manuscripts/components/sensitivity-trends.R

In cboettig/nonparametric-bayes: Nonparametric Bayes inference for ecological models

sensitivity_trends <- function(allee, sigma, seed){
  sigma_g <- sigma
  p <- c(r = p[[1]], K = p[[2]], C = allee)
  
  # seed indicates replicate training data, generated from f with parameters p  
  yields <- sapply(seed, 
                   function(seed_i){
                     set.seed(seed_i)
                     
                     x <- numeric(Tobs)
                     x[1] <- Xo
                     nz <- 1
                     for(t in 1:(Tobs-1))
                       x[t+1] = z_g() * f(x[t], h=0, p=p)
                     
                     X = c(rep(0,nz), pmax(rep(0,Tobs-1), x[1:(Tobs-1)]))
                     Y = c(rep(0,nz), x[2:Tobs])
                     
                     ## @knitr gp-priors
                     s2.p <- c(5,5)  
                     d.p = c(10, 1/0.1)
                     
                     ## @knitr gp
                     gp <- gp_mcmc(X, y=Y, n=1e5, s2.p = s2.p, d.p = d.p)
                     gp_dat <- gp_predict(gp, x_grid, burnin=1e4, thin=300)
                     
                     matrices_gp <- gp_transition_matrix(gp_dat$Ef_posterior, gp_dat$Vf_posterior, x_grid, h_grid) 
                     opt_gp <- value_iteration(matrices_gp, x_grid, h_grid, MaxT, xT, profit, delta, reward)
                     
                     ## @knitr mle-opt
                     matrices_true <- f_transition_matrix(f, p, x_grid, h_grid, sigma_g)
                     opt_true <- value_iteration(matrices_true, x_grid, h_grid, OptTime=MaxT, xT, profit, delta=delta)
                     
                     OPT = data.frame(GP = opt_gp$D, True = opt_true$D)
                     policies <- melt(data.frame(stock=x_grid, sapply(OPT, function(x) x_grid[x])), id="stock")
                     names(policies) <- c("stock", "method", "value")
                     
                     sims <- lapply(OPT, function(D){
                       set.seed(1)
                       lapply(1:100, function(i) 
                         ForwardSimulate(f, p, x_grid, h_grid, x0, D, z_g, profit=profit, OptTime=OptTime)
                              )
                       })
                     
                     dat <- melt(sims, id=names(sims[[1]][[1]]))
                     sims_data <- data.table(dat)
                     setnames(sims_data, c("L1", "L2"), c("method", "reps")) 
                     # Legend in original ordering please, not alphabetical: 
                     sims_data$method = factor(sims_data$method, ordered=TRUE, levels=names(OPT))
                     
                     Profit <- sims_data[, sum(profit), by=c("reps", "method")]
                     tmp <- dcast(Profit, reps ~ method)
                     tmp <- tmp / tmp[,"True"]
                     tmp <- melt(tmp[2:dim(tmp)[2]])
                     tmp$value[tmp$variable == "GP"]  
                     })
  
  yields_dat <- melt(yields)
  names(yields_dat) <- c("replicate", "simulation", "value")
  
  # Make ids factors, not integers
  yields_dat$replicate <- as.factor(yields_dat$replicate)
  yields_dat$simulation <- as.factor(yields_dat$simulation)
  
  
  # definitions of id codes.  In this case the id number is it's own definition.  
  rep_ids <-  levels(yields_dat$replicate)
  names(rep_ids) <- rep_ids
  sim_ids <-  levels(yields_dat$simulation)
  names(sim_ids) <- sim_ids  
  
  
  
  dat <- data.frame(allee = p[[3]], 
                    replicate = yields_dat$replicate, 
                    sim = yields_dat$simulation, 
                    value = yields_dat$value, 
                    noise = sigma_g)
}