MARSS 3.0 posted for testing

Hi MARSS users,

A version of MARSS 3.0 is now up for testing.  It should be backwards compatible with any MARSS 2.x code you have unless you use  control$diffuse or control$kf.x0.  diffuse now goes into your model list and kf.x0 is called tinitx and goes in the model list too.  control$kf.x0="x00" is now model$tinitx=0 and control$kf.x0="x10" is model$tinitx=1.

Big changes are

• Time-varying parameters are allowed.  See the Quick_Start.pdf to get a brief intro to that feature but it should be pretty self-explanatory.
• Covariates can be added in the standard way.  Again see the Quick_Start.pdf for quick intro.  See chapter in User Guide on estimating species interactions for an example.
• There is a "form" argument in the MARSS() call that allows one to specify special types of models.  Default is "marxss" which covers MARSS + covariates.  The only other form now is "dfa" for Dynamic Factor Analysis.  Check out the DFA chapter in the User Guide for an intro to the form="dfa" which allows you to do a standard DFA by just passing in m (number of states), data and covariates (if wanted).  The dfa form is basic now.  Later we will specialize its output to give loadings etc.
• The AR-p models work now with method="kem" which is much, much faster than method="BFGS".  See chapter in User Guide on AR-p models.
• You can enter things like B=diag(list("1+2*c+3*b",0,0,"2+3c"),2,2) in your list matrices and MARSS will know what to do, i.e. it will estimate B.c and B.b and it knows that B(1,1)=1+2c+3b .  I haven't seen people want to do this..., but you can.
• The print call takes a argument called "what".  Use ?print.marssMLE to see how to use it.  It'll make it easier to print things from your marssMLE objects (what you get back from a MARSS call).

Here is are the tar.gz and .zip files for the 3.0 version.   You'll find links to the User Guide and Quick_Start guide here too.

http://fishbox.iugo-cafe.org/user/e2holmes/MARSS%20Dev%20Site
  

Plan is to upload to CRAN about July 1 assuming no big issues arise. Right now all the prior examples in the User Guide 2.8 and the man files work as before.  I've included new examples with covariates using the new covariate code in the chapter on estimating spp interactions and I've added covariates to the DFA chapter.  I've included a little more code in the AR-1 chapter on estimating those models.

Feel free to try it out.  The more real-world testing it gets before being uploaded to CRAN the better.

Cheers,

Eli