
* The IPMpack homepage: http://ipmpack.r-forge.r-project.org

* Please subscribe to our list serv to ask or answer questions on using IPMpack: 
	http://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/ipmpack-users

* An introduction to IPMpack was published in Methods in Ecology and Evolution:
	http://onlinelibrary.wiley.com/doi/10.1111/2041-210x.12001/abstract
	
* See the IPMpack vignette using:  vignette('IPMpack_Vignette')
	
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Changes in 2.0:
* We have substantially streamlined IPMpack by homogenizing function naming and argument conventions and consolidating related functions in an effort to make functions easier to find and remember. 
	
* Due to name changes, some of your past IPMpack code may not function, though we've made every effort to retain functions temporarily to ease the transition to version 2.0. Some deprecated functions are now hidden, which means that they can be accessed by preceeding the function name with a '.' (e.g. .generateDataDiscrete()). Don't hesitate to contact us through the list serv to ask for tips on updating your code to 2.0. Our new naming system is now stable, unless catastrophe strikes. 
	
1. generateData(), generateDataStochastic(), generateDataDiscrete()
This is now a single function generateData with argument type that allows you to obtain the previous generateDataStochastic (type=stochastic) and generateDataDiscrete (type=discrete).

2. convergeLambda(), convergeR0(), convergeLifeExpectFirstBin/LastBin() 
This is now a single function convergeIPM with argument response that allows you to obtain the previous options. 

3. contourPlot()
Eliminated - use image.plot in the library fields.

4. createIPMPmatrix(),  createIPMFmatrix(), createIPMCmatrix(), etc
Name changed to makeIPMPmatrix, makeIPMFmatrix, etc for consistency with rest of package. Previous still there, but deprecated. 

5. makePostGrowthObj(), makePostFecObj(), makePostSurvObj()
Eliminated. Bayesian methods now longer supported (though we still like them, they just require a lot of custom coding). 

6. runSimpleModel()
Eliminated.  

7. createMPMFmatrix(), createMPMFmatrix(), createMPMFmatrix() 
Eliminated

8. argument survToDiscrete()
changed to the more descriptive moveToDiscrete

9. Added option of separating offspringObj from fecObj - i.e. the regression defining offspring size becomes its own separate object 
-new function: makeOffspringObj 
-options in makeFecObj and makeClonalObj to NOT fit offspring (doOffspring=FALSE)
-arguments in makeIPMFmatrix to include offspring object (offspringObj)
-similar adjustments in the integer versions

10. Option of imposing user-specified coefficients in making growth, surv, fec, and offspring objects via the argument coeff  in makeGrowthObj, makeFecObj, makeSurvObj and makeOffspringObj

11. The regressionType argument in makeGrowthObj and makeOffspringObj() i.e., regressionType=declineVar changed to the more accurate changingVar.

12. trackPopStructManyCov() is now an argument of stochGrowthRateManyCov

13. stochGrowthRateSampleList() altered to take as an argument densDep=TRUE, and the function stochGrowthRateSampleListDD() was eliminated

14. makeListIPMs() is now sampleSequentialIPMsList(), which is meant to be used for generating a sequence of IPMs for a stochastic environment described by a discrete covariate. 

15. Created a new function,sampleIPMsList(), which  makes a list of IPMs from lists of vital rate objects, and is used to propagate uncertainty from regressions to IPM predictions.

16. makeListPmatrix() and makeListFmatrix() are now hidden (.makeListPmatrix and .makeListFmatrix) and their functionality is replaced by the more general sampleIPMsList.

17. Created a new function, sampleVitalRateObjList(), which replaces the functionality of getListRegObjects and getListRegObjectsFec and more generally obtains samples from any type of vital rate object.

