Code Rnet 3

top <- function(v,k){
  ord <- rev(order(v)); sel <- ord[1:k]
  S <- data.frame(name=names(v[sel]),value=as.vector(v[sel]))
  return(S)
}

> wdir <- "C:/Users/batagelj/Documents/papers/2017/Moscow/Rnet/test"
> setwd(wdir)
> library(igraph)
# delete *network and empty line before *vertices
> T <- read.graph("./nets/eatRS.net",format="pajek")
> vcount(T)
[1] 23219
> ecount(T)
[1] 325624
> source("igraph+.R")
> SR <- graph.reverse(T)
> SR$indeg <- degree(SR,mode="in")
> top(SR$indeg,10)
      name value
1       ME  1074
2      MAN  1046
3     GOOD   861
4      SEX   828
5       NO   780
6    MONEY   743
7      YES   718
8     WORK   672
9  NOTHING   672
10    FOOD   665
> SR$windeg <-  strength(SR,mode="in")
> max(SR$windeg)
[1] 4387
> top(SR$windeg,20) 
> SR$awindeg <- SR$windeg/SR$indeg
> SR$awindeg[is.nan(SR$awindeg)] <- 0
> top(SR$awindeg,20)

The names and types of node shapes in Pajek (“box”,”ellipse”, “triangle”, “diamond”, …) and igraph (“square”, “circle”, “pie”, …) are different. Besides this in Pajek description holds the rule that missing shape indicates the current shape in the sequence. Sometimes we can transform the Pajek's description into igraph's description as follows

> R <- read.graph("./nets/class.net",format="pajek")
> vertex_attr(R)$shape
 [1] "box"     ""        "ellipse" ""        ""        ""        ""       
 [8] ""        ""        ""        "box"     "ellipse" "box"     ""       
[15] ""       
> sh <- "ellipse"
> for(i in 1:vcount(R)) 
+   if(V(R)$shape[i]=="") V(R)$shape[i] <- sh else sh <- V(R)$shape[i]
> V(R)$shape
 [1] "box"     "box"     "ellipse" "ellipse" "ellipse" "ellipse" "ellipse"
 [8] "ellipse" "ellipse" "ellipse" "box"     "ellipse" "box"     "box"    
[15] "box"    
> V(R)$shape[V(R)$shape=="box"] <- "square"
> V(R)$shape[V(R)$shape=="ellipse"] <- "circle"
> V(R)$shape
 [1] "square" "square" "circle" "circle" "circle" "circle" "circle" "circle"
 [9] "circle" "circle" "square" "circle" "square" "square" "square"
> plot(R)

The other option is that we forget about the shapes information

> vertex_attr(R)$shape <- NULL

SaKtrade.net, SaKtrade.clu

> library(igraph); source("igraph+.R")
> SaK <- read.graph("./nets/SaKtrade.net",format="pajek")
> SaK
IGRAPH e1d9b99 UNW- 118 2631 -- 
+ attr: id (v/c), name (v/c), weight (e/n)
+ edges from e1d9b99 (vertex names):
 [1] usa--sen usa--jor usa--yem usa--kod usa--lao can--bol can--alb can--eth
+ ... omitted several edges 
> V(SaK)$sc <- read_Pajek_clu("./nets/SaKtrade.clu",skip=7)
> col <- c("red","green","orange","blue","green","magenta","grey","black")
> V(SaK)$color <- col[V(SaK)$sc]
> Af <- extract_clusters(SaK,"sc",c(6))
> plot(Af)
> B <- interlinks(SaK,"sc",3,4,col1="yellow",col2="cyan")
> plot(B)

> R <- read.graph("./nets/class.net",format="pajek")
> vertex_attr(R)$shape <- NULL
> V(R)$deg <- degree(R)
> Cut <- vertex_cut(R,"deg",8)
> plot(Cut,vertex.size=V(Cut)$deg*3)
> E(R)$rnd <- sample(1:10,ecount(R),replace=TRUE)
> Ec <- edge_cut(R,"rnd",9)
> plot(Ec,edge.width=E(Ec)$rnd)

Rnet