I am carrying out a zero-inflated negative binomial GLM on some insect count data in R. My problem is how to get R to read my species data as one stacked column so as to preserve the zero inflation. If I subtotal and import it into R as a single row titled Abundance, I loose the zeros and the model doesn't work. Already, I have tried to:
stack the data myself (there are 80 columns * 47 rows) so with 3760 rows after stacking manually you can imagine how slow R gets when using the pscl zeroinfl() command (It takes 20mins on my computer!, It still worked)
The next problem concerns a spatial correlation. Certain samplers sampled from the same medium so as to violate independence. Can I just put medium in as a factor in the model?