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updated src
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‎src/data.R‎

Lines changed: 103 additions & 100 deletions
Original file line numberDiff line numberDiff line change
@@ -3,114 +3,117 @@
33
#
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# Vincent Labatut 04/2016
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#############################################################################################
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data.pars <- list()
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# The name in the list is later used to retrieve the needed files.
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# Each element of the list describe a given dataset with the following fields:
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# - data.folder represents the location of all these files.
12+
# - data.folder represents the folder containing all these files.
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# - rdata.filename is the name of the R data file containing the igraph objects.
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# - centrality.filenam is the file generated with MuxViz and containing reference centrality values, to be compared with opinion centrality.
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13-
#data.pars[["Arabidopsis"]] <- list(
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# data.folder="data/Arabidopsis_Multiplex_Genetic/",
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# rdata.filename="Arabidopsis.Rdata",
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# centrality.filename="Arabidopsis_centrality_table.csv")
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#data.pars[["Celegans"]] <- list(
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# data.folder="data/Celegans_Multiplex_Genetic/",
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# rdata.filename="Celegans.Rdata",
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# centrality.filename="Celegans_centrality_table.csv")
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#data.pars[["CKM"]] <- list(
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# data.folder="data/CKM-Physicians-Innovation_Multiplex_Social/",
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# rdata.filename="CKMPI.Rdata",
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# centrality.filename="CKM_centrality_table.csv")
27-
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#data.pars[["CS_Aarhus"]] <- list(
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# data.folder="data/CS-Aarhus_Multiplex_Social/",
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# rdata.filename="CSAarhus.Rdata",
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# centrality.filename="CS_Aarhus_centrality_table.csv")
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#data.pars[["Drosophila"]] <- list(
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# data.folder="data/Drosophila_Multiplex_Genetic/",
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# rdata.filename="Drosophila.Rdata",
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# centrality.filename="Drosophila_centrality_table.csv")
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38-
#data.pars[["EUAir"]] <- list(
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# data.folder="data/EUAir_Multiplex_Transport/",
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# rdata.filename="EUAir.Rdata",
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# centrality.filename="EUAir_centrality_table.csv")
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#data.pars[["FAO"]] <- list(
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# data.folder="data/FAO_Multiplex_Trade/",
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# rdata.filename="FAO.Rdata",
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# centrality.filename="FAO_centrality_table.csv")
47-
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#data.pars[["HepatitusCVirus"]] <- list(
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# data.folder="data/HepatitusCVirus_Multiplex_Genetic/",
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# rdata.filename="HepatitusCVirus.Rdata",
51-
# centrality.filename="HepatitusCVirus_centrality_table.csv")
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#data.pars[["HumanHIV1"]] <- list(
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# data.folder="data/HumanHIV1_Multiplex_Genetic/",
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# rdata.filename="HumanHIV1.Rdata",
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# centrality.filename="HumanHIV1_centrality_table.csv")
57-
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#data.pars[["Kapferer1"]] <- list(
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# data.folder="data/kaptail1-GraphML/",
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# rdata.filename="kaptail1.Rdata",
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# centrality.filename="Kapferer1_centrality_table.csv")
62-
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#data.pars[["Kapferer2"]] <- list(
64-
# data.folder="data/kaptail2-GraphML/",
65-
# rdata.filename="kaptail2.Rdata",
66-
# centrality.filename="Kapferer2_centrality_table.csv")
67-
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#data.pars[["Knoke"]] <- list(
69-
# data.folder="data/knokbur-GraphML/",
70-
# rdata.filename="knokbur.Rdata",
71-
# centrality.filename="Knoke_centrality_table.csv")
16+
data.pars[["Arabidopsis"]] <- list(
17+
data.folder="Arabidopsis_Multiplex_Genetic/",
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rdata.filename="Arabidopsis.Rdata",
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centrality.filename="Arabidopsis_centrality_table.csv")
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21+
data.pars[["Celegans"]] <- list(
22+
data.folder="Celegans_Multiplex_Genetic/",
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rdata.filename="Celegans.Rdata",
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centrality.filename="Celegans_centrality_table.csv")
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26+
data.pars[["CKM"]] <- list(
27+
data.folder="CKM-Physicians-Innovation_Multiplex_Social/",
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rdata.filename="CKMPI.Rdata",
29+
centrality.filename="CKM_centrality_table.csv")
30+
31+
data.pars[["CS_Aarhus"]] <- list(
32+
data.folder="CS-Aarhus_Multiplex_Social/",
33+
rdata.filename="CSAarhus.Rdata",
34+
centrality.filename="CS_Aarhus_centrality_table.csv")
35+
36+
data.pars[["Drosophila"]] <- list(
37+
data.folder="Drosophila_Multiplex_Genetic/",
38+
rdata.filename="Drosophila.Rdata",
39+
centrality.filename="Drosophila_centrality_table.csv")
40+
41+
data.pars[["EUAir"]] <- list(
42+
data.folder="EUAir_Multiplex_Transport/",
43+
rdata.filename="EUAir.Rdata",
44+
centrality.filename="EUAir_centrality_table.csv")
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46+
data.pars[["FAO"]] <- list(
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data.folder="FAO_Multiplex_Trade/",
48+
rdata.filename="FAO.Rdata",
49+
centrality.filename="FAO_centrality_table.csv")
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51+
data.pars[["HepatitusCVirus"]] <- list(
52+
data.folder="HepatitusCVirus_Multiplex_Genetic/",
53+
rdata.filename="HepatitusCVirus.Rdata",
54+
centrality.filename="HepatitusCVirus_centrality_table.csv")
55+
56+
data.pars[["HumanHIV1"]] <- list(
57+
data.folder="HumanHIV1_Multiplex_Genetic/",
58+
rdata.filename="HumanHIV1.Rdata",
59+
centrality.filename="HumanHIV1_centrality_table.csv")
60+
61+
data.pars[["Kapferer1"]] <- list(
62+
data.folder="kaptail1-GraphML/",
63+
rdata.filename="kaptail1.Rdata",
64+
centrality.filename="Kapferer1_centrality_table.csv")
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66+
data.pars[["Kapferer2"]] <- list(
67+
data.folder="kaptail2-GraphML/",
68+
rdata.filename="kaptail2.Rdata",
69+
centrality.filename="Kapferer2_centrality_table.csv")
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71+
data.pars[["Knoke"]] <- list(
72+
data.folder="knokbur-GraphML/",
73+
rdata.filename="knokbur.Rdata",
74+
centrality.filename="Knoke_centrality_table.csv")
7275

