Function reference • phenomix

Processing phenology data Functions for manipulating data, prior to fitting
`create_data()`	Create data file for fitting time varying run timing distributions with TMB
`limits()`	Internal function to assign upper and lower bounds to parameters, based on their names
Fitting phenological models Function for fitting the model with TMB
`fit()`	Fitting function to be called by user
Plotting output Function for plotting estimates and diagnostics
`plot_diagnostics()`	Plotting function to be called by user
Extracting output Functions for extracting estimates
`extract_means()`	Output processing function to be called by user
`extract_sigma()`	Output processing function to be called by user
`extract_lower()`	Output processing function to be called by user
`extract_upper()`	Output processing function to be called by user
`extract_theta()`	Output processing function to be called by user
`extract_all()`	Output processing function to be called by user
`extract_annual()`	Output processing function to be called by user
`fixef(<phenomix>)`	Get fixed effects parameters from model object, copying glmmTMB 'fast' implementation
`ranef(<phenomix>)`	Get random effects parameters from model object, copying glmmTMB 'fast' implementation

Reference