RMark 2.1.4 (11 Dec 2012)
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CHANGES

* threads option for MARK was moved from inp file on proc chmatrix to run command; requires newest version of mark.exe

* accumulate was added as an argument to control whether records with same values are aggregated
		
NEW FEATURES

* Code written by Ben Augustine was added to var.components to compute conf limit on process variance, shrinkage estimates and trace of G. Code was made a little smarter about finding end points for uniroot to compute process variance. Result now contains sigmsq (old sigma) with confidence interval and sigma, the sqrt of sigmsq estimate set to 0 if sigmasq<0

* Modified parameters.txt so F and FPrime in Barker model can be shared.

* A new example deer was added by Bret Collier that explains the share argument in parameter (model) specifications and gives an example for closed capture model.

* A new example for POPAN with data on white-winged doves was added by Bret Collier.

BUG FIXES

* Fixed bug in make.design.data that was improperly labeling session values for secondary parameters when the time intervals between primary sessions were not 1. Thanks to Shannon Knapp for finding and reporting this problem.


Mark 2.1.3 (18 June 2012)
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NEW FEATURES

* Added aggregation of data in make.mark.model to reduce number of capture histories that mark.exe must process in calculating likelihood. Records that have the same ch, covariates and group membership are tallied in the frequency for that group and record.

* Added argument hessian to functions mark and make.mark.model to specify use of hessian rather than second partial matrix for v-c matrix by mark.exe.


RMark 2.1.2 (8 June 2012)
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NEW FEATURES

* Added function create.mark.mcmc to read in mcmc binary file from MARK for analysis with coda package. If you download this from the github site, make sure to install coda separately. Also, to use codamenu to analyze the results you'll need to install lattice package.
 
* Made changes for new gfortran versions of mark which include mark32.exe and mark64.exe. If there is a mark.exe it will use it so you can force the use of 32 or 64 bit by renaming mark32 or mark64 to mark; otherwise if running from 64 bit R it uses mark64.exe and from 32 but R mark32.exe

* For Windows will search both Program Files and Program Files (x86) for mark executables so no need to set MarkPath unless it is not in one of those directories and not in your Path.

* The addition of mlogit0 argument in 2.1.1 was useful to reduce number of real parameters when many mlogit parameters are fixed at 0; however, it was retaining betas that were no longer needed.  These have been removed in this version.

* An argument threads was added to mark and make.mark.model to take advantage of the multiple cpu capabilities of the new mark exes. If positive, it specifies the number of cpus to use and if negative the number of cpus to remain idle. The default is -1 which uses all but one cpu.
 
* One of the side effects of the new mark executables is that setting invisible=FALSE in the Rgui will no longer work to show the iteration counter in a window. Instead regardless of the value of invisible, it creates a file fort.0 which contains the output and you can check on its progress. The fort.0 file is deleted after completing the run. I recommend using Rterm if you are going to use mark.wrapper.parallel because I'm not certain what will happen with parallel runs all using fort.0. If you run it from rterm then using invisible=FALSE will allow you to monitor the progress. The previous version of mark.exe using the Compaq compiler will work with this version of RMark but setting invisible=FALSE does nothing. 
 
* Default formula for CRDMS was changed to ~session from ~1 for N. 
 
* Functions find.possible.transitions and transition.pairs were added.  These can be useful for examining transitions in MS models. See help for an example.
 
* Added pim.type="age" to allowable values for pims in make.design.data. Now all pim types can be created: all, constant, time and age
 
* Added functions splitCH and collapseCH which can be used to split a vector of character strings into a matrix and collapse a matrix into a vector of character strings.
 
* Fixed bug in make.mark.model which did not allow a 2 in ch for RDBarker model. Thanks to Claudia Penaloza for reporting this problem.


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.