From Joachim.Topper at uib.no  Fri May 31 14:38:52 2019
From: Joachim.Topper at uib.no (=?UTF-8?Q?Joachim_Paul_T=C3=B6pper?=)
Date: Fri, 31 May 2019 14:38:52 +0200
Subject: [Ipmpack-users] makeIPMFmatrix when having discrete stages that
 fecundity functions do not contribute to
Message-ID: <0a574c0290ec4ca5521f84c267ef841d@webmail.uib.no>

Hi!

I'm building an IPM for a clonal species with 2 discrete stages. One 
stage is a seedbank (SB), and one is related to vegetative dormancy 
(VD).
The functions for entering and leaving the vegetativ dormancy stage are 
covered in the Pmatrix, but there is no vital rates related to clonality 
or fecundity that contribute to vegetative dormancy.
However, since the discreteTransitionObject contains 2 discrete stages 
and the Pmatrix thus has n+2 bins, all discrete stages must be defined 
in clonalObj and fecObj as well so that the Cmatrix and Fmatrix end up 
with the same n+2 dimensions. This worked fine for the Cmatrix, but 
makeIPMFmatrix crashed.

Error in to.discrete[i, ] <- .fecRaw(x = y, cov = chosenCov, fecObj = 
fecObj)[[2]][which(fecObj at vitalRatesPerOffspringType[,  :
   replacement has length zero

What happened is that when calculating 'to.discrete' for the veg. 
dormant stage (VD) the else-part (line 102) failed since none of the 
fecundity-functions apply to this stage (there's only zeros there, see 
vitalRatesPerOffspringType below), and thus the calculated vector for VD 
contains nothing and cause the coercing into to.discrete of course to 
crash.



vitalRatesPerOffspringType = data.frame(VD=c(0,0,0,0),
                                         SB=c(1,1,1,0),
                                         continuous=c(1,1,1,1),
                                         
row.names=c("flowering","flowers","seedsPerCap","seedlingEstablishmentRate"))


I then changed the 'else' in line 102 to

       if 
(length(which(fecObj at vitalRatesPerOffspringType[,namesDiscrete[i]] == 
1)) == 1)

so that this part works for stages with 1 applying fecfunction, while 
simply nothing happens for those stages with 0 applying fecfunctions, 
i.e. for such stages to.discrete contains only the zeros that were 
predefined in line 94.


So, now my question is, whether this is an ok solution for a potential 
bug? Or did I make a mistake to get that error in the first place?

Thanks & cheers,
Joachim