Changelog

Source: NEWS.md

bboutools 0.1.0

• added rhat argument to glance() and converged() to adjust convergence threshold, with default value of 1.05. Convergence no longer depends on ess.
• removed exclude_year argument in bb_fit_survival_ml() as failure to fit fixed year effect resolved with intercept adjustment.
• provide warning to user if start of caribou year (year_start) not matching for survival and recruitment model fits in bb_predict_growth().

bboutools 0.0.0.9007

• Added 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().
• Renamed yearling_proportion_female argument in bb_fit_recruitment() to sex_ratio. This matches bbouretro language and arguments in bb_predict_recruitment().
• Changed default value of include_uncertain_morts argument in bb_fit_survival() to TRUE. This matches default behaviour in bbouretro.
• Added article on ‘Prior Selection and Influence’.
• Added example to “Analytical Methods” article.

bboutools 0.0.0.9006

• Moved internal data checking functions to be exported function in bboudata.
• Updated bbtutorial vignette to mention the new data checking functions.

bboutools 0.0.0.9005

• 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.

bboutools 0.0.0.9004

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 ratio
• year_trend = FALSE to bb_fit_survival() and bb_fit_recruitment() to fit model with year trend
• include_random_effects = TRUE to coef()/tidy() to provide possibility of removing individual random effect estimates

bboutools 0.0.0.9003

• Switch MCMC engine from Jags to Nimble.
• Added recruitment/survival Maximum Likelihood fit functions:
  • bb_fit_survival_ml()
  • bb_fit_recruitment_ml
• Added summary methods for Maximum Likelihood output with class ‘bboufit_ml’.
• Changed how priors are passed to fit functions (e.g. priors = c(b0_mu = 4, b0_sd = 2) instead of priors = list(b0 = "dnorm(4, 2^-2)")).
• Added argument sig_fig to coef()/tidy()/predict() methods to round estimates and lower/upper bounds to set significant figures.

bboutools 0.0.0.9002

• bb_predict_growth() now handles different years and doesn’t return month.
• Adjusted default priors.

bboutools 0.0.0.9001

• Soft-deprecated bb_predict_lambda() for bb_predict_growth().
• Added bb_plot_year_growth().
• Added bb_plot_year_recruitment().
• Added bb_plot_month_survival().
• Added bb_plot_year_survival().
• Added bb_plot_month().

bboutools 0.0.0.9000

• Added a NEWS.md file to track changes to the package.