On Sun, 23 Feb 2014, Dario Strbenac wrote:
The documentation states :
An alternative parametrization (often used in ecology) is by the mean ?mu?, and
?size?, the dispersion parameter.
However, this fails :
rnbinom(10, mu = 100, size = 0)
[1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
Warning message:
In rnbinom(10, mu = 100, size = 0) : NAs produced
For dispersion set to 0, it should work like drawing from a Poisson
distribution.
No, Poisson is the case for size converging to Inf. Compare:
R> dnbinom(1:4, mu = 1, size = 1e9)
[1] 0.36787945 0.18393972 0.06131324 0.01532831
R> dpois(1:4, lambda = 1)
[1] 0.36787944 0.18393972 0.06131324 0.01532831
This is easy to see from the explanation in the manual page:
The variance is 'mu + mu^2/size' in this parametrization.
So for size = Inf this yields mu, i.e., equidispersion. And for finite
positive size, there is always overdispersion.
It also produces incorrect draws for non-zero dispersions :
rnbinom(10, mu = 100, size = 0.01)
[1] 0 0 0 0 0 0 0 0 0 0
This conforms with the documentation
The case 'size == 0' is the distribution concentrated at zero.
This is the limiting distribution for 'size' approaching zero,
even if 'mu' rather than 'prob' is held constant. Notice though,
that the mean of the limit distribution is 0, whatever the value
of 'mu'.
It also fails for underdispersed count models :
rnbinom(10, mu = 100, size = -0.1)
[1] NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN
Warning message:
In rnbinom(10, mu = 100, size = -0.1) : NAs produced
And here the manual explains:
size: target for number of successful trials, or dispersion
parameter (the shape parameter of the gamma mixing
distribution). Must be strictly positive, need not be
integer.
sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_AU.UTF-8LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8LC_MESSAGES=en_AU.UTF-8
[7] LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tools_3.0.2
--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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