diff --git a/.gitignore b/.gitignore index 32d2ae82..d85ac4a2 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,6 @@ ## System and data files *.pdf *.csv -*.txt *.DS_Store lib/ build/ @@ -9,6 +8,9 @@ build/ xcode/ *.json .vs/ +cpp_docs/doxyoutput/html +cpp_docs/doxyoutput/xml +cpp_docs/doxyoutput/latex ## R gitignore diff --git a/R/bart.R b/R/bart.R index 1b498115..e501f11e 100644 --- a/R/bart.R +++ b/R/bart.R @@ -25,26 +25,37 @@ #' that were not in the training set. #' @param rfx_basis_test (Optional) Test set basis for "random-slope" regression in additive random effects model. #' @param cutpoint_grid_size Maximum size of the "grid" of potential cutpoints to consider. Default: 100. -#' @param tau_init Starting value of leaf node scale parameter. Calibrated internally as `1/num_trees` if not set here. -#' @param alpha Prior probability of splitting for a tree of depth 0. Tree split prior combines `alpha` and `beta` via `alpha*(1+node_depth)^-beta`. -#' @param beta Exponent that decreases split probabilities for nodes of depth > 0. Tree split prior combines `alpha` and `beta` via `alpha*(1+node_depth)^-beta`. +#' @param tau_init Starting value of leaf node scale parameter. Calibrated internally as `1/num_trees_mean` if not set here. #' @param leaf_model Model to use in the leaves, coded as integer with (0 = constant leaf, 1 = univariate leaf regression, 2 = multivariate leaf regression). Default: 0. -#' @param min_samples_leaf Minimum allowable size of a leaf, in terms of training samples. Default: 5. -#' @param max_depth Maximum depth of any tree in the ensemble. Default: 10. Can be overriden with ``-1`` which does not enforce any depth limits on trees. +#' @param alpha_mean Prior probability of splitting for a tree of depth 0 in the mean model. Tree split prior combines `alpha_mean` and `beta_mean` via `alpha_mean*(1+node_depth)^-beta_mean`. Default: 0.95. +#' @param beta_mean Exponent that decreases split probabilities for nodes of depth > 0 in the mean model. Tree split prior combines `alpha_mean` and `beta_mean` via `alpha_mean*(1+node_depth)^-beta_mean`. Default: 2. +#' @param min_samples_leaf_mean Minimum allowable size of a leaf, in terms of training samples, in the mean model. Default: 5. +#' @param max_depth_mean Maximum depth of any tree in the ensemble in the mean model. Default: 10. Can be overriden with ``-1`` which does not enforce any depth limits on trees. +#' @param alpha_variance Prior probability of splitting for a tree of depth 0 in the variance model. Tree split prior combines `alpha_variance` and `beta_variance` via `alpha_variance*(1+node_depth)^-beta_variance`. Default: 0.95. +#' @param beta_variance Exponent that decreases split probabilities for nodes of depth > 0 in the variance model. Tree split prior combines `alpha_variance` and `beta_variance` via `alpha_variance*(1+node_depth)^-beta_variance` .Default: 2. +#' @param min_samples_leaf_variance Minimum allowable size of a leaf, in terms of training samples, in the variance model. Default: 5. +#' @param max_depth_variance Maximum depth of any tree in the ensemble in the variance model. Default: 10. Can be overriden with ``-1`` which does not enforce any depth limits on trees. #' @param a_global Shape parameter in the `IG(a_global, b_global)` global error variance model. Default: 0. #' @param b_global Scale parameter in the `IG(a_global, b_global)` global error variance model. Default: 0. #' @param a_leaf Shape parameter in the `IG(a_leaf, b_leaf)` leaf node parameter variance model. Default: 3. -#' @param b_leaf Scale parameter in the `IG(a_leaf, b_leaf)` leaf node parameter variance model. Calibrated internally as `0.5/num_trees` if not set here. +#' @param b_leaf Scale parameter in the `IG(a_leaf, b_leaf)` leaf node parameter variance model. Calibrated internally as `0.5/num_trees_mean` if not set here. +#' @param a_forest Shape parameter in the `IG(a_forest, b_forest)` conditional error variance model (which is only sampled if `num_trees_variance > 0`). Calibrated internally as `num_trees_variance / 1.5^2 + 0.5` if not set. +#' @param b_forest Scale parameter in the `IG(a_forest, b_forest)` conditional error variance model (which is only sampled if `num_trees_variance > 0`). Calibrated internally as `num_trees_variance / 1.5^2` if not set. #' @param q Quantile used to calibrated `lambda` as in Sparapani et al (2021). Default: 0.9. #' @param sigma2_init Starting value of global error variance parameter. Calibrated internally as `pct_var_sigma2_init*var((y-mean(y))/sd(y))` if not set. -#' @param pct_var_sigma2_init Percentage of standardized outcome variance used to initialize global error variance parameter. Default: 0.25. Superseded by `sigma2_init`. -#' @param variable_weights Numeric weights reflecting the relative probability of splitting on each variable. Does not need to sum to 1 but cannot be negative. Defaults to `rep(1/ncol(X_train), ncol(X_train))` if not set here. -#' @param num_trees Number of trees in the ensemble. Default: 200. +#' @param variance_forest_init Starting value of root forest prediction in conditional (heteroskedastic) error variance model. Calibrated internally as `log(pct_var_variance_forest_init*var((y-mean(y))/sd(y)))/num_trees_variance` if not set. +#' @param pct_var_sigma2_init Percentage of standardized outcome variance used to initialize global error variance parameter. Default: 1. Superseded by `sigma2_init`. +#' @param pct_var_variance_forest_init Percentage of standardized outcome variance used to initialize global error variance parameter. Default: 1. Superseded by `variance_forest_init`. +#' @param variance_scale Variance after the data have been scaled. Default: 1. +#' @param variable_weights_mean Numeric weights reflecting the relative probability of splitting on each variable in the mean forest. Does not need to sum to 1 but cannot be negative. Defaults to `rep(1/ncol(X_train), ncol(X_train))` if not set here. +#' @param variable_weights_variance Numeric weights reflecting the relative probability of splitting on each variable in the variance forest. Does not need to sum to 1 but cannot be negative. Defaults to `rep(1/ncol(X_train), ncol(X_train))` if not set here. +#' @param num_trees_mean Number of trees in the ensemble for the conditional mean model. Default: 200. If `num_trees_mean = 0`, the conditional mean will not be modeled using a forest and the function will only proceed if `num_trees_variance > 0`. +#' @param num_trees_variance Number of trees in the ensemble for the conditional variance model. Default: 0. Variance is only modeled using a tree / forest if `num_trees_variance > 0`. #' @param num_gfr Number of "warm-start" iterations run using the grow-from-root algorithm (He and Hahn, 2021). Default: 5. #' @param num_burnin Number of "burn-in" iterations of the MCMC sampler. Default: 0. #' @param num_mcmc Number of "retained" iterations of the MCMC sampler. Default: 100. -#' @param sample_sigma Whether or not to update the `sigma^2` global error variance parameter based on `IG(a_globa, b_global)`. Default: T. -#' @param sample_tau Whether or not to update the `tau` leaf scale variance parameter based on `IG(a_leaf, b_leaf)`. Cannot (currently) be set to true if `ncol(W_train)>1`. Default: T. +#' @param sample_sigma_global Whether or not to update the `sigma^2` global error variance parameter based on `IG(a_global, b_global)`. Default: T. +#' @param sample_sigma_leaf Whether or not to update the `tau` leaf scale variance parameter based on `IG(a_leaf, b_leaf)`. Cannot (currently) be set to true if `ncol(W_train)>1`. Default: F. #' @param random_seed Integer parameterizing the C++ random number generator. If not specified, the C++ random number generator is seeded according to `std::random_device`. #' @param keep_burnin Whether or not "burnin" samples should be included in cached predictions. Default FALSE. Ignored if num_mcmc = 0. #' @param keep_gfr Whether or not "grow-from-root" samples should be included in cached predictions. Default TRUE. Ignored if num_mcmc = 0. @@ -80,20 +91,51 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, rfx_basis_train = NULL, X_test = NULL, W_test = NULL, group_ids_test = NULL, rfx_basis_test = NULL, - cutpoint_grid_size = 100, tau_init = NULL, alpha = 0.95, - beta = 2.0, min_samples_leaf = 5, max_depth = 10, leaf_model = 0, + cutpoint_grid_size = 100, tau_init = NULL, + alpha_mean = 0.95, beta_mean = 2.0, min_samples_leaf_mean = 5, + max_depth_mean = 10, alpha_variance = 0.95, beta_variance = 2.0, + min_samples_leaf_variance = 5, max_depth_variance = 10, a_global = 0, b_global = 0, a_leaf = 3, b_leaf = NULL, - q = 0.9, sigma2_init = NULL, pct_var_sigma2_init = 0.25, - variable_weights = NULL, num_trees = 200, num_gfr = 5, - num_burnin = 0, num_mcmc = 100, sample_sigma = T, - sample_tau = T, random_seed = -1, keep_burnin = F, - keep_gfr = F, verbose = F) { + a_forest = NULL, b_forest = NULL, q = 0.9, sigma2_init = NULL, + variance_forest_init = NULL, pct_var_sigma2_init = 1, + pct_var_variance_forest_init = 1, variance_scale = 1, + variable_weights_mean = NULL, variable_weights_variance = NULL, + num_trees_mean = 200, num_trees_variance = 20, + num_gfr = 5, num_burnin = 0, num_mcmc = 100, + sample_sigma_global = T, sample_sigma_leaf = F, random_seed = -1, + keep_burnin = F, keep_gfr = F, verbose = F) { + # Determine whether conditional mean, variance, or both will be modeled + if (num_trees_variance > 0) include_variance_forest = T + else include_variance_forest = F + if (num_trees_mean > 0) include_mean_forest = T + else include_mean_forest = F + + # Set the variance forest priors if not set + if (include_variance_forest) { + a_0 <- 1.5 + if (is.null(a_forest)) a_forest <- num_trees_variance / (a_0^2) + 0.5 + if (is.null(b_forest)) b_forest <- num_trees_variance / (a_0^2) + } + + # Override tau sampling if there is no mean forest + if (!include_mean_forest) sample_tau <- F + # Variable weight preprocessing (and initialization if necessary) - if (is.null(variable_weights)) { - variable_weights = rep(1/ncol(X_train), ncol(X_train)) + if (include_mean_forest) { + if (is.null(variable_weights_mean)) { + variable_weights_mean = rep(1/ncol(X_train), ncol(X_train)) + } + if (any(variable_weights_mean < 0)) { + stop("variable_weights_mean cannot have any negative weights") + } } - if (any(variable_weights < 0)) { - stop("variable_weights cannot have any negative weights") + if (include_variance_forest) { + if (is.null(variable_weights_variance)) { + variable_weights_variance = rep(1/ncol(X_train), ncol(X_train)) + } + if (any(variable_weights_variance < 0)) { + stop("variable_weights_variance cannot have any negative weights") + } } # Preprocess covariates @@ -105,8 +147,11 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, stop("X_test must be a matrix or dataframe") } } - if (ncol(X_train) != length(variable_weights)) { - stop("length(variable_weights) must equal ncol(X_train)") + if ((ncol(X_train) != length(variable_weights_mean)) && (include_mean_forest)) { + stop("length(variable_weights_mean) must equal ncol(X_train)") + } + if ((ncol(X_train) != length(variable_weights_variance)) && (include_variance_forest)) { + stop("length(variable_weights_variance) must equal ncol(X_train)") } train_cov_preprocess_list <- preprocessTrainData(X_train) X_train_metadata <- train_cov_preprocess_list$metadata @@ -117,7 +162,12 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, # Update variable weights variable_weights_adj <- 1/sapply(original_var_indices, function(x) sum(original_var_indices == x)) - variable_weights <- variable_weights[original_var_indices]*variable_weights_adj + if (include_mean_forest) { + variable_weights_mean <- variable_weights_mean[original_var_indices]*variable_weights_adj + } + if (include_variance_forest) { + variable_weights_variance <- variable_weights_variance[original_var_indices]*variable_weights_adj + } # Convert all input data to matrices if not already converted if ((is.null(dim(W_train))) && (!is.null(W_train))) { @@ -215,32 +265,40 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, y_bar_train <- mean(y_train) y_std_train <- sd(y_train) resid_train <- (y_train-y_bar_train)/y_std_train + resid_train <- resid_train*sqrt(variance_scale) + + # Compute initial value of root nodes in mean forest + init_val_mean <- mean(resid_train) # Calibrate priors for sigma^2 and tau if (is.null(sigma2_init)) sigma2_init <- pct_var_sigma2_init*var(resid_train) - if (is.null(b_leaf)) b_leaf <- var(resid_train)/(2*num_trees) - if (is.null(tau_init)) tau_init <- var(resid_train)/(num_trees) + if (is.null(variance_forest_init)) variance_forest_init <- pct_var_variance_forest_init*var(resid_train) + if (is.null(b_leaf)) b_leaf <- var(resid_train)/(2*num_trees_mean) + if (is.null(tau_init)) tau_init <- var(resid_train)/(num_trees_mean) current_leaf_scale <- as.matrix(tau_init) current_sigma2 <- sigma2_init - + # Determine leaf model type - if (!has_basis) leaf_model <- 0 - else if (ncol(W_train) == 1) leaf_model <- 1 - else if (ncol(W_train) > 1) leaf_model <- 2 + if (!has_basis) leaf_model_mean_forest <- 0 + else if (ncol(W_train) == 1) leaf_model_mean_forest <- 1 + else if (ncol(W_train) > 1) leaf_model_mean_forest <- 2 else stop("W_train passed must be a matrix with at least 1 column") + + # Set variance leaf model type (currently only one option) + leaf_model_variance_forest <- 3 # Unpack model type info - if (leaf_model == 0) { + if (leaf_model_mean_forest == 0) { output_dimension = 1 is_leaf_constant = T leaf_regression = F - } else if (leaf_model == 1) { + } else if (leaf_model_mean_forest == 1) { stopifnot(has_basis) stopifnot(ncol(W_train) == 1) output_dimension = 1 is_leaf_constant = F leaf_regression = T - } else if (leaf_model == 2) { + } else if (leaf_model_mean_forest == 2) { stopifnot(has_basis) stopifnot(ncol(W_train) > 1) output_dimension = ncol(W_train) @@ -269,10 +327,20 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, # Sampling data structures feature_types <- as.integer(feature_types) - forest_model <- createForestModel(forest_dataset_train, feature_types, num_trees, nrow(X_train), alpha, beta, min_samples_leaf, max_depth) + if (include_mean_forest) { + forest_model_mean <- createForestModel(forest_dataset_train, feature_types, num_trees_mean, nrow(X_train), alpha_mean, beta_mean, min_samples_leaf_mean, max_depth_mean) + } + if (include_variance_forest) { + forest_model_variance <- createForestModel(forest_dataset_train, feature_types, num_trees_variance, nrow(X_train), alpha_variance, beta_variance, min_samples_leaf_variance, max_depth_variance) + } # Container of forest samples - forest_samples <- createForestContainer(num_trees, output_dimension, is_leaf_constant) + if (include_mean_forest) { + forest_samples_mean <- createForestContainer(num_trees_mean, output_dimension, is_leaf_constant, FALSE) + } + if (include_variance_forest) { + forest_samples_variance <- createForestContainer(num_trees_variance, 1, TRUE, TRUE) + } # Random effects prior parameters if (has_rfx) { @@ -306,8 +374,20 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, # Container of variance parameter samples num_samples <- num_gfr + num_burnin + num_mcmc - if (sample_sigma) global_var_samples <- rep(0, num_samples) - if (sample_tau) leaf_scale_samples <- rep(0, num_samples) + if (sample_sigma_global) global_var_samples <- rep(0, num_samples) + if (sample_sigma_leaf) leaf_scale_samples <- rep(0, num_samples) + + # Initialize the leaves of each tree in the mean forest + if (include_mean_forest) { + if (requires_basis) init_values_mean_forest <- rep(0., ncol(W_train)) + else init_values_mean_forest <- 0. + forest_samples_mean$prepare_for_sampler(forest_dataset_train, outcome_train, forest_model_mean, leaf_model_mean_forest, init_values_mean_forest) + } + + # Initialize the leaves of each tree in the variance forest + if (include_variance_forest) { + forest_samples_variance$prepare_for_sampler(forest_dataset_train, outcome_train, forest_model_variance, leaf_model_variance_forest, variance_forest_init) + } # Run GFR (warm start) if specified if (num_gfr > 0){ @@ -320,17 +400,26 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, } } - forest_model$sample_one_iteration( - forest_dataset_train, outcome_train, forest_samples, rng, feature_types, - leaf_model, current_leaf_scale, variable_weights, - current_sigma2, cutpoint_grid_size, gfr = T, pre_initialized = F - ) - if (sample_sigma) { - global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, rng, a_global, b_global) + if (include_mean_forest) { + forest_model_mean$sample_one_iteration( + forest_dataset_train, outcome_train, forest_samples_mean, rng, feature_types, + leaf_model_mean_forest, current_leaf_scale, variable_weights_mean, + a_forest, b_forest, current_sigma2, cutpoint_grid_size, gfr = T, pre_initialized = T + ) + } + if (include_variance_forest) { + forest_model_variance$sample_one_iteration( + forest_dataset_train, outcome_train, forest_samples_variance, rng, feature_types, + leaf_model_variance_forest, current_leaf_scale, variable_weights_variance, + a_forest, b_forest, current_sigma2, cutpoint_grid_size, gfr = T, pre_initialized = T + ) + } + if (sample_sigma_global) { + global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, forest_dataset_train, rng, a_global, b_global) current_sigma2 <- global_var_samples[i] } - if (sample_tau) { - leaf_scale_samples[i] <- sample_tau_one_iteration(forest_samples, rng, a_leaf, b_leaf, i-1) + if (sample_sigma_leaf) { + leaf_scale_samples[i] <- sample_tau_one_iteration(forest_samples_mean, rng, a_leaf, b_leaf, i-1) current_leaf_scale <- as.matrix(leaf_scale_samples[i]) } if (has_rfx) { @@ -362,17 +451,26 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, } } - forest_model$sample_one_iteration( - forest_dataset_train, outcome_train, forest_samples, rng, feature_types, - leaf_model, current_leaf_scale, variable_weights, - current_sigma2, cutpoint_grid_size, gfr = F, pre_initialized = F - ) - if (sample_sigma) { - global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, rng, a_global, b_global) + if (include_mean_forest) { + forest_model_mean$sample_one_iteration( + forest_dataset_train, outcome_train, forest_samples_mean, rng, feature_types, + leaf_model_mean_forest, current_leaf_scale, variable_weights_mean, + a_forest, b_forest, current_sigma2, cutpoint_grid_size, gfr = F, pre_initialized = T + ) + } + if (include_variance_forest) { + forest_model_variance$sample_one_iteration( + forest_dataset_train, outcome_train, forest_samples_variance, rng, feature_types, + leaf_model_variance_forest, current_leaf_scale, variable_weights_variance, + a_forest, b_forest, current_sigma2, cutpoint_grid_size, gfr = F, pre_initialized = T + ) + } + if (sample_sigma_global) { + global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, forest_dataset_train, rng, a_global, b_global) current_sigma2 <- global_var_samples[i] } - if (sample_tau) { - leaf_scale_samples[i] <- sample_tau_one_iteration(forest_samples, rng, a_leaf, b_leaf, i-1) + if (sample_sigma_leaf) { + leaf_scale_samples[i] <- sample_tau_one_iteration(forest_samples_mean, rng, a_leaf, b_leaf, i-1) current_leaf_scale <- as.matrix(leaf_scale_samples[i]) } if (has_rfx) { @@ -381,17 +479,25 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, } } - # Forest predictions - y_hat_train <- forest_samples$predict(forest_dataset_train)*y_std_train + y_bar_train - if (has_test) y_hat_test <- forest_samples$predict(forest_dataset_test)*y_std_train + y_bar_train + # Mean forest predictions + if (include_mean_forest) { + y_hat_train <- forest_samples_mean$predict(forest_dataset_train)*y_std_train/sqrt(variance_scale) + y_bar_train + if (has_test) y_hat_test <- forest_samples_mean$predict(forest_dataset_test)*y_std_train/sqrt(variance_scale) + y_bar_train + } + + # Variance forest predictions + if (include_variance_forest) { + sigma_x_hat_train <- forest_samples_variance$predict(forest_dataset_train) + if (has_test) sigma_x_hat_test <- forest_samples_variance$predict(forest_dataset_test) + } # Random effects predictions if (has_rfx) { - rfx_preds_train <- rfx_samples$predict(group_ids_train, rfx_basis_train)*y_std_train + rfx_preds_train <- rfx_samples$predict(group_ids_train, rfx_basis_train)*y_std_train/sqrt(variance_scale) y_hat_train <- y_hat_train + rfx_preds_train } if ((has_rfx_test) && (has_test)) { - rfx_preds_test <- rfx_samples$predict(group_ids_test, rfx_basis_test)*y_std_train + rfx_preds_test <- rfx_samples$predict(group_ids_test, rfx_basis_test)*y_std_train/sqrt(variance_scale) y_hat_test <- y_hat_test + rfx_preds_test } @@ -417,24 +523,38 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, } # Subset forest and RFX predictions - y_hat_train <- y_hat_train[,keep_indices] + if (include_mean_forest) { + y_hat_train <- y_hat_train[,keep_indices] + if (has_test) y_hat_test <- y_hat_test[,keep_indices] + } + if (include_variance_forest) { + sigma_x_hat_train <- sigma_x_hat_train[,keep_indices] + if (has_test) sigma_x_hat_test <- sigma_x_hat_test[,keep_indices] + } if (has_rfx) { rfx_preds_train <- rfx_preds_train[,keep_indices] + if (has_test) rfx_preds_test <- rfx_preds_test[,keep_indices] } - if (has_test) { - y_hat_test <- y_hat_test[,keep_indices] - if (has_rfx_test) { - rfx_preds_test <- rfx_preds_test[,keep_indices] - } - } - + # Global error variance - if (sample_sigma) sigma2_samples <- global_var_samples[keep_indices]*(y_std_train^2) + if (sample_sigma_global) sigma2_samples <- global_var_samples[keep_indices]*(y_std_train^2)/variance_scale # Leaf parameter variance - if (sample_tau) tau_samples <- leaf_scale_samples[keep_indices] + if (sample_sigma_leaf) tau_samples <- leaf_scale_samples[keep_indices] + + # Rescale variance forest prediction by sigma2_samples + if (include_variance_forest) { + if (sample_sigma) { + sigma_x_hat_train <- sapply(1:length(keep_indices), function(i) sqrt(sigma_x_hat_train[,i]*sigma2_samples[i])) + if (has_test) sigma_x_hat_test <- sapply(1:length(keep_indices), function(i) sqrt(sigma_x_hat_test[,i]*sigma2_samples[i])) + } else { + sigma_x_hat_train <- sqrt(sigma_x_hat_train*sigma2_init)*y_std_train/sqrt(variance_scale) + if (has_test) sigma_x_hat_test <- sqrt(sigma_x_hat_test*sigma2_init)*y_std_train/sqrt(variance_scale) + } + } # Return results as a list + # TODO: store variance_scale and propagate through predict function model_params <- list( "sigma2_init" = sigma2_init, "a_global" = a_global, @@ -442,6 +562,8 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, "tau_init" = tau_init, "a_leaf" = a_leaf, "b_leaf" = b_leaf, + "a_forest" = a_forest, + "b_forest" = b_forest, "outcome_mean" = y_bar_train, "outcome_scale" = y_std_train, "output_dimension" = output_dimension, @@ -458,19 +580,29 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, "has_rfx" = has_rfx, "has_rfx_basis" = has_basis_rfx, "num_rfx_basis" = num_basis_rfx, - "sample_sigma" = sample_sigma, - "sample_tau" = sample_tau + "sample_sigma_global" = sample_sigma_global, + "sample_sigma_leaf" = sample_sigma_leaf, + "include_mean_forest" = include_mean_forest, + "include_variance_forest" = include_variance_forest, + "variance_scale" = variance_scale ) result <- list( - "forests" = forest_samples, "model_params" = model_params, - "y_hat_train" = y_hat_train, "train_set_metadata" = X_train_metadata, "keep_indices" = keep_indices ) - if (has_test) result[["y_hat_test"]] = y_hat_test - if (sample_sigma) result[["sigma2_samples"]] = sigma2_samples - if (sample_tau) result[["tau_samples"]] = tau_samples + if (include_mean_forest) { + result[["mean_forests"]] = forest_samples_mean + result[["y_hat_train"]] = y_hat_train + if (has_test) result[["y_hat_test"]] = y_hat_test + } + if (include_variance_forest) { + result[["var_forests"]] = forest_samples_variance + result[["sigma_x_hat_train"]] = sigma_x_hat_train + if (has_test) result[["sigma_x_hat_test"]] = sigma_x_hat_test + } + if (sample_sigma_global) result[["sigma2_global_samples"]] = sigma2_samples + if (sample_sigma_leaf) result[["sigma2_leaf_samples"]] = tau_samples if (has_rfx) { result[["rfx_samples"]] = rfx_samples result[["rfx_preds_train"]] = rfx_preds_train @@ -480,7 +612,8 @@ bart <- function(X_train, y_train, W_train = NULL, group_ids_train = NULL, class(result) <- "bartmodel" # Clean up classes with external pointers to C++ data structures - rm(forest_model) + if (include_mean_forest) rm(forest_model_mean) + if (include_variance_forest) rm(forest_model_variance) rm(forest_dataset_train) if (has_test) rm(forest_dataset_test) if (has_rfx) rm(rfx_dataset_train, rfx_tracker_train, rfx_model) @@ -588,34 +721,51 @@ predict.bartmodel <- function(bart, X_test, W_test = NULL, group_ids_test = NULL if (!is.null(W_test)) prediction_dataset <- createForestDataset(X_test, W_test) else prediction_dataset <- createForestDataset(X_test) - # Compute forest predictions + # Compute mean forest predictions + variance_scale <- bart$model_params$variance_scale y_std <- bart$model_params$outcome_scale y_bar <- bart$model_params$outcome_mean - forest_predictions <- bart$forests$predict(prediction_dataset)*y_std + y_bar + mean_forest_predictions <- bart$mean_forests$predict(prediction_dataset)*y_std/sqrt(variance_scale) + y_bar + + # Compute variance forest predictions + if (bart$model_params$include_variance_forest) { + var_forest_predictions <- bart$variance_forests$predict(prediction_dataset)*(y_std^2)/variance_scale + } # Compute rfx predictions (if needed) if (bart$model_params$has_rfx) { - rfx_predictions <- bart$rfx_samples$predict(group_ids_test, rfx_basis_test)*y_std + rfx_predictions <- bart$rfx_samples$predict(group_ids_test, rfx_basis_test)*y_std/sqrt(variance_scale) } # Restrict predictions to the "retained" samples (if applicable) if (!predict_all) { keep_indices = bart$keep_indices - forest_predictions <- forest_predictions[,keep_indices] + mean_forest_predictions <- mean_forest_predictions[,keep_indices] + if (bart$model_params$include_variance_forest) { + variance_forest_predictions <- variance_forest_predictions[,keep_indices] + } if (bart$model_params$has_rfx) rfx_predictions <- rfx_predictions[,keep_indices] } if (bart$model_params$has_rfx) { - y_hat <- forest_predictions + rfx_predictions - result <- list( - "forest_predictions" = forest_predictions, - "rfx_predictions" = rfx_predictions, - "y_hat" = y_hat - ) - return(result) + y_hat <- mean_forest_predictions + rfx_predictions } else { - return(list("y_hat" = forest_predictions)) + y_hat <- mean_forest_predictions + } + + result <- list( + "y_hat" = y_hat, + "mean_forest_predictions" = mean_forest_predictions + ) + + if (bart$model_params$has_rfx) { + result[["rfx_predictions"]] = rfx_predictions } + + if (bart$model_params$include_variance_forest) { + result[["variance_forest_predictions"]] = variance_forest_predictions + } + return(result) } #' Extract raw sample values for each of the random effect parameter terms. diff --git a/R/bcf.R b/R/bcf.R index f99c3df2..d0c2de4d 100644 --- a/R/bcf.R +++ b/R/bcf.R @@ -526,7 +526,7 @@ bcf <- function(X_train, Z_train, y_train, pi_train = NULL, group_ids_train = NU # Sample variance parameters (if requested) if (sample_sigma_global) { - global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, rng, a_global, b_global) + global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, forest_dataset_train, rng, a_global, b_global) current_sigma2 <- global_var_samples[i] } if (sample_sigma_leaf_mu) { @@ -578,7 +578,7 @@ bcf <- function(X_train, Z_train, y_train, pi_train = NULL, group_ids_train = NU # Sample variance parameters (if requested) if (sample_sigma_global) { - global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, rng, a_global, b_global) + global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, forest_dataset_train, rng, a_global, b_global) current_sigma2 <- global_var_samples[i] } if (sample_sigma_leaf_tau) { @@ -625,7 +625,7 @@ bcf <- function(X_train, Z_train, y_train, pi_train = NULL, group_ids_train = NU # Sample variance parameters (if requested) if (sample_sigma_global) { - global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, rng, a_global, b_global) + global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, forest_dataset_train, rng, a_global, b_global) current_sigma2 <- global_var_samples[i] } if (sample_sigma_leaf_mu) { @@ -677,7 +677,7 @@ bcf <- function(X_train, Z_train, y_train, pi_train = NULL, group_ids_train = NU # Sample variance parameters (if requested) if (sample_sigma_global) { - global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, rng, a_global, b_global) + global_var_samples[i] <- sample_sigma2_one_iteration(outcome_train, forest_dataset_train, rng, a_global, b_global) current_sigma2 <- global_var_samples[i] } if (sample_sigma_leaf_tau) { diff --git a/R/cpp11.R b/R/cpp11.R index dd0b5986..cde1286f 100644 --- a/R/cpp11.R +++ b/R/cpp11.R @@ -188,8 +188,8 @@ rfx_label_mapper_to_list_cpp <- function(label_mapper_ptr) { .Call(`_stochtree_rfx_label_mapper_to_list_cpp`, label_mapper_ptr) } -forest_container_cpp <- function(num_trees, output_dimension, is_leaf_constant) { - .Call(`_stochtree_forest_container_cpp`, num_trees, output_dimension, is_leaf_constant) +forest_container_cpp <- function(num_trees, output_dimension, is_leaf_constant, is_exponentiated) { + .Call(`_stochtree_forest_container_cpp`, num_trees, output_dimension, is_leaf_constant, is_exponentiated) } forest_container_from_json_cpp <- function(json_ptr, forest_label) { @@ -284,6 +284,10 @@ set_leaf_vector_forest_container_cpp <- function(forest_samples, leaf_vector) { invisible(.Call(`_stochtree_set_leaf_vector_forest_container_cpp`, forest_samples, leaf_vector)) } +initialize_forest_model_cpp <- function(data, residual, forest_samples, tracker, init_values, leaf_model_int) { + invisible(.Call(`_stochtree_initialize_forest_model_cpp`, data, residual, forest_samples, tracker, init_values, leaf_model_int)) +} + adjust_residual_forest_container_cpp <- function(data, residual, forest_samples, tracker, requires_basis, forest_num, add) { invisible(.Call(`_stochtree_adjust_residual_forest_container_cpp`, data, residual, forest_samples, tracker, requires_basis, forest_num, add)) } @@ -332,16 +336,16 @@ forest_kernel_compute_kernel_train_test_cpp <- function(forest_kernel, covariate .Call(`_stochtree_forest_kernel_compute_kernel_train_test_cpp`, forest_kernel, covariates_train, covariates_test, forest_container, forest_num) } -sample_gfr_one_iteration_cpp <- function(data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, global_variance, leaf_model_int, pre_initialized) { - invisible(.Call(`_stochtree_sample_gfr_one_iteration_cpp`, data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, global_variance, leaf_model_int, pre_initialized)) +sample_gfr_one_iteration_cpp <- function(data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, a_forest, b_forest, global_variance, leaf_model_int, pre_initialized) { + invisible(.Call(`_stochtree_sample_gfr_one_iteration_cpp`, data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, a_forest, b_forest, global_variance, leaf_model_int, pre_initialized)) } -sample_mcmc_one_iteration_cpp <- function(data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, global_variance, leaf_model_int, pre_initialized) { - invisible(.Call(`_stochtree_sample_mcmc_one_iteration_cpp`, data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, global_variance, leaf_model_int, pre_initialized)) +sample_mcmc_one_iteration_cpp <- function(data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, a_forest, b_forest, global_variance, leaf_model_int, pre_initialized) { + invisible(.Call(`_stochtree_sample_mcmc_one_iteration_cpp`, data, residual, forest_samples, tracker, split_prior, rng, feature_types, cutpoint_grid_size, leaf_model_scale_input, variable_weights, a_forest, b_forest, global_variance, leaf_model_int, pre_initialized)) } -sample_sigma2_one_iteration_cpp <- function(residual, rng, a, b) { - .Call(`_stochtree_sample_sigma2_one_iteration_cpp`, residual, rng, a, b) +sample_sigma2_one_iteration_cpp <- function(residual, dataset, rng, a, b) { + .Call(`_stochtree_sample_sigma2_one_iteration_cpp`, residual, dataset, rng, a, b) } sample_tau_one_iteration_cpp <- function(forest_samples, rng, a, b, sample_num) { diff --git a/R/forest.R b/R/forest.R index 953aa585..8a61cf57 100644 --- a/R/forest.R +++ b/R/forest.R @@ -16,9 +16,10 @@ ForestSamples <- R6::R6Class( #' @param num_trees Number of trees #' @param output_dimension Dimensionality of the outcome model #' @param is_leaf_constant Whether leaf is constant + #' @param is_exponentiated Whether forest predictions should be exponentiated before being returned #' @return A new `ForestContainer` object. - initialize = function(num_trees, output_dimension=1, is_leaf_constant=F) { - self$forest_container_ptr <- forest_container_cpp(num_trees, output_dimension, is_leaf_constant) + initialize = function(num_trees, output_dimension=1, is_leaf_constant=F, is_exponentiated=F) { + self$forest_container_ptr <- forest_container_cpp(num_trees, output_dimension, is_leaf_constant, is_exponentiated) }, #' @description @@ -106,6 +107,26 @@ ForestSamples <- R6::R6Class( } }, + #' @description + #' Set a constant predicted value for every tree in the ensemble. + #' Stops program if any tree is more than a root node. + #' @param dataset `ForestDataset` Dataset class (covariates, basis, etc...) + #' @param outcome `Outcome` Outcome class (residual / partial residual) + #' @param forest_model `ForestModel` object storing tracking structures used in training / sampling + #' @param leaf_model_int Integer value encoding the leaf model type (0 = constant gaussian, 1 = univariate gaussian, 2 = multivariate gaussian, 3 = log linear variance). + #' @param leaf_value Constant leaf value(s) to be fixed for each tree in the ensemble indexed by `forest_num`. Can be either a single number or a vector, depending on the forest's leaf dimension. + prepare_for_sampler = function(dataset, outcome, forest_model, leaf_model_int, leaf_value) { + stopifnot(!is.null(dataset$data_ptr)) + stopifnot(!is.null(outcome$data_ptr)) + stopifnot(!is.null(forest_model$tracker_ptr)) + stopifnot(!is.null(self$forest_container_ptr)) + stopifnot(num_samples_forest_container_cpp(self$forest_container_ptr) == 0) + + # Initialize the model + initialize_forest_model_cpp(dataset$data_ptr, outcome$data_ptr, self$forest_container_ptr, + forest_model$tracker_ptr, leaf_value, leaf_model_int) + }, + #' @description #' Adjusts residual based on the predictions of a forest #' @@ -294,11 +315,12 @@ ForestSamples <- R6::R6Class( #' @param num_trees Number of trees #' @param output_dimension Dimensionality of the outcome model #' @param is_leaf_constant Whether leaf is constant +#' @param is_exponentiated Whether forest predictions should be exponentiated before being returned #' #' @return `ForestSamples` object #' @export -createForestContainer <- function(num_trees, output_dimension=1, is_leaf_constant=F) { +createForestContainer <- function(num_trees, output_dimension=1, is_leaf_constant=F, is_exponentiated=F) { return(invisible(( - ForestSamples$new(num_trees, output_dimension, is_leaf_constant) + ForestSamples$new(num_trees, output_dimension, is_leaf_constant, is_exponentiated) ))) } diff --git a/R/model.R b/R/model.R index 4811ab56..67d61499 100644 --- a/R/model.R +++ b/R/model.R @@ -68,27 +68,29 @@ ForestModel <- R6::R6Class( #' @param leaf_model_int Integer specifying the leaf model type (0 = constant leaf, 1 = univariate leaf regression, 2 = multivariate leaf regression) #' @param leaf_model_scale Scale parameter used in the leaf node model (should be a q x q matrix where q is the dimensionality of the basis and is only >1 when `leaf_model_int = 2`) #' @param variable_weights Vector specifying sampling probability for all p covariates in `forest_dataset` + #' @param a_forest Shape parameter on variance forest model (if applicable) + #' @param b_forest Scale parameter on variance forest model (if applicable) #' @param global_scale Global variance parameter #' @param cutpoint_grid_size (Optional) Number of unique cutpoints to consider (default: 500, currently only used when `GFR = TRUE`) #' @param gfr (Optional) Whether or not the forest should be sampled using the "grow-from-root" (GFR) algorithm #' @param pre_initialized (Optional) Whether or not the leaves are pre-initialized outside of the sampling loop (before any samples are drawn). In multi-forest implementations like BCF, this is true, though in the single-forest supervised learning implementation, we can let C++ do the initialization. Default: F. sample_one_iteration = function(forest_dataset, residual, forest_samples, rng, feature_types, leaf_model_int, leaf_model_scale, variable_weights, - global_scale, cutpoint_grid_size = 500, gfr = T, - pre_initialized = F) { + a_forest, b_forest, global_scale, cutpoint_grid_size = 500, + gfr = T, pre_initialized = F) { if (gfr) { sample_gfr_one_iteration_cpp( forest_dataset$data_ptr, residual$data_ptr, forest_samples$forest_container_ptr, self$tracker_ptr, self$tree_prior_ptr, rng$rng_ptr, feature_types, cutpoint_grid_size, leaf_model_scale, - variable_weights, global_scale, leaf_model_int, pre_initialized + variable_weights, a_forest, b_forest, global_scale, leaf_model_int, pre_initialized ) } else { sample_mcmc_one_iteration_cpp( forest_dataset$data_ptr, residual$data_ptr, forest_samples$forest_container_ptr, self$tracker_ptr, self$tree_prior_ptr, rng$rng_ptr, feature_types, cutpoint_grid_size, leaf_model_scale, - variable_weights, global_scale, leaf_model_int, pre_initialized + variable_weights, a_forest, b_forest, global_scale, leaf_model_int, pre_initialized ) } } diff --git a/R/variance.R b/R/variance.R index c8933b3d..d225226e 100644 --- a/R/variance.R +++ b/R/variance.R @@ -1,13 +1,14 @@ #' Sample one iteration of the (inverse gamma) global variance model #' #' @param residual Outcome class +#' @param dataset ForestDataset class #' @param rng C++ random number generator #' @param a Global variance shape parameter #' @param b Global variance scale parameter #' #' @export -sample_sigma2_one_iteration <- function(residual, rng, a, b) { - return(sample_sigma2_one_iteration_cpp(residual$data_ptr, rng$rng_ptr, a, b)) +sample_sigma2_one_iteration <- function(residual, dataset, rng, a, b) { + return(sample_sigma2_one_iteration_cpp(residual$data_ptr, dataset$data_ptr, rng$rng_ptr, a, b)) } #' Sample one iteration of the leaf parameter variance model (only for univariate basis and constant leaf!) diff --git a/cpp_docs/Doxyfile b/cpp_docs/Doxyfile new file mode 100644 index 00000000..9c0d1708 --- /dev/null +++ b/cpp_docs/Doxyfile @@ -0,0 +1,2865 @@ +# Doxyfile 1.12.0 + +# This file describes the settings to be used by the documentation system +# Doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). +# +# Note: +# +# Use Doxygen to compare the used configuration file with the template +# configuration file: +# doxygen -x [configFile] +# Use Doxygen to compare the used configuration file with the template +# configuration file without replacing the environment variables or CMake type +# replacement variables: +# doxygen -x_noenv [configFile] + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the configuration +# file that follow. 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If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# Doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, Doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, Doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which Doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where Doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, Doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the JAVADOC_BANNER tag is set to YES then Doxygen will interpret a line +# such as +# /*************** +# as being the beginning of a Javadoc-style comment "banner". If set to NO, the +# Javadoc-style will behave just like regular comments and it will not be +# interpreted by Doxygen. +# The default value is: NO. + +JAVADOC_BANNER = NO + +# If the QT_AUTOBRIEF tag is set to YES then Doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# By default Python docstrings are displayed as preformatted text and Doxygen's +# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the +# Doxygen's special commands can be used and the contents of the docstring +# documentation blocks is shown as Doxygen documentation. +# The default value is: YES. + +PYTHON_DOCSTRING = YES + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then Doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:^^" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". Note that you cannot put \n's in the value part of an alias +# to insert newlines (in the resulting output). You can put ^^ in the value part +# of an alias to insert a newline as if a physical newline was in the original +# file. When you need a literal { or } or , in the value part of an alias you +# have to escape them by means of a backslash (\), this can lead to conflicts +# with the commands \{ and \} for these it is advised to use the version @{ and +# @} or use a double escape (\\{ and \\}) + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice +# sources only. Doxygen will then generate output that is more tailored for that +# language. For instance, namespaces will be presented as modules, types will be +# separated into more groups, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_SLICE = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by Doxygen: IDL, Java, JavaScript, +# Csharp (C#), C, C++, Lex, D, PHP, md (Markdown), Objective-C, Python, Slice, +# VHDL, Fortran (fixed format Fortran: FortranFixed, free formatted Fortran: +# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser +# tries to guess whether the code is fixed or free formatted code, this is the +# default for Fortran type files). For instance to make Doxygen treat .inc files +# as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by Doxygen. When specifying no_extension you should add +# * to the FILE_PATTERNS. +# +# Note see also the list of default file extension mappings. