and duplicate edges... 45.652%
Checking for loops and duplicate edges... 47.826%
Checking for loops and duplicate edges... 50.000%
Checking for loops and duplicate edges... 52.174%
Checking for loops and duplicate edges... 54.348%
Checking for loops and duplicate edges... 56.522%
Checking for loops and duplicate edges... 58.696%
Checking for loops and duplicate edges... 60.870%
Checking for loops and duplicate edges... 63.043%
Checking for loops and duplicate edges... 65.217%
Checking for loops and duplicate edges... 67.391%
Checking for loops and duplicate edges... 69.565%
Checking for loops and duplicate edges... 71.739%
Checking for loops and duplicate edges... 73.913%
Checking for loops and duplicate edges... 76.087%
Checking for loops and duplicate edges... 78.261%
Checking for loops and duplicate edges... 80.435%
Checking for loops and duplicate edges... 82.609%
Checking for loops and duplicate edges... 84.783%
Checking for loops and duplicate edges... 86.957%
Checking for loops and duplicate edges... 89.130%
Checking for loops and duplicate edges... 91.304%
Checking for loops and duplicate edges... 93.478%
Checking for loops and duplicate edges... 95.652%
Checking for loops and duplicate edges... 97.826%
Checking for loops and duplicate edges... 100.000%
Found and removed 4 loop(s)
Found and removed 2 duplicate edge(s)
Calculating edge similarities for 41 edges... 0.00%
Calculating edge similarities for 41 edges... 2.56%
Calculating edge similarities for 41 edges... 5.13%
Calculating edge similarities for 41 edges... 7.69%
Calculating edge similarities for 41 edges... 10.26%
Calculating edge similarities for 41 edges... 12.82%
Calculating edge similarities for 41 edges... 15.38%
Calculating edge similarities for 41 edges... 17.95%
Calculating edge similarities for 41 edges... 20.51%
Calculating edge similarities for 41 edges... 23.08%
Calculating edge similarities for 41 edges... 25.64%
Calculating edge similarities for 41 edges... 28.21%
Calculating edge similarities for 41 edges... 30.77%
Calculating edge similarities for 41 edges... 33.33%
Calculating edge similarities for 41 edges... 35.90%
Calculating edge similarities for 41 edges... 38.46%
Calculating edge similarities for 41 edges... 41.03%
Calculating edge similarities for 41 edges... 43.59%
Calculating edge similarities for 41 edges... 46.15%
Calculating edge similarities for 41 edges... 48.72%
Calculating edge similarities for 41 edges... 51.28%
Calculating edge similarities for 41 edges... 53.85%
Calculating edge similarities for 41 edges... 56.41%
Calculating edge similarities for 41 edges... 58.97%
Calculating edge similarities for 41 edges... 61.54%
Calculating edge similarities for 41 edges... 64.10%
Calculating edge similarities for 41 edges... 66.67%
Calculating edge similarities for 41 edges... 69.23%
Calculating edge similarities for 41 edges... 71.79%
Calculating edge similarities for 41 edges... 74.36%
Calculating edge similarities for 41 edges... 76.92%
Calculating edge similarities for 41 edges... 79.49%
Calculating edge similarities for 41 edges... 82.05%
Calculating edge similarities for 41 edges... 84.62%
Calculating edge similarities for 41 edges... 87.18%
Calculating edge similarities for 41 edges... 89.74%
Calculating edge similarities for 41 edges... 92.31%
Calculating edge similarities for 41 edges... 94.87%
Calculating edge similarities for 41 edges... 97.44%
Calculating edge similarities for 41 edges... 100.00%
Hierarchical clustering of edges...
Calculating link densities... 0.00%
Calculating link densities... 2.56%
Calculating link densities... 5.13%
Calculating link densities... 7.69%
Calculating link densities... 10.26%
Calculating link densities... 12.82%
Calculating link densities... 15.38%
Calculating link densities... 17.95%
Calculating link densities... 20.51%
Calculating link densities... 23.08%
Calculating link densities... 25.64%
Calculating link densities... 28.21%
Calculating link densities... 30.77%
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Calculating link densities... 35.90%
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Calculating link densities... 41.03%
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Calculating link densities... 53.85%
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Calculating link densities... 58.97%
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Calculating link densities... 64.10%
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Calculating link densities... 69.23%
Calculating link densities... 71.79%
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Calculating link densities... 76.92%
Calculating link densities... 79.49%
Calculating link densities... 82.05%
Calculating link densities... 84.62%
Calculating link densities... 87.18%
Calculating link densities... 89.74%
Calculating link densities... 92.31%
Calculating link densities... 94.87%
Calculating link densities... 97.44%
Calculating link densities... 100.00%
Maximum partition density = 0.2601626
Finishing up...1/4... 12%
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Plotting...
Colouring dendrogram... 1%
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[1] 0.7306163
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