R/VCBART_ind.R

In VCBART: Fit Varying Coefficient Models with Bayesian Additive Regression Trees

VCBART_ind <- function(Y_train,
                       subj_id_train, ni_train,X_train,
                       Z_cont_train = matrix(0, nrow = 1, ncol = 1),
                       Z_cat_train = matrix(0L, nrow = 1, ncol = 1),
                       X_test = matrix(0, nrow = 1, ncol = 1),
                       Z_cont_test = matrix(0, nrow = 1, ncol = 1),
                       Z_cat_test = matrix(0, nrow = 1, ncol = 1),
                       unif_cuts = rep(TRUE, times = ncol(Z_cont_train)),
                       cutpoints_list = NULL,
                       cat_levels_list = NULL,
                       edge_mat_list = NULL,
                       graph_split = rep(FALSE, times = ncol(Z_cat_train)),
                       sparse = TRUE, 
                       M = 50,
                       mu0 = NULL, tau = NULL, nu = NULL, lambda = NULL,
                       nd = 1000, burn = 1000, thin = 1,
                       save_samples = TRUE, save_trees = TRUE,
                       verbose = TRUE, print_every = floor( (nd*thin + burn)/10))
{
  # standardize Y
  y_mean <- mean(Y_train)
  y_sd <- stats::sd(Y_train)
  std_Y_train <- (Y_train - y_mean)/y_sd 
  
  if(!is.matrix(X_train)) stop("X_train must be a matrix!")
  if(!is.matrix(Z_cont_train)) stop("Z_cont_train must be a matrix!")
  if(!is.matrix(Z_cat_train)) stop("Z_cat_train must be an integer matrix!")
  
  if(all(X_train[,1] == 1)) stop("Do not include intercept as first column of X_train")
  
  # ASSUME: first column of X_train is not the intercept
  std_X_train <- matrix(NA, nrow = nrow(X_train), ncol = 1 + ncol(X_train))
  std_X_train[,1] <- 1
  x_mean <- rep(NA, times = 1+ncol(X_train))
  x_sd <- rep(NA, times = 1+ncol(X_train))
    
  x_mean[1] <- 0
  x_sd[1] <- 1
  for(j in 1:ncol(X_train)){
    x_mean[j+1] <- mean(X_train[,j])
    x_sd[j+1] <- stats::sd(X_train[,j])
    std_X_train[,j+1] <- (X_train[,j] - x_mean[j+1])/x_sd[j+1]
  }
  
  if(length(X_test) > 1){
    # There is a valid X_test
    if(ncol(X_test) != ncol(X_train)){
      message(paste("X_train has", ncol(X_train), "columns but X_test has", ncol(X_test), "columns"))
      stop("X_train and X_test must have the same number of columns")
    } else{
      # standardize X_test using the column means and sd's from the training data
      std_X_test <- matrix(NA, nrow = nrow(X_test), ncol = 1 + ncol(X_test))
      std_X_test[,1] <- 1
      for(j in 1:ncol(X_test)) std_X_test[,j+1] <- (X_test[,j] - x_mean[j+1])/x_sd[j+1]
    }
  } else{
    # No X_test provided
    std_X_test <- matrix(0, nrow = 1, ncol = 1)
  }
  
  # Set some hyperparameters
  
  if(is.null(mu0)) mu0 <- rep(0, times = ncol(std_X_train))
  else if(length(mu0) != ncol(std_X_train)) stop("mu0 needs to have length 1 + ncol(X_train)")
  
  if(is.null(tau)) tau <- rep(0.5/sqrt(M), times = ncol(std_X_train))
  else if(length(tau) != ncol(std_X_train)) stop("tau needs to have length 1 + ncol(X_train)")
  
  if(is.null(nu)) nu <- 3
  if(is.null(lambda)) lambda <- stats::qchisq(0.1, df = nu)/nu
  
  # hyperparameters for the Dirichlet prior on splitting probs
  a_u <- 0.5
  b_u <- 1
  
 
  fit <- .vcbart_ind_fit(Y_train = std_Y_train,
                         subj_id_train = subj_id_train-1, # remember C++ is 0-indexed
                         ni_train = ni_train,
                         tX_train = t(std_X_train),
                         tZ_cont_train = t(Z_cont_train),
                         tZ_cat_train = t(Z_cat_train),
                         tX_test = t(std_X_test),
                         tZ_cont_test = t(Z_cont_test),
                         tZ_cat_test = t(Z_cat_test),
                         unif_cuts = unif_cuts,
                         cutpoints_list = cutpoints_list,
                         cat_levels_list = cat_levels_list,
                         edge_mat_list = edge_mat_list,
                         graph_split = graph_split,
                         graph_cut_type = 0, # hardcoded!
                         rc_split = FALSE, prob_rc = 0, a_rc = 1, b_rc = 1,
                         sparse = sparse, a_u = a_u, b_u = b_u,
                         mu0 = mu0, tau = tau,
                         lambda = lambda, nu = nu,
                         M = M, 
                         nd = nd, burn = burn, thin = thin,
                         save_samples = save_samples, save_trees = save_trees,
                         verbose = verbose, print_every = print_every)
  
  sigma_samples <- y_sd * fit$sigma
  
  yhat_train_mean <- y_mean + y_sd * fit$fit_train_mean
  beta_train_mean <- rescale_beta_mean(fit$beta_train_mean, y_mean, y_sd, x_mean, x_sd)
  if(save_samples){
    yhat_train <- y_mean + y_sd * fit$fit_train
    beta_train <- rescale_beta(fit$beta_train, y_mean, y_sd, x_mean, x_sd)
  }
  
  if(!is.null(fit$fit_test_mean)){
    yhat_test_mean <- y_mean + y_sd * fit$fit_test_mean
    beta_test_mean <- rescale_beta_mean(fit$beta_test_mean, y_mean, y_sd, x_mean, x_sd)
    if(save_samples){
      yhat_test <- y_mean + y_sd * fit$fit_test
      beta_test <- rescale_beta(fit$beta_test, y_mean, y_sd, x_mean, x_sd)
    }
  }
  
  results <- list()
  results[["y_mean"]] <- y_mean
  results[["y_sd"]] <- y_sd
  results[["x_mean"]] <- x_mean
  results[["x_sd"]] <- x_sd
  results[["yhat.train.mean"]] <- yhat_train_mean
  results[["betahat.train.mean"]] <- beta_train_mean
  if(save_samples){
    results[["yhat.train"]] <- yhat_train
    results[["betahat.train"]] <- beta_train
  }
  if(!is.null(fit$fit_test_mean)){
    results[["yhat.test.mean"]] <- yhat_test_mean
    results[["betahat.test.mean"]] <- beta_test_mean
    if(save_samples){
      results[["yhat.test"]] <- yhat_test
      results[["betahat.test"]] <- beta_test
    }
  }
  results[["sigma"]] <- y_sd * fit$sigma
  results[["varcounts"]] <- fit$var_count
  if(sparse) results[["theta"]] <- fit$theta
  if(save_trees) results[["trees"]] <- fit$trees
  return(results)
}