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then Doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See https://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by Doxygen, so you can +# mix Doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 6. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 6 + +# The MARKDOWN_ID_STYLE tag can be used to specify the algorithm used to +# generate identifiers for the Markdown headings. Note: Every identifier is +# unique. +# Possible values are: DOXYGEN use a fixed 'autotoc_md' string followed by a +# sequence number starting at 0 and GITHUB use the lower case version of title +# with any whitespace replaced by '-' and punctuation characters removed. +# The default value is: DOXYGEN. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +MARKDOWN_ID_STYLE = DOXYGEN + +# When enabled Doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let Doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also makes the inheritance and +# collaboration diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# https://www.riverbankcomputing.com/software) sources only. Doxygen will parse +# them like normal C++ but will assume all classes use public instead of private +# inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# Doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then Doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, Doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# Doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run Doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +# The NUM_PROC_THREADS specifies the number of threads Doxygen is allowed to use +# during processing. When set to 0 Doxygen will based this on the number of +# cores available in the system. You can set it explicitly to a value larger +# than 0 to get more control over the balance between CPU load and processing +# speed. At this moment only the input processing can be done using multiple +# threads. Since this is still an experimental feature the default is set to 1, +# which effectively disables parallel processing. Please report any issues you +# encounter. Generating dot graphs in parallel is controlled by the +# DOT_NUM_THREADS setting. +# Minimum value: 0, maximum value: 32, default value: 1. + +NUM_PROC_THREADS = 1 + +# If the TIMESTAMP tag is set different from NO then each generated page will +# contain the date or date and time when the page was generated. Setting this to +# NO can help when comparing the output of multiple runs. +# Possible values are: YES, NO, DATETIME and DATE. +# The default value is: NO. + +TIMESTAMP = NO + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, Doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual +# methods of a class will be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIV_VIRTUAL = NO + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If this flag is set to YES, the name of an unnamed parameter in a declaration +# will be determined by the corresponding definition. By default unnamed +# parameters remain unnamed in the output. +# The default value is: YES. + +RESOLVE_UNNAMED_PARAMS = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# will also hide undocumented C++ concepts if enabled. This option has no effect +# if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all friend +# declarations. If set to NO, these declarations will be included in the +# documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# With the correct setting of option CASE_SENSE_NAMES Doxygen will better be +# able to match the capabilities of the underlying filesystem. In case the +# filesystem is case sensitive (i.e. it supports files in the same directory +# whose names only differ in casing), the option must be set to YES to properly +# deal with such files in case they appear in the input. For filesystems that +# are not case sensitive the option should be set to NO to properly deal with +# output files written for symbols that only differ in casing, such as for two +# classes, one named CLASS and the other named Class, and to also support +# references to files without having to specify the exact matching casing. On +# Windows (including Cygwin) and macOS, users should typically set this option +# to NO, whereas on Linux or other Unix flavors it should typically be set to +# YES. +# Possible values are: SYSTEM, NO and YES. +# The default value is: SYSTEM. + +CASE_SENSE_NAMES = SYSTEM + +# If the HIDE_SCOPE_NAMES tag is set to NO then Doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then Doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_HEADERFILE tag is set to YES then the documentation for a class +# will show which file needs to be included to use the class. +# The default value is: YES. + +SHOW_HEADERFILE = YES + +# If the SHOW_INCLUDE_FILES tag is set to YES then Doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then Doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then Doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then Doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then Doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and Doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING Doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# Doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by Doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by Doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents Doxygen's defaults, run Doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. See also section "Changing the +# layout of pages" for information. +# +# Note that if you run Doxygen from a directory containing a file called +# DoxygenLayout.xml, Doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +# The EXTERNAL_TOOL_PATH tag can be used to extend the search path (PATH +# environment variable) so that external tools such as latex and gs can be +# found. +# Note: Directories specified with EXTERNAL_TOOL_PATH are added in front of the +# path already specified by the PATH variable, and are added in the order +# specified. +# Note: This option is particularly useful for macOS version 14 (Sonoma) and +# higher, when running Doxygen from Doxywizard, because in this case any user- +# defined changes to the PATH are ignored. A typical example on macOS is to set +# EXTERNAL_TOOL_PATH = /Library/TeX/texbin /usr/local/bin +# together with the standard path, the full search path used by doxygen when +# launching external tools will then become +# PATH=/Library/TeX/texbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin + +EXTERNAL_TOOL_PATH = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by Doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by Doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then Doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, Doxygen will generate warnings for +# potential errors in the documentation, such as documenting some parameters in +# a documented function twice, or documenting parameters that don't exist or +# using markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# If WARN_IF_INCOMPLETE_DOC is set to YES, Doxygen will warn about incomplete +# function parameter documentation. If set to NO, Doxygen will accept that some +# parameters have no documentation without warning. +# The default value is: YES. + +WARN_IF_INCOMPLETE_DOC = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, Doxygen will only warn about wrong parameter +# documentation, but not about the absence of documentation. If EXTRACT_ALL is +# set to YES then this flag will automatically be disabled. See also +# WARN_IF_INCOMPLETE_DOC +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If WARN_IF_UNDOC_ENUM_VAL option is set to YES, Doxygen will warn about +# undocumented enumeration values. If set to NO, Doxygen will accept +# undocumented enumeration values. