Extracting results from output files with Rmark

posts related to the RMark library, which may not be of general interest to users of 'classic' MARK

Extracting results from output files with Rmark

Postby LisenkadeVries » Mon Dec 17, 2018 11:40 am

Hi all,

I have been running Burnham models in RMark, using the function approach described in paragraph C.13 to create and run a set of models in Mark and return the results in a marklist in Rmark.
Unfortunately, they tested the electrical installation at last weekend, resulting in a complete power shutdown.
At that time, Rmark/Mark had run about 70% of the models. Of these models I have the .inp, .res, .vcv and .out files, so I have the results of the models. But since the function in Rmark was not fully completed, the results are not returned as a marklist in Rmark.
I have tried to create a model list using collect.models, but this results in an error stating that no mark models can be found. I guess this means that although the models were successfully run in Mark, the results were not extracted from the output file and saved to a mark object in Rmark.

Is there a way to extract the results from the output files and to create a model list for the models I was able to run?
My best guess would be to use/adapt the internal function extract.mark.output?

Many thanks in advance!
LisenkadeVries
 
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Re: Extracting results from output files with Rmark

Postby jlaake » Mon Dec 17, 2018 10:35 pm

This has arisen before and unless you use external=TRUE, I don't know of any way to do it easily. You would have to create each model with run =FALSE, set the matching Mark base filename and the extract the results. I think you woulf be better off re-running. One suggestion would be to run smaller sets and then merge the marklists. That would avoid losing too much work as long as you dod a save.image in between.Alternatively use external argument.
jlaake
 
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Re: Extracting results from output files with Rmark

Postby LisenkadeVries » Tue Dec 18, 2018 5:18 am

Thanks for your help.

Unfortunately I did not use external=TRUE, so I guess I will have to do it the hard way.
It took me about a month to run these models (they include individual covariates) so i would rather not run them again. For me it is probably quicker to just create all of the models with run=FALSE and then extract the results.

Next time I will definitely run them in batches and use the external argument. It would have saved me so much trouble. I guess you have to make mistakes before you can learn from them...
LisenkadeVries
 
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Joined: Tue May 29, 2018 4:39 am


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