Files in richelbilderbeek/gcaer
Interface to GCAE

.Rbuildignore

.github/workflows/R-CMD-check.yaml

.github/workflows/build_singularity.yaml

.github/workflows/check_bash_style.yaml

.github/workflows/check_links.yaml

.github/workflows/check_versions_match.yaml

.gitignore

CODE_OF_CONDUCT.md CONTRIBUTING.md

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/calc_mse_from_identity_line.R R/calc_nmse_from_identity_line.R R/calc_nmse_from_phenotype_predictions.R R/calc_r_squared.R R/calc_r_squared_from_phenotype_predictions.R R/check_analyse_epochs.R R/check_csv_filename.R R/check_data.R R/check_data_opts_id.R R/check_datadir.R R/check_epoch.R R/check_epochs.R R/check_evaluate_results.R R/check_file_extension.R R/check_folder_name.R R/check_gcae_args.R R/check_gcae_experiment_params.R R/check_gcae_experiment_params_filename.R R/check_gcae_experiment_results.R R/check_gcae_folder.R R/check_gcae_input_data.R R/check_gcae_input_data_data_type.R R/check_gcae_input_filenames.R R/check_gcae_input_files.R R/check_gcae_is_installed.R R/check_gcae_options.R R/check_gcae_options_filename.R R/check_gcae_python_packages_are_installed.R R/check_gcae_repo_is_cloned.R R/check_gcae_script_is_fixed.R R/check_gcae_setup.R R/check_gcae_setup_filename.R R/check_gcae_train_files_are_present.R R/check_gcae_version.R R/check_genotype_concordances_table.R R/check_gif_filename.R R/check_input_files_are_present.R R/check_labels_table.R R/check_losses_from_train_t_table.R R/check_losses_from_train_v_table.R R/check_metric.R R/check_metrics.R R/check_model.R R/check_model_filename.R R/check_model_id.R R/check_n_neurons.R R/check_nmse_in_time_table.R R/check_ormr_folder_name.R R/check_pheno_model_filename.R R/check_pheno_model_id.R R/check_phenotype_predictions_table.R R/check_png_filename.R R/check_python_version.R R/check_r_squared_in_time_table.R R/check_resume_from.R R/check_save_interval.R R/check_score_per_pop_table.R R/check_scores_table.R R/check_superpops.R R/check_train_opts_id.R R/check_train_times_table.R R/check_trainedmodeldir.R R/check_trainedmodelname.R R/clean_file_path.R R/clean_gcaer_tempfolder.R R/clone_gcae_repo.R R/create_gcae_evaluate_args.R R/create_gcae_experiment_params.R R/create_gcae_input_data.R R/create_gcae_input_filenames.R R/create_gcae_input_files_1.R R/create_gcae_input_files_2.R R/create_gcae_options.R R/create_gcae_project_args.R R/create_gcae_setup.R R/create_gcae_train_args.R R/create_gcae_train_more_args.R R/create_genotype_concordances_through_time_png.R R/create_losses_from_train_t_through_time_png.R R/create_losses_from_train_v_through_time_png.R R/create_nmse_through_time_png.R R/create_phenotype_prediction_quality_png.R R/create_phenotype_prediction_through_time_gif.R R/create_phenotype_predictions_through_time_png.R R/create_plots_from_gcae_experiment_results.R R/create_r_squared_through_time_png.R R/create_score_per_pop_through_time_png.R R/create_scores_through_time_png.R R/create_test_gcae_experiment_params.R R/create_test_gcae_experiment_results.R R/create_test_gcae_input_data.R R/create_test_gcae_input_filenames.R R/create_test_gcae_setup.R R/create_test_genotype_concordances_table.R R/create_test_losses_from_train_t_table.R R/create_test_losses_from_train_v_table.R R/create_test_model.R R/create_test_nmse_in_time_table.R R/create_test_phenotype_predictions_table.R R/create_test_r_squared_in_time_table.R