NEWS.md
rhat argument to glance() and converged() to adjust convergence threshold, with default value of 1.05. Convergence no longer depends on ess.exclude_year argument in bb_fit_survival_ml() as failure to fit fixed year effect resolved with intercept adjustment.year_start) not matching for survival and recruitment model fits in bb_predict_growth().bb_predict_calf_cow_ratio()
bb_predict_recruitment() now predicts adjusted recruitment, following methods in DeCesare (2012). Previous output of bb_predict_recruitment() can now be obtained by running bb_predict_calf_cow_ratio().yearling_proportion_female argument in bb_fit_recruitment() to sex_ratio. This matches bbouretro language and arguments in bb_predict_recruitment().include_uncertain_morts argument in bb_fit_survival() to TRUE. This matches default behaviour in bbouretro.bboudata.bb_fit_recruitment() will error if there are any NA values in the PopulationName, Year, Month and Day columns.bb_fit_survival() will error if there are any NA values in the PopulationName, Year, Month, StartTotal, MortalitiesCertain and MortalitiesUncertain columns.Added ‘Getting Started’ vignette.
Added functions:
bb_predict_survival_trend()bb_predict_recruitment_trend()bb_plot_year_trend_survival()bb_plot_year_trend_recruitment()bb_predict_population_change()bb_plot_year_population_change()plot() (plot traceplots for bboufit object)Added arguments:
year_start = 4L to bb_fit_survival() and bb_fit_recruitment() to set caribou year start month as integer - (default April)yearling_female_proportion = 0.5 to bb_fit_recruitment() to set yearling sex ratioyear_trend = FALSE to bb_fit_survival() and bb_fit_recruitment() to fit model with year trendinclude_random_effects = TRUE to coef()/tidy() to provide possibility of removing individual random effect estimatesbb_fit_survival_ml()bb_fit_recruitment_mlpriors = c(b0_mu = 4, b0_sd = 2) instead of priors = list(b0 = "dnorm(4, 2^-2)")).sig_fig to coef()/tidy()/predict() methods to round estimates and lower/upper bounds to set significant figures.bb_predict_growth() now handles different years and doesn’t return month.bb_predict_lambda() for bb_predict_growth().bb_plot_year_growth().bb_plot_year_recruitment().bb_plot_month_survival().bb_plot_year_survival().bb_plot_month().