7376
data.pars[["Lazega"]] <- list(
74-
data.folder="data/Lazega-Law-Firm_Multiplex_Social/",
77+
data.folder="Lazega-Law-Firm_Multiplex_Social/",
7578
rdata.filename="Lazega.Rdata",
7679
centrality.filename="Lazega_centrality_table.csv")
7780

78-
#data.pars[["London"]] <- list(
79-
# data.folder="data/London_Multiplex_Transport/",
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# rdata.filename="London.Rdata",
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# centrality.filename="London_centrality_table.csv")
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83-
#data.pars[["Padgett"]] <- list(
84-
# data.folder="data/padgett-GraphML/",
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# rdata.filename="padgett.Rdata",
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# centrality.filename="Padgett_centrality_table.csv")
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#data.pars[["PierreAuger"]] <- list(
89-
# data.folder="data/PierreAuger_Multiplex_Coauthorship/",
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# rdata.filename="PierreAuger.Rdata",
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# centrality.filename="PierreAuger_centrality_table.csv")
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93-
#data.pars[["Rattus"]] <- list(
94-
# data.folder="data/Rattus_Multiplex_Genetic/",
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# rdata.filename="Rattus.Rdata",
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# centrality.filename="Rattus_centrality_table.csv")
97-
98-
#data.pars[["Roethlisberger"]] <- list(
99-
# data.folder="data/wiring-GraphML/",
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# rdata.filename="wiring.Rdata",
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# centrality.filename="Roethlisberger_centrality_table.csv")
102-
103-
#data.pars[["Sampson"]] <- list(
104-
# data.folder="data/sampson-GraphML/",
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# rdata.filename="sampson.Rdata",
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# centrality.filename="Sampson_centrality_table.csv")
107-
108-
#data.pars[["Thurmann"]] <- list(
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# data.folder="data/thuroff-GraphML/",
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# rdata.filename="thuroff.Rdata",
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# centrality.filename="Thurmann_centrality_table.csv")
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#data.pars[["Wolfe"]] <- list(
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# data.folder="data/wolfe-GraphML/",
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# rdata.filename="wolfe.Rdata",
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# centrality.filename="Wolfe_centrality_table.csv")
81+
data.pars[["London"]] <- list(
82+
data.folder="London_Multiplex_Transport/",
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rdata.filename="London.Rdata",
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centrality.filename="London_centrality_table.csv")
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86+
data.pars[["Padgett"]] <- list(
87+
data.folder="padgett-GraphML/",
88+
rdata.filename="padgett.Rdata",
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centrality.filename="Padgett_centrality_table.csv")
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91+
data.pars[["PierreAuger"]] <- list(
92+
data.folder="PierreAuger_Multiplex_Coauthorship/",
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rdata.filename="PierreAuger.Rdata",
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centrality.filename="PierreAuger_centrality_table.csv")
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96+
data.pars[["Rattus"]] <- list(
97+
data.folder="Rattus_Multiplex_Genetic/",
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rdata.filename="Rattus.Rdata",
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centrality.filename="Rattus_centrality_table.csv")
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101+
data.pars[["Roethlisberger"]] <- list(
102+
data.folder="wiring-GraphML/",
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rdata.filename="wiring.Rdata",
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centrality.filename="Roethlisberger_centrality_table.csv")
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106+
data.pars[["Sampson"]] <- list(
107+
data.folder="sampson-GraphML/",
108+
rdata.filename="sampson.Rdata",
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centrality.filename="Sampson_centrality_table.csv")
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111+
data.pars[["Thurmann"]] <- list(
112+
data.folder="thuroff-GraphML/",
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rdata.filename="thuroff.Rdata",
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centrality.filename="Thurmann_centrality_table.csv")
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116+
data.pars[["Wolfe"]] <- list(
117+
data.folder="wolfe-GraphML/",
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rdata.filename="wolfe.Rdata",
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centrality.filename="Wolfe_centrality_table.csv")

