Good day all,
I was hoping that you could offer some guidance.
I am fitting a single species occupancy model from data collected during a single year between the wet and dry seasons. In total, 20 camera traps were deployed for a period of 30 days each season. In short, my aim is to evaluate temporal variation in occupancy for 13 individual species relative to three site specific covariates.
My data are as a follows:
Detection (y) <- matrix
Site_covs <- Forage cover (percentage), forage nutritive quality, distance to nearest rivers (m).
Obs_covs <- Habitat type (LRB) and season (wet vs dry)
I have attempted a variety of different approaches however it seems as if I am going around in circles. For example, I have evaluated temporal variation in occupancy on a per season (1) basis using the following code:
m3 <- stan_occu(~Season:Habitat ~Season:Habitat + Season:scale(Grass_cover) + Season:scale(Shrub_cover) + Season:scale(Tree_cover) + Season:scale(Grass_quality) + Season:scale(Shrub_quality) + Season:scale(Tree_quality) + Season:scale(Distance_to_rivers), umf, chains=4, iter=10000)
Similarly, I have evaluated temporal variation in occupancy relative to habitat (2) using the following code:
m4 <- stan_occu(~Season:Habitat ~Season:Habitat + Habitat:scale(Grass_cover) + Habitat:scale(Shrub_cover) + Habitat:scale(Tree_cover) + Habitat:scale(Grass_quality) + Habitat:scale(Shrub_quality) + Habitat:scale(Tree_quality) + Habitat:scale(Distance_to_rivers), umf, chains=4, iter=10000)
Both approaches suggest that no covariates have an effect on the species occupancy. My question is two part:
1) Will I be able to infer reliable estimates using the above approach?
2) Is it necessary for met to scale my grass, shrub and tree cover variables given that these are estimated percentage estimates on a per site basis? For example:
m22 <- stan_occu(~Season:Habitat ~Season:Habitat + Season:Grass_cover + Season:scale(Grass_quality), umf, chains=4, iter=10000)
If I do this, the results suggest a significant effect however I receive a warning about covariates not being standardized (1) and divergent transitions (2).
Any help would be greatly appreciated!
Regards
Gareth