Hello,
I would appreciate some help in a question regarding statistical analysis.
I'm looking at species count data where sampling was carried out over
multiple years in repeated sites. So each year was sampled at six different
sites for example. The years were categorized into a temperature group with
two factors:warm or cold. However, I'm only interested in exploring
community differences between temp. groups and across years. I used the
vegan package in R for calculating diversity metrics(abundance, richness,
diversity index, evenness) and want to statistically check differences
among metrics from factors of group and year.
I have been using the manyglm-mvabund package with negative binomial
distribution, but there is the issue that mvabund doesn't fit non-integer
data well, and I'm worried its incorrectly computing diversity and evenness
stats. Additionally, I'm wondering if the repeated sites should be added
as a fixed effect to mitigate this? Or if it's even considered a
random effect actually and a mixed model is more appropriate, using glmmTMB
instead in this case? I'm not terribly familiar with using mixed models in
R so any help is appreciated.
Thank you for your help
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