Man pages for eyeris
Flexible, Extensible, & Reproducible Pupillometry Preprocessing
| add_unique_event_identifiers | Add unique event identifiers to handle duplicate event... |
| add_unique_identifiers_to_df | Add unique identifiers to a single events data frame |
| bidsify | Save out pupil time series data in a BIDS-like structure |
| bin | Bin pupil time series by averaging within time bins |
| bin_pupil | Bin pupil data into specified time bins |
| boilerplate | Generate a reproducible, copy-and-paste-ready methods... |
| boilerplate_license_note | Creative Commons CC BY 4.0 license note for the methods... |
| bp_num | Format a numeric value for inclusion in prose |
| build_boilerplate_md | Build the Markdown methods boilerplate for an eyeris object |
| calc_euclidean_dist | Calculate Euclidean distance between points |
| calculate_epoched_confounds | Calculate confounds for epoched data |
| check_and_create_dir | Check and create directory if it doesn't exist |
| check_arrow | Check for Arrow availability |
| check_baseline_epoch_counts | Check baseline and epoch counts match |
| check_baseline_inputs | Check baseline input arguments |
| check_baseline_mean | Check if baseline mean is zero |
| check_column | Check if column exists in data frame |
| check_data | Check if object is of class eyeris |
| check_duckdb | Check for DuckDB availability |
| check_epoch_input | Check epoch input for plotting |
| check_epoch_manual_input_data | Check epoch manual input data structure |
| check_epoch_manual_input_dfs | Check epoch manual input data frame format |
| check_epoch_msg_values | Check epoch message values against available events |
| check_input | Check if input argument is provided |
| check_limits | Check limits in wildcard mode |
| check_pupil_cols | Check if pupil_raw column exists |
| check_start_end_timestamps | Check start and end timestamps are balanced |
| check_time_monotonic | Check time series monotonicity |
| clean_string | Clean string by removing non-alphanumeric characters |
| cleanup_run_dir_images | Clean up individual image files in run directories after HTML... |
| cleanup_source_figures_post_render | Clean up source figures after report generation |
| cleanup_temp_database | Cleanup temporary database |
| compute_baseline | Compute baseline correction for epoch data |
| compute_run_data_loss | Compute percent data lost for a given run/block |
| connect_eyeris_database | Create or connect to eyeris project database |
| convert_nested_dt | Convert nested data.table objects to tibbles |
| count_epochs | Count epochs and validate data is epoched |
| counter_bar | Create a counter progress bar |
| create_epoch_images_zip | Create zip file from epoch images |
| create_table_name | Create table name for eyeris data |
| create_temp_eyeris_database | Create temporary database for parallel processing |
| deblink | NA-pad blink events / missing data |
| deblink_pupil | Internal function to remove blink artifacts from pupil data |
| describe_boilerplate_step | Describe a single pipeline step as a methods-section sentence |
| describe_boilerplate_steps | Describe each recorded pipeline step as a methods-section... |
| detransient | Remove pupil samples that are physiologically unlikely |
| detransient_pupil | Internal function to remove transient artifacts from pupil... |
| detrend | Detrend the pupil time series |
| detrend_pupil | Internal function to detrend pupil data |
| disconnect_eyeris_database | Disconnect from eyeris database |
| downsample | Downsample pupil time series with anti-aliasing filtering |
| downsample_pupil | Internal function to downsample pupil data |
| draw_na_lines | Draw vertical lines at NA positions |
| draw_random_epochs | Draw random epochs for plotting |
| epoch | Epoch (and baseline) pupil data based on custom event message... |
| epoch_and_baseline_block | Block-by-block epoch and baseline handler |
| epoch_manually | Manually epoch using provided start/end data frames of... |
| epoch_only_start_msg | Epoch based on a single event message (without explicit... |
| epoch_pupil | Main epoching and baselining logic |
| epoch_start_end_msg | Epoch using a start and an end message (explicit timestamps) |
| epoch_start_msg_and_limits | Epoch using a start message with fixed limits around it |
| error_handler | Handle errors with custom error classes |
| evaluate_pipeline_step_params | Evaluate pipeline step parameters |
| export_confounds_to_csv | Export confounds data to CSV files and/or database |
| extract_baseline_epochs | Extract baseline epochs from time series data |
| extract_event_ids | Extract event identifiers from event messages |
| eyelink_asc_binocular_demo_dataset | Access example EyeLink .asc binocular mock dataset file... |
| eyelink_asc_demo_dataset | Access example EyeLink .asc demo dataset file provided by the... |
| eyelogger | Run 'eyeris' commands with automatic logging of R console's... |
| eyeris_color_palette | Default color palette for eyeris plotting functions |
| eyeris_db_collect | Extract and aggregate eyeris data across subjects from... |
| eyeris_db_connect | Connect to eyeris project database (user-facing) |
| eyeris_db_disconnect | Disconnect from eyeris database (user-facing) |
