From 0e9d7733258a3bf3af255cd799e6ac96dde30f47 Mon Sep 17 00:00:00 2001 From: Martin Date: Thu, 15 Feb 2024 14:31:11 +0100 Subject: [PATCH] update docs --- man/Specified_masks_mask_generator.Rd | 5 +++-- man/vaeac_check_activation_func.Rd | 2 +- man/vaeac_check_cuda.Rd | 2 +- man/vaeac_check_epoch_values.Rd | 2 +- man/vaeac_check_extra_named_list.Rd | 2 +- man/vaeac_check_logicals.Rd | 2 +- man/vaeac_check_mask_gen.Rd | 2 +- man/vaeac_check_masking_ratio.Rd | 2 +- man/vaeac_check_parameters.Rd | 2 +- man/vaeac_check_positive_integers.Rd | 2 +- man/vaeac_check_positive_numerics.Rd | 2 +- man/vaeac_check_probabilities.Rd | 2 +- man/vaeac_check_save_names.Rd | 2 +- man/vaeac_check_save_parameters.Rd | 2 +- man/vaeac_check_verbose.Rd | 2 +- man/vaeac_check_which_vaeac_model.Rd | 2 +- man/vaeac_check_x_train_names.Rd | 2 +- man/vaeac_get_current_save_state.Rd | 2 +- man/vaeac_get_data_objects.Rd | 2 +- man/vaeac_get_evaluation_criteria.Rd | 2 +- man/vaeac_get_extra_para_default.Rd | 2 +- man/vaeac_get_full_state_list.Rd | 2 +- man/vaeac_get_mask_generator_name.Rd | 2 +- man/vaeac_get_model_from_checkp.Rd | 2 +- man/vaeac_get_n_decimals.Rd | 2 +- man/vaeac_get_optimizer.Rd | 2 +- man/vaeac_get_save_file_names.Rd | 2 +- man/vaeac_get_x_explain_extended.Rd | 2 +- man/vaeac_plot_evaluation_criteria.Rd | 2 +- man/vaeac_plot_imputed_ggpairs.Rd | 2 +- man/vaeac_print_train_summary.Rd | 2 +- man/vaeac_save_state.Rd | 2 +- man/vaeac_train_model_auxiliary.Rd | 2 +- man/vaeac_update_para_locations.Rd | 2 +- man/vaeac_update_pretrained_model.Rd | 2 +- 35 files changed, 37 insertions(+), 36 deletions(-) diff --git a/man/Specified_masks_mask_generator.Rd b/man/Specified_masks_mask_generator.Rd index a2b12cab5..e35ce969e 100644 --- a/man/Specified_masks_mask_generator.Rd +++ b/man/Specified_masks_mask_generator.Rd @@ -37,11 +37,12 @@ Initialize a specified masks mask generator. \examples{ \dontrun{ masks <- torch_tensor(matrix(c(0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1), - nrow = 3, ncol = 4, byrow = TRUE)) + nrow = 3, ncol = 4, byrow = TRUE +)) masks_probs <- c(3, 1, 6) mask_gen <- Specified_masks_mask_generator(masks = masks, masks_probs = masks_probs) empirical_prob <- - table(as.array(mask_gen(torch::torch_randn(c(10000, ncol(masks))))$sum(-1))) + table(as.array(mask_gen(torch::torch_randn(c(10000, ncol(masks))))$sum(-1))) empirical_prob / sum(empirical_prob) masks_probs / sum(masks_probs) } diff --git a/man/vaeac_check_activation_func.Rd b/man/vaeac_check_activation_func.Rd index 3ff035f55..75ac2973a 100644 --- a/man/vaeac_check_activation_func.Rd +++ b/man/vaeac_check_activation_func.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_activation_func} \alias{vaeac_check_activation_func} \title{Function that checks the provided activation function} diff --git a/man/vaeac_check_cuda.Rd b/man/vaeac_check_cuda.Rd index 113cfacff..b85777b77 100644 --- a/man/vaeac_check_cuda.Rd +++ b/man/vaeac_check_cuda.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_cuda} \alias{vaeac_check_cuda} \title{Function that checks for access to CUDA} diff --git a/man/vaeac_check_epoch_values.Rd b/man/vaeac_check_epoch_values.Rd index 45d87817b..767de3302 100644 --- a/man/vaeac_check_epoch_values.Rd +++ b/man/vaeac_check_epoch_values.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_epoch_values} \alias{vaeac_check_epoch_values} \title{Function that checks provided epoch arguments} diff --git a/man/vaeac_check_extra_named_list.Rd b/man/vaeac_check_extra_named_list.Rd index 9bafc52d0..32cd1228c 100644 --- a/man/vaeac_check_extra_named_list.Rd +++ b/man/vaeac_check_extra_named_list.