Internal igraph vertex ids start from 0 in C, and from 1 in R, and
they are never negative. The not very helpful error message is coming
from the igraph C library and is a consequence of some other error,
probably in the R package, or maybe a bug in igraph.
Your data is not very big, actually, so if you save it with save() and
send it to me with the complete code that you used, I can probably
help you. Assuming you are allowed to share the data.
Gabor
On Wed, Nov 13, 2013 at 9:59 PM, <address@hidden> wrote:
I have a problem with the function bipartite.projection() which
returns
Error in bipartite.projection(igraph_bi) :
At structure_generators.c:84 : Invalid (negative) vertex id, Invalid
vertex id
when trying to project my bipartite graph.
Unfortunately my graph is very large (IGRAPH DN-B 154626 448387 -- )
so I
can't easily reproduce the error in a minimum working example to
share.
What I tried to do was to have a look at the dataframes that I used to
create the graph object in the first place with
graph.data.frame(edges, directed=TRUE, vertices=nodes)
I checked the "id" column of my "nodes" df along with the "from"
column of
my "edges" df for negative values. (By the way, both "id" and "from"
columns
are character vectors, not numeric). Indeed I found 25 "negative"
strings in
my "id" column of the "nodes" df--it depends on the first character,
non-alphanumerics make for a negative value of the string. But still
after
removing all the negative strings, and after double-checking again
both "id"
and "from" columns, I keep getting the same error from
bipartite.projection()
Error in bipartite.projection(igraph_bi) :
At structure_generators.c:84 : Invalid (negative) vertex id, Invalid
vertex id
Now my problem is to understand how to find where the negative values
that
trigger the error are hidden.
Is the value of the column "id" used as id of the node without any
transformation (and same for the column "from" for edges) by the
function
graph.data.frame?
How can I get the id values out of the graph object to check for
negative
values?
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