‎src/main.R‎

Lines changed: 25 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -18,11 +18,12 @@ source('src/misc.R')
1818

1919

2020

21-
# init the data list
22-
source('src/data.R')
21+
# init the data-related variables
22+
data.folder <- "data/" # location of the data in this project
23+
source('src/data.R') # init the list of considered networks
2324

2425

25-
# select the previously processed centrality measures
26+
# select the centrality measures previously processed in MuxViz (or an other tool)
2627
measures <- c(
2728
"Degree",
2829
# "DegreeIn", # MuxViz cannot process this one for certain networks
@@ -38,7 +39,7 @@ measures <- c(
3839
alpha.vals <- seq(from=0,to=1,by=0.25) # distinct values of alpha
3940
alpha.vals <- alpha.vals[alpha.vals!=0]
4041
alpha.vals <- c(alpha.vals,seq(from=2,to=5,by=1))
41-
l <- length(alpha.vals) # number of distinct values of alpha
42+
l <- length(alpha.vals) # number of distinct values of alpha
4243
#round(c(1:l)/(l-3),2)
4344

4445
# plot folder
@@ -49,6 +50,13 @@ formats <- c( # file format of the plots
4950
"PNG"
5051
)
5152

53+
# init time measurement matrix
54+
elapsed.times <- matrix(NA,nrow=length(data.pars),ncol=length(alpha.vals))
55+
rownames(elapsed.times) <- names(data.pars)
56+
colnames(elapsed.times) <- alpha.vals
57+
time.file <- paste(data.folder,"elapsed-times.csv")
58+
59+
5260
# process each multiplex network
5361
network.names <- names(data.pars)
5462
for(multiplex.index in 1:length(data.pars))
@@ -57,7 +65,7 @@ for(multiplex.index in 1:length(data.pars))
5765
data.par <- data.pars[[network.name]]
5866

5967
# load network
60-
net.file <- paste(data.par$data.folder,data.par$rdata.filename,sep="")
68+
net.file <- paste(data.folder,data.par$data.folder,data.par$rdata.filename,sep="")
6169
multiplex.network <- retrieve.rdata.object(net.file)
6270
number.layers <- length(multiplex.network)
6371
number.nodes <- vcount(multiplex.network[[1]])
@@ -88,11 +96,16 @@ for(multiplex.index in 1:length(data.pars))
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8997
# load previously processed centralities
9098
centr.file <- paste(data.par$data.folder,data.par$centrality.filename,sep="")
91-
mutiplex.centralities <- read.csv(file=centr.file,sep=";")
99+
if(file.exists(centr.fil))
100+
multiplex.centralities <- read.csv(file=centr.file,sep=";")
101+
else
102+
{ cat("WARNING: did not find the file containing the centrality values for external measures (MuxViz)\n")
103+
multiplex.centralities <- matrix(NA,nrow=number.nodes,ncol=length(measures))
104+
}
92105

93106
# init centrality tables
94107
opinion.centralities <- array(0,c(l,number.nodes))
95-
other.centralities <- as.matrix(mutiplex.centralities)[(number.layers*number.nodes+1):((number.layers+1)*number.nodes),measures]
108+
other.centralities <- as.matrix(multiplex.centralities)[(number.layers*number.nodes+1):((number.layers+1)*number.nodes),measures]
96109
class(other.centralities) <- "numeric"
97110

98111
# init plot folder
@@ -102,7 +115,7 @@ for(multiplex.index in 1:length(data.pars))
102115
# init correlation table
103116
correlation.values <- matrix(NA, nrow=l, ncol=length(measures))
104117
colnames(correlation.values) <- measures
105-
118+
106119
# process our centrality measure
107120
cat(" Processing the opinion centrality\n",sep="")
108121
for(i in 1:l)
@@ -111,7 +124,11 @@ for(multiplex.index in 1:length(data.pars))
111124
#print(alpha)
112125

113126
####### process opinion centrality measure
127+
elapsed.time <- system.time(
114128
centrality <- process.opinion.centrality(network=multiplex.network, alpha, budget=1, personal.opinion)
129+
)
130+
elapsed.times[multiplex.index,i] <- elapsed.time["elapsed"]
131+
write.csv2(elapsed.times, file=time.file)
115132

116133
opinion.centralities[i,] <- t(centrality)
117134
stdev <- sd(opinion.centralities[i,])

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