Man pages for richelbilderbeek/gcaer
Interface to GCAE

calc_mse_from_identity_line	Calculate the mean squared error from the identity line.
calc_nmse_from_identity_line	Calculate the normalized mean squared error from the identity...
calc_nmse_from_phenotype_predictions	Calculate the normalized mean squared error through time from...
calc_r_squared	Calculate the 'r_squared'
calc_r_squared_from_phenotype_predictions	Calculate the 'r_squared' through time from the phenotype...
check_analyse_epochs	Check if the 'analyse_epochs' is valid
check_csv_filename	Check if the 'csv_filename' is valid
check_data	Check if the 'data' is valid
check_datadir	Check if the 'datadir' is valid
check_data_opts_id	Check if the 'data_opts_id' is valid
check_epoch	Check if the 'epoch' is valid
check_epochs	Check if the 'epochs' is valid
check_evaluate_results	Check if the 'evaluate_results' are valid.
check_file_extension	Check if the 'file_extension' is valid
check_folder_name	Check if the 'folder_name' is valid
check_gcae_args	Check if the arguments to call GCAE are valid.
check_gcae_experiment_params	Check if the options to run GCAE are valid.
check_gcae_experiment_params_filename	Check if the 'gcae_experiment_params_filename' is valid
check_gcae_experiment_results	Check if the 'gcae_experiment_results' is valid.
check_gcae_folder	Check if the 'gcae_folder' is valid
check_gcae_input_data	Check if the 'gcae_input_data' is valid, i.e. can be run by...
check_gcae_input_data_data_type	Check if the data type of 'gcae_input_data' is valid
check_gcae_input_filenames	Check if the GenoCAE input filenames list is valid.
check_gcae_input_files	Check if the GenoCAE input files are valid.
check_gcae_is_installed	Check if GCAE is installed
check_gcae_options	Check if the options to run GCAE are valid.
check_gcae_options_filename	Check if the 'gcae_options_filename' is valid
check_gcae_python_packages_are_installed	Check if all the GCAE Python packages are installed.
check_gcae_repo_is_cloned	Check if the GCAE repo is cloned. Will stop if not.
check_gcae_script_is_fixed	Check if the GCAE script is fixed
check_gcae_setup	Check if the options to run GCAE are valid.
check_gcae_setup_filename	Check if the 'gcae_setup_filename' is valid
check_gcae_train_files_are_present	Check if the files to run gcae_train are present.
check_gcae_version	Check if the GCAE version is valid, will stop if not
check_genotype_concordances_table	Create a 'genotype_concordances_table' to be used in testing
check_gif_filename	Check if the 'gif_filename' is valid
check_input_files_are_present	Check if all the files needed for do_gcae_experiment are...
check_labels_table	Check if the 'labels_table' is valid
check_losses_from_train_t_table	Check if the 'losses_from_train_t_table' is valid
check_losses_from_train_v_table	Check if the 'losses_from_train_v_table' is valid
check_metric	Check if the 'metric' is valid
check_metrics	Check if the 'metrics' is valid
check_model	Check if the 'model' is valid
check_model_filename	Check if the 'model_filename' is valid
check_model_id	Check if the 'model_id' is valid
check_nmse_in_time_table	Check if the 'nmse_in_time_table' is valid
check_n_neurons	Check if the 'n_neurons' is valid
check_ormr_folder_name	Check if the 'ormr_folder_name' is valid
check_pheno_model_filename	Check if the 'pheno_model_filename' is valid
check_pheno_model_id	Check if the 'pheno_model_id' is valid
check_phenotype_predictions_table	Check if the 'phenotype_predictions_table' is valid
check_png_filename	Check if the 'png_filename' is valid
check_python_version	Check if the 'python_version' is valid
check_resume_from	Check if the 'resume_from' is valid
check_r_squared_in_time_table	Check if the 'r_squared_in_time_table' is valid
check_save_interval	Check if the 'save_interval' is valid
check_score_per_pop_table	Create a 'score_per_pop_table' to be used in testing
check_scores_table	Check if the 'scores_table' is valid
check_superpops	Check if the 'superpops' is valid
check_trainedmodeldir	Check if the 'trainedmodeldir' is valid
check_trainedmodelname	Check if the 'trainedmodelname' is valid
check_train_opts_id	Check if the 'train_opts_id' is valid
check_train_times_table	Check if the 'train_times_table' is valid
clean_file_path	Cleans up a file path
clean_gcaer_tempfolder	Remove all 'gcaer' temporary files
clone_gcae_repo	Clone the GCAE repo
create_gcae_evaluate_args	Create the CLI arguments to evaluate the 'GCAE' training
create_gcae_experiment_params	Create the parameters for a GCAE experiment
create_gcae_input_data	Create a 'gcae_input_data'.
