问题
I am trying to create valued bipartite projection from my data which looks like the 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 the above data and call it data1
Then I do the following:
##create graph object from data1
graph1 <- graph.data.frame(data1)
#check if it is bipartite
is.bipartite(graph1)
FALSE
##convert to bipartite graph
V(graph1)$type <- V(graph1)$name %in% data1[,1]
##check again if it is bipartite
is.bipartite(graph1)
TRUE
##create biparite projection
##the multiplicity argument is suppose to count the number of
##edges
proj<-bipartite.projection(graph1, V(graph1)$type,multiplicity = TRUE)
##get adjacency matrix from second projection
get.adjacency(proj$proj2)
I get the 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 and Calvin having 2 edges through ***rid***s 13580 and 11800, Phineas appears twice. And the plot of the "rid" projection shows only 1 edge between 13580 and 11800. The plot for the "Name" shows Phineas twice.
I appreciate any suggestions to modify this code to get valued projection and adjacency matrix. thank you!
EDIT #1: Phineas was appearing twice because of some type of formatting issue where two "Phinease-s" were being recognized as separate names. BUT, fixing this still does not solve the main problem. The output still gives only 1 edge between Phineas and Calvin and between 13580 and 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 a namespace (and not attached):
[1] grid_3.1.0 lattice_0.20-29 magrittr_1.5 Matrix_1.1-3 tools_3.1.0
\
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 .
回答1:
I do not know what you have done. Probably some more information is necessary: sessionInfo() to check what system were you using and what version of the packages.
This is what I've found in my PC (see below the 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 the data
head(data1)
dim(data1)
str(data1)
plot(data1)
Call the library
library(igraph)
Create graph object from data1
graph1 <- graph.data.frame(data1)
Check if it is bipartite
is.bipartite(graph1) ### FALSE
Convert to bipartite graph
V(graph1)$type <- V(graph1)$name %in% data1[,1]
Check again if it is bipartite
is.bipartite(graph1) ### TRUE
Create biparite projection The multiplicity argument is suppose to count the number of edges
proj<-bipartite.projection(graph1, V(graph1)$type,multiplicity = TRUE)
Get adjacency matrix from the first projection
t1 <- get.adjacency(proj$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 from 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 your 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 a namespace (and not attached): [1] grid_3.0.2 lattice_0.20-24
来源：https://stackoverflow.com/questions/32300263/valued-bipartite-projection-using-r-igraph