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: NO. + +WARN_IF_UNDOC_ENUM_VAL = NO + +# If the WARN_AS_ERROR tag is set to YES then Doxygen will immediately stop when +# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS +# then Doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but +# at the end of the Doxygen process Doxygen will return with a non-zero status. +# If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS_PRINT then Doxygen behaves +# like FAIL_ON_WARNINGS but in case no WARN_LOGFILE is defined Doxygen will not +# write the warning messages in between other messages but write them at the end +# of a run, in case a WARN_LOGFILE is defined the warning messages will be +# besides being in the defined file also be shown at the end of a run, unless +# the WARN_LOGFILE is defined as - i.e. standard output (stdout) in that case +# the behavior will remain as with the setting FAIL_ON_WARNINGS. +# Possible values are: NO, YES, FAIL_ON_WARNINGS and FAIL_ON_WARNINGS_PRINT. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that Doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# See also: WARN_LINE_FORMAT +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# In the $text part of the WARN_FORMAT command it is possible that a reference +# to a more specific place is given. To make it easier to jump to this place +# (outside of Doxygen) the user can define a custom "cut" / "paste" string. +# Example: +# WARN_LINE_FORMAT = "'vi $file +$line'" +# See also: WARN_FORMAT +# The default value is: at line $line of file $file. + +WARN_LINE_FORMAT = "at line $line of file $file" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). In case the file specified cannot be opened for writing the +# warning and error messages are written to standard error. When as file - is +# specified the warning and error messages are written to standard output +# (stdout). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = + +# This tag can be used to specify the character encoding of the source files +# that Doxygen parses. Internally Doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: +# https://www.gnu.org/software/libiconv/) for the list of possible encodings. +# See also: INPUT_FILE_ENCODING +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# This tag can be used to specify the character encoding of the source files +# that Doxygen parses The INPUT_FILE_ENCODING tag can be used to specify +# character encoding on a per file pattern basis. Doxygen will compare the file +# name with each pattern and apply the encoding instead of the default +# INPUT_ENCODING) if there is a match. The character encodings are a list of the +# form: pattern=encoding (like *.php=ISO-8859-1). +# See also: INPUT_ENCODING for further information on supported encodings. + +INPUT_FILE_ENCODING = + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by Doxygen. +# +# Note the list of default checked file patterns might differ from the list of +# default file extension mappings. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cxxm, +# *.cpp, *.cppm, *.ccm, *.c++, *.c++m, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, +# *.idl, *.ddl, *.odl, *.h, *.hh, *.hxx, *.hpp, *.h++, *.ixx, *.l, *.cs, *.d, +# *.php, *.php4, *.php5, *.phtml, *.inc, *.m, *.markdown, *.md, *.mm, *.dox (to +# be provided as Doxygen C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, +# *.f18, *.f, *.for, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cxxm \ + *.cpp \ + *.cppm \ + *.ccm \ + *.c++ \ + *.c++m \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which Doxygen is +# run. + +EXCLUDE = src/cpp11.cpp \ + src/py_stochtree.cpp \ + src/R_data.cpp \ + src/R_random_effects.cpp \ + src/sampler.cpp \ + src/serialization.cpp \ + src/stochtree_types.h + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = */test/* \ + */tools/* \ + */vignettes/* \ + */R/* \ + */nlohmann/* \ + */debug/* \ + */demo/* \ + */deps/* \ + */venv/* \ + */xcode/* \ + */build/* \ + */docs/* \ + */stochtree.egg-info/* + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# ANamespace::AClass, ANamespace::*Test + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that Doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that Doxygen will use the data processed and written to standard output +# for further processing, therefore nothing else, like debug statements or used +# commands (so in case of a Windows batch file always use @echo OFF), should be +# written to standard output. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by Doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by Doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the Doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +# The Fortran standard specifies that for fixed formatted Fortran code all +# characters from position 72 are to be considered as comment. A common +# extension is to allow longer lines before the automatic comment starts. The +# setting FORTRAN_COMMENT_AFTER will also make it possible that longer lines can +# be processed before the automatic comment starts. +# Minimum value: 7, maximum value: 10000, default value: 72. + +FORTRAN_COMMENT_AFTER = 72 + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# multi-line macros, enums or list initialized variables directly into the +# documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct Doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# entity all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of Doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see https://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by Doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then Doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The IGNORE_PREFIX tag can be used to specify a prefix (or a list of prefixes) +# that should be ignored while generating the index headers. The IGNORE_PREFIX +# tag works for classes, function and member names. The entity will be placed in +# the alphabetical list under the first letter of the entity name that remains +# after removing the prefix. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, Doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = NO + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank Doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that Doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that Doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of Doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank Doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that Doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank Doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that Doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by Doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). +# Note: Since the styling of scrollbars can currently not be overruled in +# Webkit/Chromium, the styling will be left out of the default doxygen.css if +# one or more extra stylesheets have been specified. So if scrollbar +# customization is desired it has to be added explicitly. For an example see the +# documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE tag can be used to specify if the generated HTML output +# should be rendered with a dark or light theme. +# Possible values are: LIGHT always generates light mode output, DARK always +# generates dark mode output, AUTO_LIGHT automatically sets the mode according +# to the user preference, uses light mode if no preference is set (the default), +# AUTO_DARK automatically sets the mode according to the user preference, uses +# dark mode if no preference is set and TOGGLE allows a user to switch between +# light and dark mode via a button. +# The default value is: AUTO_LIGHT. