added function

DESCRIPTION

@@ -13,7 +13,7 @@ Description: drjacoby is an R package for performing Bayesian inference via
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LinkingTo: 
     Rcpp
 Imports: 

NAMESPACE

@@ -16,6 +16,7 @@ export(plot_scatter)
 export(plot_trace)
 export(run_mcmc)
 export(sample_chains)
+export(tune_rungs)
 import(dplyr)
 import(ggplot2)
 importFrom(GGally,ggpairs)
@@ -25,6 +26,7 @@ importFrom(coda,geweke.diag)
 importFrom(coda,mcmc)
 importFrom(grDevices,grey)
 importFrom(magrittr,"%>%")
+importFrom(stats,approx)
 importFrom(stats,cor)
 importFrom(stats,pnorm)
 importFrom(stats,quantile)

R/main.R

@@ -609,6 +609,58 @@ deploy_chain <- function(args) {
   return(ret)
 }
 
+#------------------------------------------------
+#' @title Tune mcmc rungs
+#'
+#' @description Takes a completed mcmc object that has been run with parallel
+#'   tempering, and uses the acceptance rates to recalculate the optimal number
+#'   and distribution of rungs.
+#'   
+#' @param x an object of class \code{drjacoby_output}, with the MCMC completed
+#'   and run with parallel tempering over multiple rungs.
+#' @param target_acceptance the target acceptance rate between rungs. Higher
+#'   values will lead to more rungs being needed.
+#'
+#' @importFrom stats approx
+#' @export
+
+tune_rungs <- function(x, target_acceptance = 0.23) {
+
+  # avoid "no visible binding" note
+  link <- value <- NULL
+
+  # check inputs
+  assert_class(x, "drjacoby_output")
+  assert_neq(length(x$diagnostics$mc_accept), 1, message = "run_mcmc() must have been run with multiple temperature rungs")
+  assert_single_bounded(target_acceptance)
+
+  # get acceptance rates and check all non-zero
+  acceptance <- x$diagnostics$mc_accept |>
+    group_by(link) |>
+    summarise(value = mean(value)) |>
+    pull(value)
+
+  assert_gr(acceptance, 0, message = "acceptance rates must be positive for all pairs of rungs")
+  n_rungs <- length(acceptance) + 1
+
+  # calculate cumulative barrier Lambda
+  Lambda <- sum(1 - acceptance)
+
+  # calculate new number of rungs
+  n_rungs_new <- ceiling(Lambda / (1 - target_acceptance)) + 1
+
+  # calculate new distribution of rungs by linear interpolation
+  beta_old <- x$parameters$beta_manual
+  y_old <- c(0, cumsum(1 - acceptance))
+  #plot(beta_old, y_old)
+  y_new <- seq(0, Lambda, l = n_rungs_new)
+  result <- approx(y_old, beta_old, xout = y_new)
+  #points(result$y, result$x, col = 2)
+  beta_new <- result$y
+
+  return(beta_new)
+}
+
 #------------------------------------------------
 # update progress bar
 # pb_list = list of progress bar objects
@@ -625,5 +677,7 @@ update_progress <- function(pb_list, name, i, max_i, close = TRUE) {
   }
 }
 
+#------------------------------------------------
 # Deal with user input cpp not being defined
 globalVariables(c("create_xptr"))
+

R_ignore/deploy.R

@@ -42,7 +42,17 @@ mcmc <- run_mcmc(data = list(x = x),
                  loglike = r_loglike,
                  logprior = r_logprior,
                  burnin = 1e3,
-                 samples = 1e3)
+                 samples = 1e3,
+                 chains = 2,
+                 beta_manual = beta_tuned)
+
+plot_mc_acceptance(mcmc)
+
+beta_tuned
+
+beta_tuned
+
+beta_tuned <- interleave_with_halfway(beta_tuned)
 
 plot_trace(mcmc, show = "mu", phase = "burnin")