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_extra_named_list} \alias{vaeac_check_extra_named_list} \title{Check vaeac.extra_parameters list} diff --git a/man/vaeac_check_logicals.Rd b/man/vaeac_check_logicals.Rd index d246bed7c..41e31d065 100644 --- a/man/vaeac_check_logicals.Rd +++ b/man/vaeac_check_logicals.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_logicals} \alias{vaeac_check_logicals} \title{Function that checks logicals} diff --git a/man/vaeac_check_mask_gen.Rd b/man/vaeac_check_mask_gen.Rd index 138e76d29..fc5209010 100644 --- a/man/vaeac_check_mask_gen.Rd +++ b/man/vaeac_check_mask_gen.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_mask_gen} \alias{vaeac_check_mask_gen} \title{Function that checks the specified masking scheme} diff --git a/man/vaeac_check_masking_ratio.Rd b/man/vaeac_check_masking_ratio.Rd index c1e29e83c..7a7defd21 100644 --- a/man/vaeac_check_masking_ratio.Rd +++ b/man/vaeac_check_masking_ratio.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_masking_ratio} \alias{vaeac_check_masking_ratio} \title{Function that checks that the masking ratio argument is valid} diff --git a/man/vaeac_check_parameters.Rd b/man/vaeac_check_parameters.Rd index 02044dc12..0fe3f3d8f 100644 --- a/man/vaeac_check_parameters.Rd +++ b/man/vaeac_check_parameters.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_parameters} \alias{vaeac_check_parameters} \title{Function that calls all vaeac parameters check functions} diff --git a/man/vaeac_check_positive_integers.Rd b/man/vaeac_check_positive_integers.Rd index 78fefb0fd..c532b516b 100644 --- a/man/vaeac_check_positive_integers.Rd +++ b/man/vaeac_check_positive_integers.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_positive_integers} \alias{vaeac_check_positive_integers} \title{Function that checks positive integers} diff --git a/man/vaeac_check_positive_numerics.Rd b/man/vaeac_check_positive_numerics.Rd index e3bf30071..cfc61dc70 100644 --- a/man/vaeac_check_positive_numerics.Rd +++ b/man/vaeac_check_positive_numerics.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_positive_numerics} \alias{vaeac_check_positive_numerics} \title{Function that checks positive numerics} diff --git a/man/vaeac_check_probabilities.Rd b/man/vaeac_check_probabilities.Rd index 1e6986d46..ccbffc729 100644 --- a/man/vaeac_check_probabilities.Rd +++ b/man/vaeac_check_probabilities.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_probabilities} \alias{vaeac_check_probabilities} \title{Function that checks probabilities} diff --git a/man/vaeac_check_save_names.Rd b/man/vaeac_check_save_names.Rd index 984ad2df1..e2bb63648 100644 --- a/man/vaeac_check_save_names.Rd +++ b/man/vaeac_check_save_names.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_save_names} \alias{vaeac_check_save_names} \title{Function that checks that the save folder exists and for a valid file name} diff --git a/man/vaeac_check_save_parameters.Rd b/man/vaeac_check_save_parameters.Rd index b6c1edf10..4736dd14b 100644 --- a/man/vaeac_check_save_parameters.Rd +++ b/man/vaeac_check_save_parameters.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_save_parameters} \alias{vaeac_check_save_parameters} \title{Function that gives a warning about disk usage} diff --git a/man/vaeac_check_verbose.Rd b/man/vaeac_check_verbose.Rd index 0ba09d4ee..c5aecac15 100644 --- a/man/vaeac_check_verbose.Rd +++ b/man/vaeac_check_verbose.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_verbose} \alias{vaeac_check_verbose} \title{Function the checks the verbose parameter} diff --git a/man/vaeac_check_which_vaeac_model.Rd b/man/vaeac_check_which_vaeac_model.Rd index 525dae517..3a3d89ac2 100644 --- a/man/vaeac_check_which_vaeac_model.Rd +++ b/man/vaeac_check_which_vaeac_model.