[R] Zero Inflated Models - Plotting Results

[Achim Zeileis]

On Tue, 2 Oct 2012, lieslpe wrote:

> Dear SamiC,
>
> I am also attempting to plot my zero inflated model on my data. Did you 
> find a solution? Does anyone else on this list have a solution?

If you want to compare observed and fitted frequencies for the counts 0, 
1, 2, ..., then a common approach is use a rootogram or some variant of 
it. Below is a code snippet that works for "zeroinfl" and "hurdle" objects 
from pscl. But it's fairly straightforward to extend this yourself.

If you want to visualize dependence on covariates, you can either use 
scatterplots for continuity-corrected logs (as the countreg vignette of 
pscl does) or separately visualize factor(y > 0) ~ x and log(y) ~ x, 
subset = y > 0 or so.

hth,
Z

rootogram <- function(obj, max = NULL, ...) {
   y <- model.response(model.frame(obj))
   tab <- table(factor(y, levels = 0:max(y)))
   tab2 <- colSums(predprob(obj))
   if(is.null(max)) {
     max <- if(all(tab2 >= 1)) max(y) else max(ceiling(mean(y)), min(which(tab2 < 1)) - 1)
   }
   max <- min(max, length(tab) - 1) + 1
   obsrvd <- sqrt(tab[1:max])
   expctd <- sqrt(tab2[1:max])
   res <- obsrvd - expctd
   x <- barplot(obsrvd, offset = -res, xlab = "Count", ylab = "sqrt(Frequency)")
   lines(x, expctd, col = 2, type = ifelse(max > 25, "l", "b"), pch = 19)
   abline(h = 0)
   invisible(cbind(observed = tab, expected = tab2))
}


> Thanks,
> Liesl
>
> Message from SamiC Jun 30, 2011:
> I am fitting a zero inflated negative binomial model to my data.  I have
> pretty much got my selected model and now i am wanting to plot the model to
> the origional data.
>
> Example.
>
> f8<-formula(Birds~Tide+Fish+Zooplankton+Chlorophylla|StratificationIndex)
> Nb8<-zeroinfl(f8, dist="negbin", link= "logit", data=ocean)
>
> Tide is a factor, so i assume i have to plot a different graph for each
> level of the factor.
>
> what i essentially want to do is plot a graph for each variables against
> birds with the fitted line of the model.
>
> I have been using the predict function, but i get the same trend for every
> graph and variable.  I was reading that the predict function gives a mean
> across all the values (or something to this effect).
>
> Does anyone know how to code for this in R.  from the above model i want to
> plot birds~fish (the original data) and then fit the line of the
> relationship from the model.
>
>
>
>
> --
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>
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