Use of several distances with ABC-SMC

library(BRREWABC)

Model definition

compute_dist <- function(x, ss_obs) {
  ss_sim <- c(x[["alpha"]] + x[["beta"]] + rnorm(1, 0, 0.1),
              x[["alpha"]] * x[["beta"]] + rnorm(1, 0, 0.1))
  dist <- (ss_sim - ss_obs)^2 # the function returns a vector of 2 values
  return(c(dist))
}

model_list <- list("m1" = compute_dist)

Define prior distribution

prior_dist <- list("m1" = list(c("alpha", "unif", 0, 4),
                               c("beta", "unif", 0, 1)))

Create a reference trajectory

sum_stat_obs <- c(2.0, 0.75)

Run abc smc procedure

res <- abcsmc(model_list = model_list,
              prior_dist = prior_dist,
              ss_obs = sum_stat_obs,
              max_number_of_gen = 15,
              nb_acc_prtcl_per_gen = 2000,
              new_threshold_quantile = 0.8,
              nb_threshold = 2, # the number of thresholds/distances used has to be indicated
              experiment_folderpath = "svrldist",
              max_concurrent_jobs = 5,
              verbose = FALSE)
#> The distance threshold(s) (epsilon(s)) fall(s) below the predetermined min value!
#> [1] 0.009986183 0.003752885

Plot results

all_accepted_particles <- res$particles
all_thresholds <- res$thresholds
plot_abcsmc_res(data = all_accepted_particles, prior = prior_dist,
                filename = "svrldist/res/figs/svrldist_pairplot_all.png", colorpal = "YlGnBu")
#> [1] "Plot saved as '.png'."
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2
plot_densityridges(data = all_accepted_particles, prior = prior_dist,
                   filename = "svrldist/res/figs/svrldist_densityridges.png", colorpal = "YlGnBu")
#> [1] "Plot saved as '.png'."
plot_thresholds(data = all_thresholds, nb_threshold = 2, # the number of thresholds/distances used has to be indicated
                filename = "svrldist/res/figs/svrldist_thresholds.png", colorpal = "YlGnBu")
#> [1] "Plot saved as 'png'."

Pairplot of all iterations

Threshold evolution over iterations (1)

Threshold evolution over iterations (2)

Density estimates for alpha

Density estimates for beta