I am confused how to analyze this dataset in R: There are 2 islands, 2 sites were selected (nonrandom) per each island, 6 transects randomly were located on each site, then the number of corals was counted in three categories: bleached, partial-bleached and health. The data are collected for 2 years.
The transect (random effect) is nested within sites, and sites (fixed effect) within island (fixed effect), but I have counted on categorical data. I am confused which analyses should I use to compare the spatial and temporal variation in each category of health condition. I think generalized linear mixed model is perfect but multivariate abundance model may be the best. Which test (analysis) in which package is the best fit to my data? How should I deal with the categories, is it fixed effect factor?
Any suggestion would be appreciated.
I ran the model as:
model <- glmer(No.coral ~ island + health_status + (1|island:site:transect), data = data, family=poisson) summary(model) Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) ['glmerMod'] Family: poisson ( log ) Formula: No.coral ~ island + health_status + (1 | island:site:transect) Data: data AIC BIC logLik deviance df.resid 33065.5 33100.5 -16527.8 33055.5 8059 Scaled residuals: Min 1Q Median 3Q Max -1.733 -0.961 -0.567 -0.284 117.509 Random effects: Groups Name Variance Std.Dev. island:site:transect (Intercept) 0.1081 0.3289 Number of obs: 8064, groups: island:site:transect, 32 Fixed effects: Estimate Std. Error z value Pr(>|z|) (Intercept) -2.99554 0.10110 -29.63 <2e-16 *** islandL 1.38643 0.12018 11.54 <2e-16 *** health_statusM 2.29915 0.05599 41.06 <2e-16 *** health_statusS 2.31649 0.05595 41.40 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Correlation of Fixed Effects: (Intr) islndL hlth_M islandL -0.618 helth_sttsM -0.503 0.000 helth_sttsS -0.503 0.000 0.909
My questions are: Is my model written correctly? why the model output is dismissed 'health_status_H'? Also, I don't know how to show the variation (increasing/decreasing) of each health status during the 4 years of observation (not only show the significance of variations as above)? (before, I told that the samplings were conducted during 2 years, by mistake). I also need comparisons ONLY among years at each island and each site. Many thanks.