Create summary table of demographic rates from survival and recruitment surveys

Create summary table of demographic rates from survival and recruitment surveys

Usage

estimateBayesianRates(
  surv_data,
  recruit_data,
  N0 = NA,
  disturbance = NULL,
  priors = NULL,
  shiny_progress = FALSE,
  return_mcmc = FALSE,
  i18n = NULL,
  niters = formals(bboutools::bb_fit_survival)$niters,
  nthin = formals(bboutools::bb_fit_survival)$nthin,
  ...
)

Arguments

surv_data

dataframe. Survival data in bboudata format

recruit_data

dataframe. Recruitment data in bboudata format

N0

dataframe. Optional. Initial population estimates, required columns are PopulationName and N0

disturbance

dataframe. Optional. If provided, fit a Beta model that includes disturbance covariates.

priors

list. Optional. If disturbance is NA, this should be list(priors_survival=c(...),priors_recruitment=c(...)); see bboutools::bb_priors_survival and bboutools::bb_priors_recruitment for details. If disturbance is not NA, see betaNationalPriors for details.

shiny_progress

logical. Should shiny progress bar be updated. Only set to TRUE if using in an app.

return_mcmc

boolean. If TRUE return fitted survival and recruitment models. Default FALSE.

niters

integer. The number of iterations per chain after thinning and burn-in.

nthin

integer. The number of the thinning rate.

...

Other parameters passed on to bboutools::bb_fit_survival and bboutools::bb_fit_recruitment.

Value

If return_mcmc is TRUE then a list with results and fitted models, if FALSE just the results summaries are returned.

See also

Caribou demography functions: bayesianScenariosWorkflow(), bayesianTrajectoryWorkflow(), betaNationalPriors(), caribouPopGrowth(), compareTrajectories(), compositionBiasCorrection(), convertTrajectories(), dataFromSheets(), demographicProjectionApp(), estimateNationalRate(), getNationalCoefficients(), getScenarioDefaults(), plotCompareTrajectories(), plotSurvivalSeries(), plotTrajectories(), popGrowthTableJohnsonECCC, simulateObservations(), trajectoriesFromBayesian(), trajectoriesFromNational(), trajectoriesFromSummary(), trajectoriesFromSummaryForApp()

Examples

s_data <- rbind(bboudata::bbousurv_a, bboudata::bbousurv_b)
r_data <- rbind(bboudata::bbourecruit_a, bboudata::bbourecruit_b)
estimateBayesianRates(s_data, r_data, N0 = 500)
#>   PopulationName     R_bar       R_sd R_iv_mean R_iv_shape R_bar_lower
#> 1              A 0.1892526 0.07960512 0.3156477   26.15747   0.1660519
#> 2              B 0.2037054 0.10782358 0.3156477   26.15747   0.1704809
#>   R_bar_upper     S_bar      S_sd S_iv_mean S_iv_shape S_bar_lower S_bar_upper
#> 1   0.2144154 0.8815656 0.2352747 0.5053561   13.72423   0.8252899   0.9231215
#> 2   0.2399635 0.9078586 0.2977726 0.5053561   13.72423   0.8486475   0.9467159
#>    N0 nCollarYears nSurvYears nCowsAllYears nRecruitYears
#> 1 500          900         31          2353            27
#> 2 500          519         18          2001            15