[R-sig-eco] hurdle model for experiment anlysis

[Ben Bolker]

  A few comments:

  are the habitats replicated? If not, you have a fairly serious
experimental design problem -- you can't statistically distinguish
between the measured covariates and other, unmeasured/unintentional
differences among the habitats ...

  * are you willing to treat complexity as a continuous variable, or do
you not want to assume that the 'distance' between neighboring
values of complexity is the same (an ordinal variable)?

 * for colour and water, you should probably simply leave these as
single categorical variables and let R sort out the construction of
dummy variables for you.

 * you should think about whether you want to look for regular/monotonic
trends with time (i.e. code time as a continuous
variable) or allow for any possible temporal variable (code time a
fixed, or possibly random-effect, categorical variable)
  if habitats are indeed replicated you probably want something like

MCMCglmm(fixed=number_in_habitat~complexity+colour+water+time,random=~habitat,
   family=zipoisson,data=...)

  you have a few options for the family depending on how you want to
treat the zeros (hurdle vs. zero-inflated)

  are you sure the data are zero-inflated  (Warton, D. I. 2005. Many
zeros do not mean zero inflation: comparing the goodness-of-fit of
parametric models to multivariate abundance data. Environmetrics
16:275-289. doi: 10.1002/env.702 <http://dx.doi.org/10.1002/env.702>.  ) ?



Renke Lühken wrote:
>  Hi all,
> I want to analyse an experiment at which insects were allowed to
> choose between four habitats with different characteristics (see
> below). Number of individuals per habitat were resampled six times
> (every 5 min). I want to know which variables and which interactions
> of the variables have an influence on the number of individuals in the
> habitats.
>
> Problem: The response variable shows a zero inflation (>50% of the
> data) by true zeros (100% detectability).
>
> Question: Can I use a hurdle model (ZAP) for that or do you recommend
> another method for the data analysis?
>
> Thanks in advance,
> Renke Lühken
>
>
> Response variables
> Number of individuals in the habitat
>
> Explanatory variables:
> Complexity of the habitat (4 levels)
> Habitat has the Colour 1 (yes/no)
> Habitat has the Colour 2 (yes/no)
> Habitat has the Colour 3 (yes/no)
> Habitat has the Colour 4 (yes/no)
> Water additive 1 (yes/no)
> Water additive 2 (yes/no)
> Time (6 levels: 5-30 min [resampling every 5 min])
>
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