I'll be updating this over time. Feel free to comment and tell me if there is something to add or fix.
Formatting
Formatting
- First year occupancy can utilize only site-level covariates
- Colonization and extinction can utilize both site-level and yearly-covariates, but the site-covariates must be formatted as yearly-covariates
- Detection can utilize site, yearly, and sample covariates.
- Yearly covariates must be formatted as a matrix of M rows and T columns, where M = number of sites, and T = number of primary sampling periods.
- Yearly covariates cannot have any missing values.
- When formatting your unmarkedDataFrame, yearlySiteCovs and obsCovs must be lists. This isn't required for siteCovs.
- In the colext vignette, the example code uses Predicted+1.96*SE to manually calculate 95% confidence intervals. Richard Chandler has stated that he isn't sure why he did that in the example, and recommends using the provided values (upper and lower) that the predict() function provides.
- Use predict() instead of backtransform() and linearcomb(). See https://groups.google.com/d/msg/unmarked/huPAwnC99SQ/ujbmQDxRAQAJ for more information.