Individual covariate length <10 characters

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Individual covariate length <10 characters

Postby jlaake » Mon Nov 14, 2016 1:43 pm

I'm fairly certain this has been posted before but when I did a search I couldn't find it. In working with an individual offlist, it became apparent that the newest version of MARK 8.1 is failing if the individual covariate name is > 10 characters. I'm using June 2014 version of MARK and that is not happening. I guess I should update.

Anyhow, anytime you see the following:

STOP ERROR
MARK did not run properly. If error message was not shown, re-run MARK with invisible=FALSE

Model output is not available

You should check the most recent .out file in your working directory. RMark is telling you that something is wrong with the .out file that MARK created such that it can't find the values it expects. Any R errors after that point are not relevant. I'm going to change the message so it specifically says to check the .out file. In this case the .out ended with

INPUT --- design matrix constraints=10 covariates=11;
INPUT --- 1 allgrass400 0 0 0 0 0 0 0 0 0;
ERROR -- Error with floating point read of ALLGRASS400

MARK gave the error while reading in the design matrix. MARK doesn't allow very long variable names. When the user changed the variable name to have fewer than 10 characters the problem went away. I thought I had a check in the RMark code for this but if I do it is not working. I'll check and add it to avoid this issue. Regardless always use individual covariate names with <10 characters. Variable names in the design data can be of any length because R doesn't have this restriction and they are used in model.matrix to create the DM and the names don't appear in the DM.

regards --jeff
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Re: Individual covariate length <10 characters

Postby cooch » Mon Nov 14, 2016 4:52 pm

Got the following from Gary:

The interface does not allow entry of a covariate name with more than 10 characters. So if Jeff allows longer names in Rmark, there is likely a problem. In the interface, a check is also made to be sure that there are not duplicate names.
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Re: Individual covariate length <10 characters

Postby bacollier » Mon Nov 14, 2016 6:15 pm

cooch wrote:Got the following from Gary:

The interface does not allow entry of a covariate name with more than 10 characters. So if Jeff allows longer names in Rmark, there is likely a problem. In the interface, a check is also made to be sure that there are not duplicate names.



Actually, I remember that Jeff, Gary and I worked this out offlist a while back when I had names that exceeded 10 characters based on some spatial covariates or something and the error in MARK through me. Jeff, if memory serves this was a fix in RMark in 2012 or 2013 based on the NEWS file.

\bret
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Re: Individual covariate length <10 characters

Postby jlaake » Mon Nov 14, 2016 7:03 pm

I just looked at the code and I think the problem you were remembering was that the covariates were not unique through the first 10 characters because they were time varying and the value of time was being added as a suffix to the base covariate name. For example, if the covariate was named "grassdens" and time was up to 2 digits, some names would be longer than 10 characters. I added a check to see if any of the names were duplicates which they would be with names grassdens10, grassdens11, etc.

But MARK was allowing names greater than 10 characters and was truncating. Apparently MARK is now failing if the covariate name is longer than 10 characters. I'll add a restriction to RMark so it will fail if a covariate name is greater than 10 characters with an appropriate message.

--jeff
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