inst/doc/determining-convergence.R

In carbondate: Calibration and Summarisation of Radiocarbon Dates

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  dev='png',
  fig.width=7, 
  fig.height=5.5 # ,
  # dev.args=list(antialias = "none")
)

## ----setup--------------------------------------------------------------------
library(carbondate)

## ----calculate_gr_multiple, results=FALSE, eval=FALSE-------------------------
# all_outputs <- list()
# for (i in 1:3) {
#   set.seed(i + 1)
#   all_outputs[[i]] <- PolyaUrnBivarDirichlet(
#       kerr$c14_age, kerr$c14_sig, intcal20, n_iter = 1e4)
# }
# PlotGelmanRubinDiagnosticMultiChain(all_outputs)

## ----out.width= "100%", echo = FALSE------------------------------------------
knitr::include_graphics("figures-convergence/calculate_gr_multiple-1.png")

## ----calculate_gr, results=FALSE, eval=FALSE----------------------------------
# set.seed(3)
# output <- PolyaUrnBivarDirichlet(
#     kerr$c14_age, kerr$c14_sig, intcal20, n_iter = 2e4)
# 
# PlotGelmanRubinDiagnosticSingleChain(output, n_burn = 5e3)

## ----out.width= "100%", echo = FALSE------------------------------------------
knitr::include_graphics("figures-convergence/calculate_gr-1.png")

## ----calculate_polya_kerr, results=FALSE, eval=FALSE--------------------------
# outputs <- list()
# for (i in 1:3) {
#   set.seed(i+1)
#   outputs[[i]] <- PolyaUrnBivarDirichlet(
#       rc_determinations = kerr$c14_age,
#       rc_sigmas = kerr$c14_sig,
#       calibration_curve=intcal20,
#       n_iter = 1e4)
#   outputs[[i]]$label <- paste("Seed =", i)
# }
# PlotPredictiveCalendarAgeDensity(
#   outputs, n_posterior_samples = 500, denscale = 2, interval_width = "1sigma")

## ----out.width= "100%", echo = FALSE------------------------------------------
knitr::include_graphics("figures-convergence/calculate_polya_kerr-1.png")

## ----calculate_polya_normals, results=FALSE, eval=FALSE-----------------------
# outputs <- list()
# for (i in 1:3) {
#   set.seed(i + 1)
#   outputs[[i]] <- PolyaUrnBivarDirichlet(
#   rc_determinations = two_normals$c14_age,
#   rc_sigmas = two_normals$c14_sig,
#   calibration_curve=intcal20,
#   n_iter = 1e4)
#   outputs[[i]]$label <- paste("Seed =", i)
# }
# PlotPredictiveCalendarAgeDensity(
#   outputs, n_posterior_samples = 500, denscale = 2, interval_width = "1sigma")

## ----out.width= "100%", echo = FALSE------------------------------------------
knitr::include_graphics("figures-convergence/calculate_polya_normals-1.png")

## ----calculate_kld, results=FALSE, eval=FALSE---------------------------------
# set.seed(50)
# output <- WalkerBivarDirichlet(
#     rc_determinations = kerr$c14_age,
#     rc_sigmas = kerr$c14_sig,
#     calibration_curve=intcal20,
#     n_iter = 1e5)
# 
# PlotConvergenceData(output)

## ----out.width= "100%", echo = FALSE------------------------------------------
knitr::include_graphics("figures-convergence/calculate_kld-1.png")