create_gcae_input_filenames	Create a 'gcae_input_filenames'
create_gcae_input_files_1	Create setting 1 for GCAE
create_gcae_input_files_2	Create setting 2 for GCAE
create_gcae_options	Create the options to run GCAE
create_gcae_project_args	Create the CLI arguments to project with 'GCAE'
create_gcae_setup	Create the GCAE setup
create_gcae_train_args	Create the CLI arguments to train with GCAE
create_gcae_train_more_args	Create the CLI arguments to resume training the 'GCAE'
create_genotype_concordances_through_time_png	Create a PNG file of the genotype concordance through time
create_losses_from_train_t_through_time_png	Create a PNG file of the losses from training through time,...
create_losses_from_train_v_through_time_png	Create a PNG file of the losses from training through time,...
create_nmse_through_time_png	Create a PNG file of the NMSE through time
create_phenotype_prediction_quality_png	Create a PNG file of the phenotype predictions at that time
create_phenotype_predictions_through_time_png	Create a PNG file of the phenotypic predictions through time
create_phenotype_prediction_through_time_gif	Create a GIF file of the phenotype predictions through time
create_plots_from_gcae_experiment_results	Create plots from the saved GCAE experiment's results
create_r_squared_through_time_png	Create a PNG file of the 'r_squared' through time
create_score_per_pop_through_time_png	Create a PNG file of the F1 scores per population through...
create_scores_through_time_png	Create a PNG file of the F1 scores through time
create_test_gcae_experiment_params	Create the parameters for a GCAE experiment
create_test_gcae_experiment_results	Create a 'gcae_experiment_results' to be used in testing
create_test_gcae_input_data	Create a 'gcae_input_data' to be used in testing.
create_test_gcae_input_filenames	Create a 'gcae_input_filenames' to be used in testing
create_test_gcae_setup	Create a GCAE setup to be used in testing
create_test_genotype_concordances_table	Create a 'genotype_concordances_table' to be used in testing
create_test_losses_from_train_t_table	Create a 'losses_from_train_t_table' to be used in testing
create_test_losses_from_train_v_table	Create a 'losses_from_train_v_table' to be used in testing
create_test_model	Create a GCAE model to be used in testing
create_test_nmse_in_time_table	Create a 'nmse_in_time_table' to be used in testing
create_test_phenotype_predictions_table	Create a 'phenotype_predictions_table' to be used in testing
create_test_r_squared_in_time_table	Create a 'r_squared_in_time_table' to be used in testing
create_test_score_per_pop_table	Create a 'score_per_pop_table' to be used in testing
create_test_scores_table	Create a 'scores_table' to be used in testing
create_test_train_times_table	Create a 'train_times_table' to be used in testing
create_train_times_through_time_png	Create a PNG file of the training times through time
default_params_doc	This function does nothing. It is intended to inherit is...
