From 75b783507ede9a6849d95f1dc8805208df0d5ead Mon Sep 17 00:00:00 2001 From: Seb Dalgarno Date: Thu, 11 Apr 2024 22:51:04 -0700 Subject: [PATCH] document --- man/bb_plot_year_recruitment.Rd | 7 +++++++ man/bb_predict_growth.Rd | 5 ++++- man/bb_predict_population_change.Rd | 5 ++++- man/bb_predict_recruitment.Rd | 12 +++++++++++- man/bb_predict_recruitment_trend.Rd | 3 +++ man/params.Rd | 2 ++ man/predict.bboufit_recruitment.Rd | 3 +++ 7 files changed, 34 insertions(+), 3 deletions(-) diff --git a/man/bb_plot_year_recruitment.Rd b/man/bb_plot_year_recruitment.Rd index 36767df..cf1380c 100644 --- a/man/bb_plot_year_recruitment.Rd +++ b/man/bb_plot_year_recruitment.Rd @@ -23,6 +23,7 @@ bb_plot_year_recruitment(x, ...) } \description{ Plot annual recruitment estimates with credible limits. +Recruitment is adjusted following DeCesare et al. (2012) methods. } \section{Methods (by class)}{ \itemize{ @@ -31,3 +32,9 @@ Plot annual recruitment estimates with credible limits. \item \code{bb_plot_year_recruitment(bboufit_recruitment)}: Plot annual recruitment estimates for a bboufit_recruitment object. }} +\references{ +DeCesare, Nicholas J., Mark Hebblewhite, Mark Bradley, Kirby G. Smith, +David Hervieux, and Lalenia Neufeld. 2012 “Estimating Ungulate Recruitment +and Growth Rates Using Age Ratios.” The Journal of Wildlife Management +76 (1): 144–53 https://doi.org/10.1002/jwmg.244. +} diff --git a/man/bb_predict_growth.Rd b/man/bb_predict_growth.Rd index bc1c68f..86640ff 100644 --- a/man/bb_predict_growth.Rd +++ b/man/bb_predict_growth.Rd @@ -8,6 +8,7 @@ bb_predict_growth( survival, recruitment, + sex_ratio = 0.5, conf_level = 0.95, estimate = median, sig_fig = 3 @@ -24,7 +25,9 @@ bb_predict_lambda( \arguments{ \item{survival}{An object of class 'bboufit_survival' (output of \code{\link[=bb_fit_survival]{bb_fit_survival()}}).} -\item{recruitment}{An object of class 'bboufit_recruitment' (output of \code{\link[=bb_fit_recruitment]{bb_fit_recruitment()}}).} +\item{recruitment}{An object of class 'bboufit_recruitment' (output of \code{\link[=bb_fit_recruitment]{bb_fit_recruitment()}})} + +\item{sex_ratio}{A number between 0 and 1 of the proportion of females at birth.} \item{conf_level}{A number between 0 and 1 of the confidence level.} diff --git a/man/bb_predict_population_change.Rd b/man/bb_predict_population_change.Rd index 0c2a389..87e9060 100644 --- a/man/bb_predict_population_change.Rd +++ b/man/bb_predict_population_change.Rd @@ -7,6 +7,7 @@ bb_predict_population_change( survival, recruitment, + sex_ratio = 0.5, conf_level = 0.95, estimate = median, sig_fig = 3 @@ -15,7 +16,9 @@ bb_predict_population_change( \arguments{ \item{survival}{An object of class 'bboufit_survival' (output of \code{\link[=bb_fit_survival]{bb_fit_survival()}}).} -\item{recruitment}{An object of class 'bboufit_recruitment' (output of \code{\link[=bb_fit_recruitment]{bb_fit_recruitment()}}).} +\item{recruitment}{An object of class 'bboufit_recruitment' (output of \code{\link[=bb_fit_recruitment]{bb_fit_recruitment()}})} + +\item{sex_ratio}{A number between 0 and 1 of the proportion of females at birth.} \item{conf_level}{A number between 0 and 1 of the confidence level.