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_which_vaeac_model} \alias{vaeac_check_which_vaeac_model} \title{Function that checks for valid \code{vaeac} model name} diff --git a/man/vaeac_check_x_train_names.Rd b/man/vaeac_check_x_train_names.Rd index 9d70aeaa4..1c2bab9a7 100644 --- a/man/vaeac_check_x_train_names.Rd +++ b/man/vaeac_check_x_train_names.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_check_x_train_names} \alias{vaeac_check_x_train_names} \title{Function that checks the feature names of data and \code{vaeac} model} diff --git a/man/vaeac_get_current_save_state.Rd b/man/vaeac_get_current_save_state.Rd index 1f53c3f05..230eb4d92 100644 --- a/man/vaeac_get_current_save_state.Rd +++ b/man/vaeac_get_current_save_state.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_current_save_state} \alias{vaeac_get_current_save_state} \title{Function that extracts additional objects from the environment to the state list} diff --git a/man/vaeac_get_data_objects.Rd b/man/vaeac_get_data_objects.Rd index 0b08136b1..bac7e5d16 100644 --- a/man/vaeac_get_data_objects.Rd +++ b/man/vaeac_get_data_objects.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_data_objects} \alias{vaeac_get_data_objects} \title{Function to set up data loaders and save file names} diff --git a/man/vaeac_get_evaluation_criteria.Rd b/man/vaeac_get_evaluation_criteria.Rd index 8cbfaaa4a..7925c7285 100644 --- a/man/vaeac_get_evaluation_criteria.Rd +++ b/man/vaeac_get_evaluation_criteria.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_evaluation_criteria} \alias{vaeac_get_evaluation_criteria} \title{Extract the Training VLB and Validation IWAE from a list of explanations objects using the vaeac approach} diff --git a/man/vaeac_get_extra_para_default.Rd b/man/vaeac_get_extra_para_default.Rd index 12677e61b..870f2a774 100644 --- a/man/vaeac_get_extra_para_default.Rd +++ b/man/vaeac_get_extra_para_default.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_extra_para_default} \alias{vaeac_get_extra_para_default} \title{Function to specify the extra parameters in the \code{vaeac} model} diff --git a/man/vaeac_get_full_state_list.Rd b/man/vaeac_get_full_state_list.Rd index 3495191b7..59418372e 100644 --- a/man/vaeac_get_full_state_list.Rd +++ b/man/vaeac_get_full_state_list.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_full_state_list} \alias{vaeac_get_full_state_list} \title{Function that extracts the state list objects from the environment} diff --git a/man/vaeac_get_mask_generator_name.Rd b/man/vaeac_get_mask_generator_name.Rd index 5e695f77e..67db3c993 100644 --- a/man/vaeac_get_mask_generator_name.Rd +++ b/man/vaeac_get_mask_generator_name.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_mask_generator_name} \alias{vaeac_get_mask_generator_name} \title{Function that determines which mask generator to use} diff --git a/man/vaeac_get_model_from_checkp.Rd b/man/vaeac_get_model_from_checkp.Rd index 077c76b69..cb2a3d2b4 100644 --- a/man/vaeac_get_model_from_checkp.Rd +++ b/man/vaeac_get_model_from_checkp.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_model_from_checkp} \alias{vaeac_get_model_from_checkp} \title{Function to load a \code{vaeac} model and set it in the right state and mode} diff --git a/man/vaeac_get_n_decimals.Rd b/man/vaeac_get_n_decimals.Rd index c6b9befed..4e1445e8e 100644 --- a/man/vaeac_get_n_decimals.Rd +++ b/man/vaeac_get_n_decimals.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_n_decimals} \alias{vaeac_get_n_decimals} \title{Function to get string of values with specific number of decimals} diff --git a/man/vaeac_get_optimizer.Rd b/man/vaeac_get_optimizer.Rd index eda90beb2..256d7704e 100644 --- a/man/vaeac_get_optimizer.Rd +++ b/man/vaeac_get_optimizer.