How do I run this model in RMark?

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

How do I run this model in RMark?

Postby jlaake » Fri Apr 13, 2012 4:47 pm

Every once in awhile I get this question posed to me as I just did via email. If you ask me this question there is a good chance I probably won't know. RMark is automated to the point that I really don't have to know the intricacies of each model -- Gary does all that hard work. This is my typical response:

I've never used this model. It is quite easy for me to program these models into RMark without knowing anything about them because all I do is to create the input file for MARK and as of August 2011 that is quite automated. Each model is defined in MarkModels.pdf, models.txt and each parameter in each model is defined in parameters.txt. Those files are located in the RMark directory in your R library. Implementing each model in RMark is really no different. Once you have learned how to setup one type of model it is the same as any other model, other than the parameters that are defined for the model and maybe some model-specific parameters (eg subtract.stratum for MS models). You can see the parameters in each model by looking at the MarkModels.pdf with the exception that ' and '' are spelled out as Prime and DoublePrime. You can also look at parameters.txt. Note do not change this file without knowing what you are doing. About the only thing you would want to change would be the default link or the default formula but if you change it on your machine then it will be reset any time you load a new version of RMark. If you change any of the other settings, the model may stop working correctly.

The best place to look for help with a model is the Cooch and White book and failing that the help files that accompany MARK. While I'd like to have a help file in RMark for each type of model, I simply do not have the time at present to create one. If you would like to create one for a model that does not have an example, I'll gladly include it in the package so that others can benefit from it and will acknowledge your help. Several folks have already done this. For example, see ?crdms and ?mallard.

regards --jeff
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