} diff --git a/man/bb_predict_recruitment.Rd b/man/bb_predict_recruitment.Rd index 839f390..805d3a3 100644 --- a/man/bb_predict_recruitment.Rd +++ b/man/bb_predict_recruitment.Rd @@ -7,6 +7,7 @@ bb_predict_recruitment( recruitment, year = TRUE, + sex_ratio = 0.5, conf_level = 0.95, estimate = median, sig_fig = 3 @@ -17,6 +18,8 @@ bb_predict_recruitment( \item{year}{A flag indicating whether to predict by year.} +\item{sex_ratio}{A number between 0 and 1 of the proportion of females at birth.} + \item{conf_level}{A number between 0 and 1 of the confidence level.} \item{estimate}{A function to calculate the estimate.} @@ -27,8 +30,15 @@ bb_predict_recruitment( A tibble of the predicted estimates. } \description{ -Predict DeCesare adjusted recruitment by year, assuming a 50\% sex ratio. +Predict adjusted recruitment by year using DeCesare et al. (2012) methods. If year is FALSE, predictions are made for a 'typical' year. +See \code{\link[=bb_predict_calf_cow_ratio]{bb_predict_calf_cow_ratio()}} for unadjusted recruitment. +} +\references{ +DeCesare, Nicholas J., Mark Hebblewhite, Mark Bradley, Kirby G. Smith, +David Hervieux, and Lalenia Neufeld. 2012 “Estimating Ungulate Recruitment +and Growth Rates Using Age Ratios.” The Journal of Wildlife Management +76 (1): 144–53 https://doi.org/10.1002/jwmg.244. } \seealso{ Other analysis: diff --git a/man/bb_predict_recruitment_trend.Rd b/man/bb_predict_recruitment_trend.Rd index fa7c1df..c0abd3a 100644 --- a/man/bb_predict_recruitment_trend.Rd +++ b/man/bb_predict_recruitment_trend.Rd @@ -6,6 +6,7 @@ \usage{ bb_predict_recruitment_trend( recruitment, + sex_ratio = 0.5, conf_level = 0.95, estimate = median, sig_fig = 5 @@ -14,6 +15,8 @@ bb_predict_recruitment_trend( \arguments{ \item{recruitment}{An object of class 'bboufit_recruitment' (output of \code{\link[=bb_fit_recruitment]{bb_fit_recruitment()}})} +\item{sex_ratio}{A number between 0 and 1 of the proportion of females at birth.} + \item{conf_level}{A number between 0 and 1 of the confidence level.} \item{estimate}{A function to calculate the estimate.} diff --git a/man/params.Rd b/man/params.Rd index e456863..72f534f 100644 --- a/man/params.Rd +++ b/man/params.Rd @@ -33,6 +33,8 @@ Year trend cannot be fit if there is also a fixed year effect (as opposed to ran If NULL, the proportion is estimated from the data (i.e., \code{Cows ~ Binomial(adult_female_proportion, Cows + Bulls)}) and a prior of dbeta(65, 35) is used. This prior can be changed via the \code{priors} argument.} +\item{sex_ratio}{A number between 0 and 1 of the proportion of females at birth.} + \item{year}{A flag indicating whether to predict by year.} \item{month}{A flag indicating whether to predict by month.} diff --git a/man/predict.bboufit_recruitment.Rd b/man/predict.bboufit_recruitment.Rd index 05a2593..738eb2b 100644 --- a/man/predict.bboufit_recruitment.Rd +++ b/man/predict.bboufit_recruitment.Rd @@ -7,6 +7,7 @@ \method{predict}{bboufit_recruitment}( object, year = TRUE, + sex_ratio = 0.5, conf_level = 0.95, estimate = median, sig_fig = 3, @@ -18,6 +19,8 @@ \item{year}{A flag indicating whether to predict by year.} +\item{sex_ratio}{A number between 0 and 1 of the proportion of females at birth.} + \item{conf_level}{A number between 0 and 1 of the confidence level.} \item{estimate}{A function to calculate the estimate.}