[Ipmpack-users] IPMpack v2.0

[Eelke Jongejans]

Dear IPMpack-users list subscribers,

two weeks ago v2.0 of IPMpack came online. I would like to draw your 
attention to the main changes, outlined below. Please let us know via 
this users list if there are any issues with v2.0.

best wishes,
Eelke


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 ÒgenerateDataÓ with argument ÒtypeÓ that 
allows you to obtain the previous generateDataStochastic 
(type=ÓstochasticÓ) and generateDataDiscrete (type=ÓdiscreteÓ).

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

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

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.