[Ipmpack-users] help with IPMpack

[Bruce Kendall]

Note that the sim.CI object returned by stock.growth.rate() is not a confidence interval in the statistical sense; rather, it is a measure of convergence (it goes to zero as the length of your simulation goes to infinity).

A confidence interval that reflected uncertainty in your estimate of demography (e.g., the fact that you only have four annual IPMs) would involve resampling your data/models and then running the stochastic growth rate calculation to an adequate level of convergence for each sample. In your case, if you are resampling the annual IPMs, then there are only 4^4 = 256 equally likely possible combinations, so you could simply calculate them all (you could be more efficient by simulating only with the unique unordered sets and weighting by the appropriate binomial coefficient).

Bruce

> On Jul 27, 2016, at 10:23 AM, Eelke Jongejans <e.jongejans at science.ru.nl> wrote:
> 
> Dear Elena,
> 
> the function stochGrowthRateSampleList only returns the mean of the per-time-step population growth rates in a stochastic simulation. If you want to know the distribution of these per-time-step population growth rates you could write your own version of this function and make sure that that distribution is stored as well. On the other hand if you want a CI for the resulting mean stochastic population growth rate, you code write code in which stochGrowthRateSampleList is called multiple times, and analyse the resulting distribution of mean stochastic population growth rates. If other people have other solutions, please share them! 
> 
> Please also note the description of the stochGrowthRateSampleList function, that reads "Note that the function stoch.growth.rate in the package popbio does this more efficiently and with more useful output; but may fail for large bin numbers.".
> 
> I hope this helps,
> 
> Eelke
> 
> 
> 
> 
> On 20-Jul-16 1:48 PM, Elena S. wrote:
>> 
>> Hi,
>> 
>> I try to calculate CI (confidence intervals) for my stochastic population growth rate. I started with 4 IPM (four years of study), then I run the following function:
>> 
>> exp(stochGrowthRateSampleList(list(IPM9,IPM10,IPM11,IPM12),nRunIn = 100, tMax = 5000))
>> 
>> or the following ones, based on the IPMpack manual (Metcalf et al. 2014):
>> 
>> exp(stochGrowthRateSampleList(nRunIn=100,tMax=5000,listIPMmatrix=list(IPM9,IPM10,IPM11,IPM12),
>>                               listPmatrix=list(Pmatrix9,Pmatrix10,Pmatrix11,Pmatrix12), 
>>                               listFmatrix=list(Fmatrix9,Fmatrix10,Fmatrix11,Fmatrix12),
>>                               seedList=NULL,
>>                               densDep=FALSE))
>> 
>> and I obtained a stochastic lambda of 1.25, but, at the moment, I don't know how to calculate the confidence intervals.
>> 
>> Anyone can help me?
>> 
>> Thanks in advance,
>> 
>> best regards,
>> 
>> Elena
>> 
>> 
>> 
>> _________________________________________________________
>> Dott.ssa Elena Sulis, PhD
>> Centro Conservazione Biodiversità (CCB)
>> Sezione Botanica - Dipartimento di Scienze della Vita e dell'Ambiente (DISVA)
>> Università degli Studi di Cagliari
>> V.le Sant'Ignazio da Laconi, 11-13
>> 09123 Cagliari (ITALIA)
>> Tel:  +39-0706753509
>> E-mail: elenasulis at hotmail.it <mailto:elenasulis at hotmail.it> 
>> Skype: elena.sulis
>> 
>> 
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> 
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--
Bruce Kendall
kendall at bren.ucsb.edu <mailto:kendall at bren.ucsb.edu>
http://kendall.bren.ucsb.edu <http://kendall.bren.ucsb.edu/> 
Skype: brucekendall64

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