RMark v2.1.7

[jlaake]

V2.1.7 was posted to CRAN. It should start showing up on various repositories in the next 24 hours. Below is a list of changes/additions/fixes. Note changes to pent parameters in some models and MultScalOcc model. These were all changes in MARK. Also note patch for a serious bug for cases in which many individual covariates were used in multiple formula.

regards --jeff

RMark 2.1.7 (15 Dec 2013)
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NEW FEATURES
* added arguments allgroups, strata.labels, and counts to mark function which are passed to process.data.
* added support for RDMSOpenMCSeas model
* modified code in convert.inp so it would work with url
* added example larksparrrow for MultScalOcc model; note change in MultScalOcc model below under changes

CHANGES
* removed model list from documentation; currently supported models are listed in MarkModels.pdf
* fixed problem in mark which prevented use of retry with fixed parameters. Thanks to Tommy Garrison for reporting this problem.
* fixed make.mark.model so indices of singular parameters were correct with fixed parameters; thanks to Bret Collier for reporting this problem.
* in extract.mark.output code was added to handle very long model formula in extracting LnL.
* in make.mark.model, code was changed to output data on multiple lines as in MARK interface; also model name truncated to 160 characters.
* added test in make.mark.model for duplicate names in the design matrix which should not happen. It reports the duplicated names with a message to contact me.
* modified structure of MultScalOcc model to match changes in MARK (Psi, Theta (primary), p(secondary); note that previous structure is no longer valid.
* modified parameters.txt for p parameter in RDMSOccRepro so time file would be numbered correctly. Also, changed definition of pent for all models except POPAN such that it aligns with MARK in that the last pent is computed by subtraction. This just changed values for design data.

BUG FIXES
* Fixed a serious bug in make.mark.model which was passing individual covariate data out of synch with the variable names when there were more than one individual covariates used in the formulas and they same covariates were used in multiple formula. Thanks to Jonathon Cohen who reported a discrepancy when the model was exported to MARK, re-run and the results were different because MARK passes all covariate data to the inp file in the same order for all models.
* Fixed bug in make.design.data which removed time,age from pi parameters that were not mixture parameters.