Re: [igraph] Can't get same results from newer layout.fruchterman.reingold

[Gábor Csárdi]

On Tue, Feb 11, 2014 at 10:56 AM, HIGUCHI Koichi <address@hidden> wrote:

Hi, thank you very much for your reply!

I use "start" option in "layout.fruchterman.reingold()" command in the
test code to avoid random start. So "set.seed()" does not have any
effect on the results, does it?

The algorithm is randomized, in the sense that tiny random displacement values might be added to the coordinates in each iteration. So you need to set the seed to get the same result, although if your graph is not too dense, then you might get away without randomization.

I guess the algorism has been improved and I need to use old version
to get the same result. Maybe I can run secondary R instance with
older Igraph to do layout, or just move to the improved layout
function.

You can install another version of the same package into a different R library directory, you just cannot load them at the same time.

Gabor 

 

Thanks again.
Best regards.

2014-02-12 0:39 GMT+09:00 Gábor Csárdi <address@hidden>:

> Hi, you also need to specify the random seed via set.seed.
>
> That said, you still might get different layouts with different igraph
> versions, because we are trying to improve the algorithms. If setting the
> seed does not work, then you can generate the layout in the old version,
> save the coordinates and then use them with the new version.
>
> Unfortunately R does not really support using different versions of the same
> package at the same time.
>
> Best,
> Gabor
>
>
> On Tue, Feb 11, 2014 at 10:35 AM, HIGUCHI Koichi <address@hidden>
> wrote:
>>
>> Does anybody have any ideas?
>>
>> Thanks.
>>
>> 2013-08-29 15:32 GMT+09:00 HIGUCHI Koichi <address@hidden>:
>> > Hello.
>> >
>> > I am using igraph R package and moving from igraph 0.5.5 to 0.6.5.
>> >
>> > But I found that I can't get the same result from
>> > layout.fruchterman.reingold function of 0.6.5 even if I specified the
>> > same network object and the same starting positions. The output
>> > layouts are different between 0.5.5 and 0.6.5.
>> >
>> > Is there any way to reproduce the same result as 0.5.5 using 0.6.5??
>> >
>> > Here is my test code:
>> > http://koichi.nihon.to/psnl/tmp/net_test.r
>> >
>> > igraph 0.5.5 result:
>> > http://koichi.nihon.to/psnl/tmp/055.png
>> >
>> > igraph 0.6.5 result:
>> > http://koichi.nihon.to/psnl/tmp/065.png
>> >
>> > New layout is not bad at all, but I would like to have the same
>> > results when I input the same data.
>> >
>> > Thank you! And sorry for my poor English.
>> >
>> > BTW, I am developing a content analysis (text data mining) software
>> > using the igraph package. Igraph package is really useful and nice
>> > software! Thank you very much for the effort!
>> > http://khc.sourceforge.net/en/gallery/
>> >
>> > Koichi, Higuchi
>>
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>
>
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