R/create_test_score_per_pop_table.R R/create_test_scores_table.R R/create_test_train_times_table.R R/create_train_times_through_time_png.R R/default_params_doc.R R/do_gcae_experiment.R R/evaluate_phenotype_prediction.R R/fix_gcae_script.R R/gcae_animate.R R/gcae_evaluate.R R/gcae_options_to_str.R R/gcae_plot.R R/gcae_project.R R/gcae_setup_to_str.R R/gcae_train.R R/gcae_train_more.R R/gcaer.R R/gcaer_report.R R/get_default_github_repo_branch_name.R R/get_default_github_repo_url.R R/get_default_ormr_folder_name.R R/get_gcae_data_opts_filename.R R/get_gcae_data_opts_filenames.R R/get_gcae_data_opts_ids.R R/get_gcae_example_filename.R R/get_gcae_example_filenames.R R/get_gcae_experiment_results_filenames.R R/get_gcae_folder.R R/get_gcae_help_text.R R/get_gcae_input_filenames.R R/get_gcae_model_filename.R R/get_gcae_model_filenames.R R/get_gcae_model_ids.R R/get_gcae_output_subfolder.R R/get_gcae_pheno_model_filename.R R/get_gcae_pheno_model_filenames.R R/get_gcae_pheno_model_ids.R R/get_gcae_required_python_packages.R R/get_gcae_train_opts_filename.R R/get_gcae_train_opts_filenames.R R/get_gcae_train_opts_ids.R R/get_gcae_trainedmodelname.R R/get_gcae_version.R R/get_gcaer_filename.R R/get_gcaer_filenames.R R/get_gcaer_folder.R R/get_gcaer_tempfilename.R R/get_gcaer_theme.R R/get_n_neurons_in_latent_layer.R R/get_n_neurons_in_latent_layer_from_gcae_experiment_params.R R/get_n_neurons_in_latent_layer_from_model.R R/get_run_gcae_py_path.R R/get_test_data.R R/get_test_datadir.R R/get_test_labels_table.R R/has_cloned_gcae_repo.R R/install_gcae.R R/install_gcae_requirements.R R/is_equal_json.R R/is_gcae_experiment_params.R R/is_gcae_installed.R R/is_gcae_repo_cloned.R R/is_gcae_script_fixed.R R/is_model.R R/is_tensorboard_installed.R R/normalize_true_and_estimated_values.R R/parse_evaluate_filenames.R R/parse_genotype_concordances_file.R R/parse_losses_from_project_file.R R/parse_losses_from_train_t_file.R R/parse_losses_from_train_v_file.R R/parse_project_files.R R/parse_score_per_pop_file.R R/parse_train_filenames.R R/parse_train_times_file.R R/plot_genotype_concordances_from_file.R R/plot_losses_from_train_t_from_file.R R/plot_losses_from_train_v_from_file.R R/plot_model.R R/plot_nmse_in_time_from_file.R R/plot_phenotype_predictions_from_file.R R/plot_r_squared_in_time_from_file.R R/plot_score_per_pop_from_file.R R/plot_scores_from_file.R R/plot_train_times_from_file.R R/project.R R/read_gcae_experiment_params_file.R R/read_gcae_input_files.R R/read_gcae_options_file.R R/read_gcae_setup_file.R R/read_genotype_concordances_file.R R/read_labels_file.R R/read_losses_from_train_t_file.R R/read_losses_from_train_v_filename.R R/read_model_file.R R/read_nmse_in_time_file.R R/read_pheno_model_file.R R/read_phenotype_predictions_file.R R/read_r_squared_in_time_file.R R/read_score_per_pop_file.R R/read_scores_file.R R/read_train_times_file.R R/remove_gcaer_tempfolder.R R/rename_files.R R/resize_to_shared_individuals_from_data.R R/resize_to_shared_individuals_from_files.R R/run_gcae.R R/run_tensorboard.R R/save_gcae_experiment_params.R R/save_gcae_experiment_results.R R/save_gcae_input_data.R R/save_gcae_options.R R/save_gcae_setup.R R/save_labels_table.R R/save_model.R R/save_model_plot.R R/set_n_neurons_in_latent_layer.R R/summarise_gcae_input_data.R R/summarise_gcae_input_files.R R/uninstall_gcae.R README.md

