graph - valued bipartite projection using R igraph -

i trying create valued bipartite projection data looks following:

                 name   rid                 emile    17560                 lou     11800                 luther   11800                 tot     11800                 phineas   11800                 phineas   13580                 calvin    13580                 calvin    11800                   les      11800                  jeff      11800                  sonny     13580                   leon      13580                   red       13580 

i imported above data , call data1

then following:

##create graph object data1 graph1 <- graph.data.frame(data1)  #check if bipartite is.bipartite(graph1) false  ##convert bipartite graph v(graph1)$type <- v(graph1)$name %in% data1[,1]  ##check again if bipartite is.bipartite(graph1) true  ##create biparite projection  ##the multiplicity argument suppose count number of   ##edges  proj<-bipartite.projection(graph1, v(graph1)$type,multiplicity = true)  ##get adjacency matrix second projection get.adjacency(proj$proj2) 

i following ouput

 11 x 11 sparse matrix of class "dgcmatrix"   [[ suppressing 11 column names ‘emile ’, ‘lou ’, ‘luther ’ ... ]]     emile    . . . . . . . . . . .    lou      . . 1 1 1 . 1 1 1 . .    luther   . 1 . 1 1 . 1 1 1 . .    tot      . 1 1 . 1 . 1 1 1 . .    phineas  . 1 1 1 . . 1 1 1 . .    phineas  . . . . . . 1 . . 1 1    calvin   . 1 1 1 1 1 . 1 1 1 1    les      . 1 1 1 1 . 1 . 1 . .    jeff     . 1 1 1 1 . 1 1 . . .    sonny    . . . . . 1 1 . . . 1    leon     . . . . . 1 1 . . 1 . 

and

     3 x 3 sparse matrix of class "dgcmatrix"                 17560 11800 13580         17560     .     .     .         11800     .     .     1        13580     .     1     . 

instead of phineas , calvin having 2 edges through ***rid***s 13580 , 11800, phineas appears twice. , plot of "rid" projection shows 1 edge between 13580 , 11800. plot "name" shows phineas twice.

i appreciate suggestions modify code valued projection , adjacency matrix. thank you!

edit #1: phineas appearing twice because of type of formatting issue 2 "phinease-s" being recognized separate names. but, fixing still not solve main problem. output still gives 1 edge between phineas , calvin , between 13580 , 11800.

edit #2: session info results

r version 3.1.0 (2014-04-10) platform: i386-w64-mingw32/i386 (32-bit)  locale: [1] lc_collate=english_united states.1252  lc_ctype=english_united        states.1252    lc_monetary=english_united states.1252 [4] lc_numeric=c                           lc_time=english_united states.1252      attached base packages: [1] stats     graphics  grdevices utils     datasets  methods   base        other attached packages:   [1] igraph_1.0.1    loaded via namespace (and not attached):   [1] grid_3.1.0      lattice_0.20-29 magrittr_1.5    matrix_1.1-3        tools_3.1.0     

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edit #3

desired output   3 x 3 sparse matrix of class "dgcmatrix"                 17560 11800 13580         17560     .     .     .         11800     .     .     2        13580     .     2     .    11 x 11 sparse matrix of class "dgcmatrix"   [[ suppressing 11 column names ‘emile ’, ‘lou ’, ‘luther ’ ... ]]     emile    . . . . . . . . . . .    lou      . . 1 1 1 . 1 1 1 . .    luther   . 1 . 1 1 . 1 1 1 . .    tot      . 1 1 . 1 . 1 1 1 . .    phineas  . 1 1 1 . 2 1 1 1 1    calvin   . 1 1 1 2 1 . 1 1 1 1    les      . 1 1 1 1 . 1 . 1 . .    jeff     . 1 1 1 1 . 1 1 . . .    sonny    . . . . . 1 1 . . . 1    leon     . . . . . 1 1 . . 1 . 

i not know have done. more information necessary: sessioninfo() check system using , version of packages.

this i've found in pc (see below result of sessioninfo()

the data

data1 <- read.table(text="name   rid            emile    17560              lou     11800              luther   11800              tot     11800              phineas   11800              phineas   13580              calvin    13580              calvin    11800                les      11800               jeff      11800               sonny     13580                leon      13580                red       13580", header=true) 

check data

head(data1) dim(data1) str(data1) plot(data1) 

call library

library(igraph) 

create graph object data1

graph1 <- graph.data.frame(data1) 

check if bipartite

is.bipartite(graph1)        ### false 

convert bipartite graph

v(graph1)$type <- v(graph1)$name %in% data1[,1] 

check again if bipartite

is.bipartite(graph1)        ### true 

create biparite projection multiplicity argument suppose count number of edges

proj<-bipartite.projection(graph1, v(graph1)$type,multiplicity = true) 

get adjacency matrix first projection

t1 <- get.adjacency(proj$proj1) t1 

loading required package: matrix

11 x 11 sparse matrix of class "dgcmatrix"

[[ suppressing 11 column names ‘emile’, ‘lou’, ‘luther’ ... ]]

emile . . . . . . . . . . .

lou . . 1 1 1 1 1 1 . . .

luther . 1 . 1 1 1 1 1 . . .

tot . 1 1 . 1 1 1 1 . . .

phineas . 1 1 1 . 1 1 1 1 1 1

calvin . 1 1 1 1 . 1 1 1 1 1

les . 1 1 1 1 1 . 1 . . .

jeff . 1 1 1 1 1 1 . . . .

sonny . . . . 1 1 . . . 1 1

leon . . . . 1 1 . . 1 . 1

red . . . . 1 1 . . 1 1 .

get adjacency matrix second projection

t2 <- get.adjacency(proj$proj2) t2 

3 x 3 sparse matrix of class "dgcmatrix"

  17560 11800 13580 

17560 . . .

11800 . . 1

13580 . 1 .

plot matrix

g1 <- graph.adjacency(t1)  plot(g1) 

result of sessioninfo() r version 3.0.2 (2013-09-25) platform: x86_64-w64-mingw32/x64 (64-bit)

locale: [1] lc_collate=italian_italy.1252  lc_ctype=italian_italy.1252    [3] lc_monetary=italian_italy.1252 lc_numeric=c                   [5] lc_time=italian_italy.1252      attached base packages:[1] stats     graphics  grdevices utils        datasets  methods   base      other attached packages: [1] matrix_1.1-0 igraph_0.6.6 loaded via namespace (and not attached): [1] grid_3.0.2      lattice_0.20-24