Re: [igraph] vcount(g) and V(g) with missing items

[Tamas Nepusz]

Hi,

Two things. First, when you do this:

> g <- graph.empty(n=max_items, directed=TRUE)
> g <- graph( igraph_data,n=max_items, directed=TRUE )

This means that first you construct an empty graph with 9 items, then you 
construct another one from your given data and throw the first one away. The 
first call to graph.empty is unnecessary.

Second, note that igraph uses numeric vertex IDs by default, and they must 
always be consecutive (i.e. from 0 to |V|-1, where |V| is the number of 
vertices). When using the graph() constructor, igraph_data is assumed to 
contain vertex IDs. Since the largest number in igraph_data is 9, this means 
that |V| = 10, even though not all of the IDs are used. I suggest you use the 
graph.data.frame constructor instead, this constructs a graph from a data frame 
that contains a *symbolic* edge list. In this case, the numbers in the data 
frame will not be interpreted as edge IDs directly; igraph will invent edge IDs 
on the fly and assign the numbers to a vertex attribute called "name":

> m <- matrix(c(0,1,1,2,4,5,5,6,6,7,7,8,8,9,0,9), ncol=2, byrow=T)
> m
     [,1] [,2]
[1,]    0    1
[2,]    1    2
[3,]    4    5
[4,]    5    6
[5,]    6    7
[6,]    7    8
[7,]    8    9
[8,]    0    9
> g <- graph.data.frame(m)
> vcount(g)
[1] 9
> V(g)$name
[1] "0" "1" "4" "5" "6" "7" "8" "2" "9"

-- 
Tamas