robin.R
In robin: ROBustness in Network

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#install.packages("robin")

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# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# BiocManager::install("gprege")
# 
# install.packages("robin")

## ----message=FALSE, warning=FALSE, paged.print=TRUE---------------------------
library("robin")

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my_network <- system.file("example/football.gml", package="robin")
# downloaded from: http://www-personal.umich.edu/~mejn/netdata/
graph <- prepGraph(file=my_network, file.format="gml")
graph

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plotGraph(graph)

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methodCommunity(graph=graph, method="fastGreedy") 

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membershipCommunities(graph=graph, method="fastGreedy") 

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members <- membershipCommunities(graph=graph, method="fastGreedy")
plotComm(graph=graph, members=members)

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graphRandom <- random(graph=graph)
graphRandom

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proc <- robinRobust(graph=graph, graphRandom=graphRandom, measure="vi", 
                  method="louvain", type="independent")

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plotRobin(graph=graph, model1=proc$Mean, model2=proc$MeanRandom,
legend=c("real data", "null model"))

## ----message=FALSE, warning=FALSE---------------------------------------------
robinFDATest(graph=graph, model1=proc$Mean, model2=proc$MeanRandom, 
            legend=c("real graph", "random graph"))

## ----message=FALSE, warning=FALSE---------------------------------------------
robinGPTest(model1=proc$Mean, model2=proc$MeanRandom)

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robinAUC(graph=graph, model1=proc$Mean, model2=proc$MeanRandom)

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membersFast <- membershipCommunities(graph=graph, method="fastGreedy")
membersLouv <- membershipCommunities(graph=graph, method="louvain")
plotComm(graph=graph, members=membersFast)
plotComm(graph=graph, members=membersLouv)

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comp <- robinCompare(graph=graph, method1="fastGreedy",
                method2="louvain", measure="vi", type="independent")

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plotRobin(graph=graph, model1=comp$Mean1, model2=comp$Mean2, 
legend=c("fastGreedy", "louvain"), title="FastGreedy vs Louvain")

## ----message=FALSE, warning=FALSE---------------------------------------------
robinFDATest(graph=graph, model1=comp$Mean1, model2=comp$Mean2)


## ----message=FALSE, warning=FALSE---------------------------------------------
robinGPTest(model1=comp$Mean1, model2=comp$Mean2)

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robinAUC(graph=graph, model1=comp$Mean1, model2=comp$Mean2)