Singularity

doc/README.md doc/installation.md

gcaer.Rproj

inst/extdata/M0.json

inst/extdata/f1_score_3.csv

inst/extdata/f1_score_5.csv

inst/extdata/f1_scores_pops_epoch_1.csv

inst/extdata/gcae_input_files_1.bed

inst/extdata/gcae_input_files_1.bim

inst/extdata/gcae_input_files_1.fam

inst/extdata/gcae_input_files_1.phe

inst/extdata/gcae_input_files_1_labels.csv

inst/extdata/gcae_input_files_2_0.bed

inst/extdata/gcae_input_files_2_0.bim

inst/extdata/gcae_input_files_2_0.fam

inst/extdata/gcae_input_files_2_0.phe

inst/extdata/gcae_input_files_2_0_labels.csv

inst/extdata/gcae_input_files_2_1000.bed

inst/extdata/gcae_input_files_2_1000.bim

inst/extdata/gcae_input_files_2_1000.fam

inst/extdata/gcae_input_files_2_1000.phe

inst/extdata/gcae_input_files_2_1000_labels.csv

inst/extdata/gcaer_issue_6_bin.bed

inst/extdata/gcaer_issue_6_bin.bim

inst/extdata/gcaer_issue_6_bin.fam

inst/extdata/gcaer_issue_6_bin.log

inst/extdata/gcaer_issue_6_bin.phe

inst/extdata/gcaer_issue_6_text.map

inst/extdata/gcaer_issue_6_text.ped

inst/extdata/genotype_concordances.csv

inst/extdata/losses_from_project.csv

inst/extdata/losses_from_train_t.csv

inst/extdata/losses_from_train_v.csv

inst/extdata/p0.json

inst/extdata/sim_data_1.bed

inst/extdata/sim_data_1.bim

inst/extdata/sim_data_1.fam

inst/extdata/sim_data_1.phe

inst/extdata/sim_data_1_labels.csv

inst/extdata/sim_data_issue_18_experiment_params.csv

inst/extdata/train_times.csv

man/figures/AppVeyor.png

man/figures/Codecov.png

man/figures/GitHubActions.png

man/figures/example_architecture.png

man/figures/example_dimred.png

man/figures/legend_HO_tiny.png

scripts/.gitignore

scripts/bug_report_create_conda.R scripts/bug_report_install_miniconda.R

scripts/build_cran.sh

scripts/build_singularity_container.sh

scripts/check_versions_match.R scripts/demo_container.R scripts/demo_container_create_gcae_input_files_2.R scripts/demo_container_lite.R

scripts/gcaer_report.sh

scripts/install_gcae.sh

scripts/install_gcae_prerequisites.sh

scripts/issue_6.R

scripts/issues/13/run.sh

scripts/run_container.sh

scripts/run_gcae.py

scripts/scribbles.R

scripts/tensorflow_example.py

scripts/upload_singularity_container.sh

tests/testthat.R

tests/testthat/.gitignore

tests/testthat/setting_1.bed

tests/testthat/setting_1.bim

tests/testthat/setting_1.fam

tests/testthat/setting_1.phe

tests/testthat/setting_1_labels.csv

vignettes/.gitignore

vignettes/example_plink.Rmd vignettes/example_tiny.Rmd

vignettes/example_tiny_ae_output.png

richelbilderbeek/gcaer documentation built on March 25, 2024, 3:08 p.m.

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richelbilderbeek/gcaer
Interface to GCAE

Files in richelbilderbeek/gcaer
Interface to GCAE

R Package Documentation

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richelbilderbeek/gcaer Interface to GCAE

Files in richelbilderbeek/gcaer Interface to GCAE

R Package Documentation

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We want your feedback!

richelbilderbeek/gcaer
Interface to GCAE

Files in richelbilderbeek/gcaer
Interface to GCAE