do_gcae_experiment	Do a full 'GCAE' experiment
evaluate_phenotype_prediction	Determine how well the quantitative trait prediction worked
fix_gcae_script	Fix the GCAE script
gcae_animate	Animate
gcae_evaluate	Use 'GCAE' its evaluate
gcae_options_to_str	Convert a 'gcae_options' to a string
gcae_plot	Plot
gcae_project	Project
gcaer	gcaer: An R interface to 'GCAE'.
gcaer_report	Create a gcaer report, to be used when reporting bugs
gcae_setup_to_str	Convert a 'gcae_setup' to a string
gcae_train	Train model, and save its state at certain epochs to disk.
gcae_train_more	Continue training a model, and save its state at certain...
get_default_github_repo_branch_name	Get the name of the default GitHub repository branch
get_default_github_repo_url	Get the default GitHub repository URL
get_default_ormr_folder_name	Get the default ormr folder used by 'gcaer'
get_gcae_data_opts_filename	Get the filename to the GCAE data options
get_gcae_data_opts_filenames	Get the filenames for all the 'GCAE' phenotypic model...
get_gcae_data_opts_ids	Get the 'data_opts' IDs for all the 'GCAE' phenotype...
get_gcae_example_filename	Get the path to a gcaer file
get_gcae_example_filenames	Get the paths to all 'GCAE' example files
get_gcae_experiment_results_filenames	Get a list of filenames the GCAE results will be saved to
get_gcae_folder	Get the path to the default 'GCAE' folder as used by gcaer
get_gcae_help_text	Get the text of the gcae help file
get_gcae_input_filenames	Create a 'gcae_input_filenames'
get_gcae_model_filename	Get the filename to the GCAE model
get_gcae_model_filenames	Get the filenames for all the 'GCAE' autoencoder...
get_gcae_model_ids	Get the model IDs for all the 'GCAE' autoencoder...
get_gcae_output_subfolder	Get the path to the GCAE output subfolder
get_gcae_pheno_model_filename	Get the filename to the 'GCAE' phenotype model
get_gcae_pheno_model_filenames	Get the filenames for all the 'GCAE' phenotypic model...
get_gcae_pheno_model_ids	Get the 'pheno_model' IDs for all the 'GCAE' phenotype...
get_gcae_required_python_packages	Get the names and version of all the Python packages GCAE...
get_gcaer_filename	Get the path to a gcaer file
get_gcaer_filenames	Get the full paths to all gcaer files
get_gcaer_folder	Get the folder where gcaer stores its temporary files
get_gcaer_tempfilename	Get a temporary filename
get_gcaer_theme	Get the 'gcaer' theme
get_gcae_trainedmodelname	Get the GCAE 'trainedmodelname'
get_gcae_train_opts_filename	Get the filename to the GCAE training options
get_gcae_train_opts_filenames	Get the filenames for all the 'GCAE' phenotypic model...
get_gcae_train_opts_ids	Get the 'train_opts' IDs for all the 'GCAE' phenotype...
get_gcae_version	Get the version of GCAE
get_n_neurons_in_latent_layer	Get the number of neurons in the layent layer
get_n_neurons_in_latent_layer_from_gcae_experiment_params	Get the number of neurons in the layent layer from a...
get_n_neurons_in_latent_layer_from_model	Get the number of neurons in the layent layer from a 'model'
get_run_gcae_py_path	Get the full path to 'run_gcae.py'
get_test_data	Get the 'data' for use in testing.
get_test_datadir	Get the 'datadir' for use in testing.
get_test_labels_table	Get a 'labels_table' for use in testing.
has_cloned_gcae_repo	Determines if the GCAE repo has been cloned already
install_gcae	Install a specific version of GCAE
install_gcae_requirements	Install the GCAE requirements
is_equal_json	Determine if two JSON objects are the same
is_gcae_experiment_params	Determine if the 'gcae_experiment_params' is indeed a...
is_gcae_installed	Determine if 'GCAE' is installed
is_gcae_repo_cloned	Determine if 'GCAE"s repo is cloned
is_gcae_script_fixed	Clone the GCAE repo
is_model	Determine if the 'model' is indeed a 'model'
is_tensorboard_installed	Determine if TensorBoard is installed
normalize_true_and_estimated_values	Normalize the true and estimated values
parse_evaluate_filenames	Parse the data from the files produced by gcae_evaluate
parse_genotype_concordances_file	Parse the 'genotype_concordances.csv' file
parse_losses_from_project_file	Parse the 'losses_from_project.csv' file
parse_losses_from_train_t_file	Parse the 'losses_from_train_t.csv' file
parse_losses_from_train_v_file	Parse the 'losses_from_train_v.csv' file
parse_project_files	Parse the data from the files produced by gcae_project
parse_score_per_pop_file	Parse the f1_scores_pops_epoch_[x].csv file produced by...
parse_train_filenames	Parse the data from the files produced by gcae_train
parse_train_times_file	Parse the 'train_times.csv' file
plot_genotype_concordances_from_file	Plot the genotype concordances in time, from file
plot_losses_from_train_t_from_file	Plot the losses from training in time, for the training set,...
plot_losses_from_train_v_from_file	Plot the losses from training in time, for the validation...
plot_model	Plot a 'GCAE' autoencoder architecture, from file
plot_nmse_in_time_from_file	Plot the NMSE in time, from file
plot_phenotype_predictions_from_file	Plot the phenotype predictions in time, from file
plot_r_squared_in_time_from_file	Plot the 'r_squared' in time, from file
plot_score_per_pop_from_file	Plot the scores per population in time, from file
plot_scores_from_file	Plot the F1 scores in time, from file
plot_train_times_from_file	Plot the train times, from file
project	Project
read_gcae_experiment_params_file	Read a 'gcae_experiment_params' from file
read_gcae_input_files	Read the GenoCAE input filenames
read_gcae_options_file	Read a 'gcae_options' from file
read_gcae_setup_file	Read a 'gcae_setup' from file
read_genotype_concordances_file	Read a 'genotype_concordances_table' from file
read_labels_file	Read a 'GCAE' labels file
read_losses_from_train_t_file	Read a 'losses_from_train_t_table' from file
read_losses_from_train_v_file	Read a 'losses_from_train_v_table' from file
read_model_file	Read a 'GCAE' autoencoder architecture file
read_nmse_in_time_file	Read a 'nmse_in_time_table' from file
read_pheno_model_file	Read a 'GCAE' phenotypic model file
read_phenotype_predictions_file	Read a 'phenotype_predictions_table' from file
read_r_squared_in_time_file	Read a 'r_squared_in_time_table' from file
read_score_per_pop_file	Read a 'score_per_pop_table' from file
read_scores_file	Read a 'scores_table' from file
read_train_times_file	Read a 'train_times_table' from file
remove_gcaer_tempfolder	Remove the 'gcaer' temporary folder
rename_files	Rename multiple files
resize_to_shared_individuals_from_data	Resize the 'gcae_input_data' to only contain the shared...
resize_to_shared_individuals_from_files	Resize the 'gcae_input_data' to only contain the shared...
run_gcae	Run GCAE from arguments
run_tensorboard	Run TensorBoard
save_gcae_experiment_params	Save a 'gcae_experiment_params' to file
save_gcae_experiment_results	Save a 'gcae_experiment_results' to file
save_gcae_input_data	Save a 'gcae_input_data'
save_gcae_options	Save a 'gcae_options' to file
save_gcae_setup	Save a 'gcae_setup' to file
save_labels_table	Save a 'GCAE' labels file
save_model	Save a 'GCAE' autoencoder architecture file
save_model_plot	Save a 'GCAE' autoencoder architecture file
set_n_neurons_in_latent_layer	Set the number of neurons in the latent layer
summarise_gcae_input_data	Summarise the 'gcae_input_data'
summarise_gcae_input_files	Summarise the GCAE input files
uninstall_gcae	Uninstall GCAE