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE = AUTO_LIGHT + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a color-wheel, see +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use gray-scales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via JavaScript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have JavaScript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# If the HTML_CODE_FOLDING tag is set to YES then classes and functions can be +# dynamically folded and expanded in the generated HTML source code. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_CODE_FOLDING = YES + +# If the HTML_COPY_CLIPBOARD tag is set to YES then Doxygen will show an icon in +# the top right corner of code and text fragments that allows the user to copy +# its content to the clipboard. Note this only works if supported by the browser +# and the web page is served via a secure context (see: +# https://www.w3.org/TR/secure-contexts/), i.e. using the https: or file: +# protocol. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COPY_CLIPBOARD = YES + +# Doxygen stores a couple of settings persistently in the browser (via e.g. +# cookies). By default these settings apply to all HTML pages generated by +# Doxygen across all projects. The HTML_PROJECT_COOKIE tag can be used to store +# the settings under a project specific key, such that the user preferences will +# be stored separately. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_PROJECT_COOKIE = + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: +# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To +# create a documentation set, Doxygen will generate a Makefile in the HTML +# output directory. Running make will produce the docset in that directory and +# running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy +# genXcode/_index.html for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag determines the URL of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDURL = + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then Doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# on Windows. In the beginning of 2021 Microsoft took the original page, with +# a.o. the download links, offline the HTML help workshop was already many years +# in maintenance mode). You can download the HTML help workshop from the web +# archives at Installation executable (see: +# http://web.archive.org/web/20160201063255/http://download.microsoft.com/downlo +# ad/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe). +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by Doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# Doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the main .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# The SITEMAP_URL tag is used to specify the full URL of the place where the +# generated documentation will be placed on the server by the user during the +# deployment of the documentation. The generated sitemap is called sitemap.xml +# and placed on the directory specified by HTML_OUTPUT. In case no SITEMAP_URL +# is specified no sitemap is generated. For information about the sitemap +# protocol see https://www.sitemaps.org +# This tag requires that the tag GENERATE_HTML is set to YES. + +SITEMAP_URL = + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location (absolute path +# including file name) of Qt's qhelpgenerator. If non-empty Doxygen will try to +# run qhelpgenerator on the generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine tune the look of the index (see "Fine-tuning the output"). As an +# example, the default style sheet generated by Doxygen has an example that +# shows how to put an image at the root of the tree instead of the PROJECT_NAME. +# Since the tree basically has the same information as the tab index, you could +# consider setting DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = NO + +# When both GENERATE_TREEVIEW and DISABLE_INDEX are set to YES, then the +# FULL_SIDEBAR option determines if the side bar is limited to only the treeview +# area (value NO) or if it should extend to the full height of the window (value +# YES). Setting this to YES gives a layout similar to +# https://docs.readthedocs.io with more room for contents, but less room for the +# project logo, title, and description. If either GENERATE_TREEVIEW or +# DISABLE_INDEX is set to NO, this option has no effect. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FULL_SIDEBAR = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# Doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# When the SHOW_ENUM_VALUES tag is set doxygen will show the specified +# enumeration values besides the enumeration mnemonics. +# The default value is: NO. + +SHOW_ENUM_VALUES = NO + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, Doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# If the OBFUSCATE_EMAILS tag is set to YES, Doxygen will obfuscate email +# addresses. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +OBFUSCATE_EMAILS = YES + +# If the HTML_FORMULA_FORMAT option is set to svg, Doxygen will use the pdf2svg +# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see +# https://inkscape.org) to generate formulas as SVG images instead of PNGs for +# the HTML output. These images will generally look nicer at scaled resolutions. +# Possible values are: png (the default) and svg (looks nicer but requires the +# pdf2svg or inkscape tool). +# The default value is: png. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FORMULA_FORMAT = png + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# Doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands +# to create new LaTeX commands to be used in formulas as building blocks. See +# the section "Including formulas" for details. + +FORMULA_MACROFILE = + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# https://www.mathjax.org) which uses client side JavaScript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# With MATHJAX_VERSION it is possible to specify the MathJax version to be used. +# Note that the different versions of MathJax have different requirements with +# regards to the different settings, so it is possible that also other MathJax +# settings have to be changed when switching between the different MathJax +# versions. +# Possible values are: MathJax_2 and MathJax_3. +# The default value is: MathJax_2. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_VERSION = MathJax_2 + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. For more details about the output format see MathJax +# version 2 (see: +# http://docs.mathjax.org/en/v2.7-latest/output.html) and MathJax version 3 +# (see: +# http://docs.mathjax.org/en/latest/web/components/output.html). +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility. This is the name for Mathjax version 2, for MathJax version 3 +# this will be translated into chtml), NativeMML (i.e. MathML. Only supported +# for MathJax 2. For MathJax version 3 chtml will be used instead.), chtml (This +# is the name for Mathjax version 3, for MathJax version 2 this will be +# translated into HTML-CSS) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from https://www.mathjax.org before deployment. The default value is: +# - in case of MathJax version 2: https://cdn.jsdelivr.net/npm/mathjax@2 +# - in case of MathJax version 3: https://cdn.jsdelivr.net/npm/mathjax@3 +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# for MathJax version 2 (see +# https://docs.mathjax.org/en/v2.7-latest/tex.html#tex-and-latex-extensions): +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# For example for MathJax version 3 (see +# http://docs.mathjax.org/en/latest/input/tex/extensions/index.html): +# MATHJAX_EXTENSIONS = ams +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with JavaScript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: +# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled Doxygen will generate a search box for +# the HTML output. The underlying search engine uses JavaScript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the JavaScript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /