In quang-huynh/RBassess: An Age- And Length-Based Assessment Model for Rainbow Trout in British Columbia, Canada

knitr::opts_chunk$set(
  collapse = TRUE, echo = FALSE, message = FALSE,
  fig.width = 6, fig.height = 4.5,
  out.width = "650px",
  comment = "#>"
)

Summary of MCMC chain {.tabset}

Data and Model Fits

plot_age_length(x@.MISC$RBfit@RBdata, stan_obj = x, bubble = bubble)

plot_length(x@.MISC$RBfit@RBdata)

plot_stocking_density(x@.MISC$RBfit@RBdata)

plot_Lstart(x@.MISC$RBfit@RBdata)

plot(x@.MISC$RBfit@RBdata@Age, x@.MISC$RBfit@RBdata@Age_adjust, xlab = "Integer Age", ylab = "Accumulated growing degree time (years)",
     typ = "o", pch = 16)
abline(a = 0, b = 1, lty = 2)

Parameter Estimates

Table 1. Posterior means, standard deviation (SD), and coefficients of variation (CV).

generate_summary_table(x)

plot_selectivity(x@.MISC$RBfit, x)

Posterior Distribution

if(is.null(y)) {
  plot_pars(RBdata = x@.MISC$RBfit@RBdata, stan_obj = x, plot.title = "", plot_type = "MCMC")
} else plot_pars(RBdata = x@.MISC$RBfit@RBdata, stan_obj = x, stan_prior = y, plot.title = "", plot_type = "MCMC_both")

MCMC Diagnostics

rstan::stan_ac(x)

rstan::stan_trace(x)

Table 2. Diagnostic statistics n_eff (effective sample size) and Rhat (Gelman-Rubin statistic) for the parameters in the model.

as.data.frame(summary(x)[[1]][, 9:10])

Note: Additional diagnostics are available through the Shiny app in the shinystan package: shinystan::launch_shinystan()

R version

This report was generated on: r Sys.time()

r R.version.string
RBassess version r packageVersion('RBassess')

quang-huynh/RBassess documentation built on May 8, 2019, 7:30 a.m.