RMark 2.1.1 and new MARK update

[jlaake]

If you get the newest version of MARK (7 May 2012) Gary is now using gfortran and creates a mark32.exe and a mark64.exe and it uses the one most appropriate for your machine. However, there is no mark.exe as RMark is expecting, so you'll need to copy the one you want to use and name it mark.exe to get the link to work. Note that you should do a full setup and not an update as the markxx.exe need a dll that only gets installed under the full setup.

The newest version of RMark is on CRAN. Here is a list of changes. If you are using multi-state models then you'll definitely want to update and look at the new argument mlogit0. Below are the list of changes/fixes:

RMark 2.1.1 (3 May 2012)
--------------------------

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.

[cooch]

If you get the newest version of MARK (7 May 2012) Gary is now using gfortran and creates a mark32.exe and a mark64.exe and it uses the one most appropriate for your machine. However, there is no mark.exe as RMark is expecting, so you'll need to copy the one you want to use and name it mark.exe to get the link to work.

Instead of copying either mark32.exe or mark64.exe to mark.exe, you can also use a symbolic link (yes, this is quite feasible under Windows 7). The following is for people who might want to go this route.

1\ open up a command window -- give it administrator privileges. (If you don't know how, you should probably stop here

2\ within the CMD window, navigate to the MARK directory. If you do a dir mark*.exe, you'll see mark32.exe and mark64.exe.

3\ simply create a symbolic link from either mark32.exe or mark64.exe to mark.exe. To do this, use the mklink command. Pretty easy to use. If you want to create a symbolic link from mark.exe to mark64.exe (for example), simply type

Code: Select all

mklink mark.exe mark64.exe


Although I haven't tried it, rmark should pick up mark.exe as if it actually existed as a 'real file'.

So, either copy mark64.exe or mark32.exe to mark.exe, or use a symbolic link, as described.

[jlaake]

Following Evan's post about new mark being in beta, I'd suggest not using it yet with RMark as there may be some issues. Let me test it out before you upgrade to new mark.

--jeff