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Re: [igraph] igraph issue with massive matrices

From: address@hidden
Subject: Re: [igraph] igraph issue with massive matrices
Date: Thu, 5 Dec 2019 07:57:43 +0000

Hi Tamas,


Here is an example of the input data and the output which contains the errors



I have a very large transition matrix and I have a shapefile of point location which I want to compute travel time to, with the following code

# Required Packages






T.GC.zone.filename  <- “global_4.T.GC

target.filename <- “targets.shp”

output.filename”<- “output.tif”


#read in transition matrix

T.GC.zone <- readRDS(T.GC.zone.filename)

#read in targetpoints

targets <- readOGR(target.filename)

#compute accumulated cost from every location to the nearest target

output.raster <- accCost(T.GC.zone, targets.zone)

#save output

writeRaster(output.raster, output.filename, format="GTiff", overwrite=TRUE)


The output should be a GeoTIFF with travel time estimates in minutes to the nearest point location and hence every point location should have a travel time of zero, with travel time values increasing with distance/travel from each point.  The snapshot below shows a small part of the output with the points in green, and the travel time raster in shades of gray. I have highlighted travel time raster cells in red when their value is zero.  You can see two points where they – for some unknown reason – have not been used in the travel time computation, but they were part of the dataset and should have been included.  In other runs I have cases where the output raster has values of zero when there is no target in that cell. And that is also an error.


I have not been able to track down this error, but I am suspecting that this error happens with very large matrices.  Unfortunately for my analysis, I really need these large matrices.








Andy Nelson Professor, Spatial Agriculture and Food Security & Head of Department

Department of Natural Resources (Room 4-144)

ITC - Faculty of Geo-Information Science and Earth Observation of the University of Twente

PO Box 217, 7500 AE Enschede, the Netherlands.

Tel: +31 (0) 53 489 3072

Natural Resources Management Research and MSc programmes at ITC





From: igraph-help <igraph-help-bounces+a.nelson=address@hidden> On Behalf Of Tamas Nepusz
Sent: 29 November 2019 12:46
To: Help for igraph users <address@hidden>
Subject: Re: [igraph] igraph issue with massive matrices


I am not sure why this happens.  On one hand, I may be running into a memory limit in R, but the other behaviours may be related to limits within igraph.


Would you have some insight or advice on this issue? 

It's hard to say anything at this stage; it could well be a bug on igraph's side, but the only way I could test it is if I could reproduce it on my side. Is there some small, self-contained example that reproduces the bug and that you could share with us?


All the best,


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