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_optimizer} \alias{vaeac_get_optimizer} \title{Function to create the optimizer used to train \code{vaeac}} diff --git a/man/vaeac_get_save_file_names.Rd b/man/vaeac_get_save_file_names.Rd index 01690cfab..18ff47925 100644 --- a/man/vaeac_get_save_file_names.Rd +++ b/man/vaeac_get_save_file_names.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_save_file_names} \alias{vaeac_get_save_file_names} \title{Function that creates the save file names for the \code{vaeac} model} diff --git a/man/vaeac_get_x_explain_extended.Rd b/man/vaeac_get_x_explain_extended.Rd index d532ebc05..91b76a56b 100644 --- a/man/vaeac_get_x_explain_extended.Rd +++ b/man/vaeac_get_x_explain_extended.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_get_x_explain_extended} \alias{vaeac_get_x_explain_extended} \title{Function to extend the explicands and apply all relevant masks/coalitions} diff --git a/man/vaeac_plot_evaluation_criteria.Rd b/man/vaeac_plot_evaluation_criteria.Rd index a38ad64ed..40dfa309d 100644 --- a/man/vaeac_plot_evaluation_criteria.Rd +++ b/man/vaeac_plot_evaluation_criteria.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_plot_evaluation_criteria} \alias{vaeac_plot_evaluation_criteria} \title{Plot the training VLB and validation IWAE for \code{vaeac} models} diff --git a/man/vaeac_plot_imputed_ggpairs.Rd b/man/vaeac_plot_imputed_ggpairs.Rd index 02a56715d..b667281f6 100644 --- a/man/vaeac_plot_imputed_ggpairs.Rd +++ b/man/vaeac_plot_imputed_ggpairs.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_plot_imputed_ggpairs} \alias{vaeac_plot_imputed_ggpairs} \title{Plot Pairwise Plots for Imputed and True Data} diff --git a/man/vaeac_print_train_summary.Rd b/man/vaeac_print_train_summary.Rd index 40528fe54..ab9a8a560 100644 --- a/man/vaeac_print_train_summary.Rd +++ b/man/vaeac_print_train_summary.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_print_train_summary} \alias{vaeac_print_train_summary} \title{Function to printout a training summary for the \code{vaeac} model} diff --git a/man/vaeac_save_state.Rd b/man/vaeac_save_state.Rd index 10103604d..5da0eaa0e 100644 --- a/man/vaeac_save_state.Rd +++ b/man/vaeac_save_state.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_save_state} \alias{vaeac_save_state} \title{Function that saves the state list and the current save state of the \code{vaeac} model} diff --git a/man/vaeac_train_model_auxiliary.Rd b/man/vaeac_train_model_auxiliary.Rd index c94bca24e..6c8a6cc21 100644 --- a/man/vaeac_train_model_auxiliary.Rd +++ b/man/vaeac_train_model_auxiliary.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_train_model_auxiliary} \alias{vaeac_train_model_auxiliary} \title{Function used to train a \code{vaeac} model} diff --git a/man/vaeac_update_para_locations.Rd b/man/vaeac_update_para_locations.Rd index 8fe9566a2..d8e3e53f1 100644 --- a/man/vaeac_update_para_locations.Rd +++ b/man/vaeac_update_para_locations.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_update_para_locations} \alias{vaeac_update_para_locations} \title{Move \code{vaeac} parameters to correct location} diff --git a/man/vaeac_update_pretrained_model.Rd b/man/vaeac_update_pretrained_model.Rd index b949faf1c..d60785518 100644 --- a/man/vaeac_update_pretrained_model.Rd +++ b/man/vaeac_update_pretrained_model.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/approach_vaeac_extra_functions.R +% Please edit documentation in R/approach_vaeac.R \name{vaeac_update_pretrained_model} \alias{vaeac_update_pretrained_model} \title{Function that checks and adds a pre-trained \code{vaeac} model}