RMark 2.1.1 (3 May 2012)
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NEW FEATURES

* In extract.indices, parameter and df can be NULL and all indices are provided for a parameter (df=NULL and parameter specified) or all parameters if parameter is NULL.
 
* In make.mark.model, the simplify argument was added back but only for building a model and not running it.

* In make.design.data, par.index and model.index are now added to the design data. par.index is a numeric row number within the parameter and model.index is the unique index across all parameters. par.index can be used in place of as.numeric(row.names(ddl[[parameter]]) in the various examples.

* In concert with above change two new arguments parm.specific and input.links were added to make.mark.model and mark.  These are useful for user specified link functions vary within a parameter. See end of help for ?dipper for an example.

* Added code to make.mark.model that sets link to Logit for Mlogit parameters that are fixed to 0. This should make these types of models run far more quickly because the number of real parameters will be reduced. This code will only run if the argument mlogit0 is set to TRUE.  Some beta values of the mlogit parameters may change but the real estimates should remain the same. Thanks to Gary White, Glenn Stauffer and Bret Collier with their help. 
 
BUG FIXES

* Fixed bug in make.mark.model for mlogit specification with pi and Omega parameters in RDMSMisClass models with more than 2 observable strata.  Thanks to Claudia Penaloza for reporting this problem.

* Modified values in parameters.txt to enable model RDHFHet to work. Thanks to Darryl McKenzie for reporting this problem.

* Removed one of the example models in edwards.eberhardt because it does not converge with the Feb 2012 version of mark.exe. It was a poor example giving a very large N with previous versions of mark.exe

* Function collect.model.names is now exported.

* make.mark.model will now issue an error and stop if any covariates are not unique within the first 10 characters which is a MARK limit.

RMark 2.1.0 (27 Jan 2012)
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NEW FEATURES

* In process.data the restriction of having only one non-unobservable state for robust designs was removed but a note is still issued when this occurs. 

* Also, in process.data a warning is issued if you specify more than one value in the vector for initial.ages but an age variable is not identified in the groups. 

* A "." is now allowed in Royle count occupancy models.

* An argument run was added to mark function which if set to FALSE will not run the model after it is created.  

BUG FIXES

* Patch was made to run.mark.model so that a filename can be specified to pick up orphaned MARK output files for a model that was run but not saved. This used to work but when I added code to allow user-specified prefixes (ie something other than marknnn) the change I made broke the other feature.  Thanks to Kelly Hastings for bringing this to my attention.

* Patch was made to make.mark.model to allow design data to be deleted on shared parameters. Thanks to Claudia Penaloza for reporting this issue.

RMark 2.0.9 (1 Dec 2011)
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* For changes in v2.0.9 or earlier, see Whatsnew in the RMark help file.