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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy bugs >> BGM coevolution error message http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1380731252 Message started by daven on Oct 2^nd, 2013 at 9:27am

Title: BGM coevolution error message
Post by daven on Oct 2^nd, 2013 at 9:27am

Hello Sergei and Art,

I am using HYPHYMP from hyphy-2.2 both on a linux server and on my macbook pro.

In both cases, when I run a BGM coevolution analysis I always get the following error message:

Running a BGM on 159 nodes with
                  2 maximum parents per node
               10000 burn-in steps
               100000 chain length
                  90 samples
Error:
The left hand side expression does not contain an object reference in the following context: 'BGM gen_bgm=<ERROR HERE>(discreteNodes,continuou'

Function call stack
1 : BGM gen_bgm=(discreteNodes,continuousNodes)
-------
2 : ml_bgm_results=runBGM(_bgm_data)
-------

Thanks in advance for any help on this problem.

David.

Title: Re: BGM coevolution error message
Post by Sergei on Oct 9^th, 2013 at 11:42am

Hi David,

I think this is because I compiled Art's new BGM definition syntax into the 2.2 distribution but haven't updated all the files.

Try replacing BGM with BayesianGraphicalModel in the corresponding batch file and see if that helps. I'll try to issue a fix on GitHub soon.

Sergei

Title: Re: BGM coevolution error message
Post by Jedson Cardoso on Jan 24^th, 2014 at 8:27am

Someone has a solution to this problem, because I have the same message of error.

Title: Re: BGM coevolution error message
Post by Art F. Poon on Jan 27^th, 2014 at 4:26pm

Hi Jedson, David,

Sorry I haven't been on top of this, I haven't been checking these boards that frequently.

I've attached an include file (bayesgraph.ibf) that provides support for using BGMs in HyPhy2.x

To create a BGM object, you use the following batch code:

Code (]
ExecuteAFile (path+"bayesgraph.ibf");
nodes={};
for (i = 0; i <3; i=i+1) {
nodes[Abs(nodes)):

= add_discrete_node ("", 2, 0, 2);
}
BayesianGraphicalModel alarm_bgm = (nodes);

Best,
- Art.

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=bayesgraph.ibf (19 KB | 4 )

Title: Re: BGM coevolution error message
Post by daven on Feb 24^th, 2015 at 11:34am

Hi Art, I don't really understand what needs to be done with the file and code you provided. I don't understand what creating a BGM object means.

Do I just run the batch with HYPHYMP? I did this, then tried to use BGM again but there was no change.

Thanks for any help. I am really close to give up on trying to use BGM really.