| eyeris_db_list_tables | List available tables in eyeris database |
| eyeris_db_read | Read eyeris data from database |
| eyeris_db_reconstruct_from_chunks | Reconstruct eyerisdb from chunked files |
| eyeris_db_split_for_sharing | Split eyerisdb for data sharing and distribution |
| eyeris_db_summary | Get summary statistics for eyeris database |
| eyeris_db_to_chunked_files | Export eyeris database to chunked files |
| eyeris_db_to_parquet | Split eyeris database into N parquet files by data type |
| eyeris-package | eyeris: Flexible, Extensible, & Reproducible Pupillometry... |
| filter_epochs | Filter epoch names from eyeris object |
| filter_task_run_dirs | Filter run-directory basenames to a single task |
| find_baseline_structure | Find baseline structure name for a given epoch |
| format_call_stack | Format call stack information for display |
| get_block_numbers | Extract block numbers from eyeris object or character vector |
| get_confounds_for_step | Calculate confounds for a single pupil data step |
| get_log_timestamp | Get formatted timestamp for logging |
| get_pre_decimation_block | Retrieve the preserved full-resolution data for a block |
| get_timestamps | Obtain timestamps from events data |
| glassbox | The opinionated "glass box" 'eyeris' pipeline |
| glassbox_internal | Internal glassbox function for processing individual eyes |
| index_metadata | Index metadata from data frame |
| interpolate | Interpolate missing pupil samples |
| interpolate_pupil | Interpolate missing pupil data using linear interpolation |
| is_binocular_object | Check if object is a binocular eyeris object |
| is_decimated_col | Identify decimated (downsample/bin) pupil columns |
| load_asc | Load and parse SR Research EyeLink '.asc' files |
| log_error | Log an error message and abort |
| logging | Standardized logging functions for eyeris |
| log_info | Log an informational message |
| log_message | Core logging function with timestamp and glue support |
| log_success | Log a success message |
| log_warn | Log a warning message |
| lpfilt | Lowpass filtering of time series data |
| lpfilt_pupil | Internal function to lowpass filter pupil data |
| make_baseline_label | Create baseline label for epoch data |
| make_bids_fname | Make a BIDS-compatible filename |
| make_epoch_label | Generate epoch label from events and data |
| make_gallery | Create interactive epoch gallery report |
| make_md_table | Create markdown table from data frame |
| make_md_table_multiline | Create multiline markdown table from data frame |
| make_prog_summary_plot | Create progressive preprocessing summary plot |
| make_report | Create eyeris report |
| make_run_dir_name | Build the canonical run-directory basename |
| merge_events_with_timeseries | Process event messages and merge with time series |
| merge_temp_database | Merge temporary database into main database |
| normalize_gaze_coords | Normalize gaze coordinates to screen-relative units |
| parse_call_stack | Parse call stack information |
| parse_eyelink_info | Parse EyeLink version and model information |
| pipeline_handler | Build a generic operation (extension) for the 'eyeris'... |
| plot_binocular_correlation | Plot binocular correlation between left and right eye data |
| plot_detrend_overlay | Internal helper to plot detrending overlay |
| plot.eyeris | Plot pre-processed pupil data from 'eyeris' |
| plot_gaze_heatmap | Create gaze heatmap of eye coordinates |
| plot_pupil_distribution | Plot pupil distribution histogram |
| plot_with_seed | Plot with seed handling for glassbox pipeline |
| print.eyeris_boilerplate | Print method for 'eyeris' methods boilerplate |
| print_lightbox_img_html | Print lightbox image HTML for zip-based gallery |
| print_lightbox_img_html_legacy | Print lightbox image HTML (legacy) |
| print_plots | Print plots in markdown format |
| process_chunked_query | Process large database query in chunks |
| process_epoch_and_baselines | Epoch and baseline processor |
| process_eyeris_data | Process eyeris data and create eyeris object |
| progress_bar | Create a progress bar for tracking operations |
| prompt_user | Prompt user for continuation |
| read_eyeris_parquet | Read parquet files back into R |
| render_report | Render R Markdown report |
| robust_plot | Robust plotting function with error handling |
| run_bidsify | Internal function to run bidsify on a single eye |
| run_dir_pattern | Regex matching run-directory basenames |
| sanitize_event_tag | Sanitize event tag string into canonical epoch label |
| save_detrend_plots | Save detrend plots for each block |
| save_progressive_summary_plots | Save progressive summary plots for each block |
| should_omit_parameter | Check if a parameter should be omitted from call stack... |
| should_plot_binoc_cors | Check if binocular correlations should be plotted |
| slice_epoch | Slice epoch from raw time series data |
| slice_epochs_no_limits | Slice epochs with no explicit limits |
| slice_epochs_with_limits | Slice epochs with explicit limits |
| slice_epoch_window | Slice a fixed time window out of a time series for previewing |
| speed | Calculate pupil speed using finite differences |
| summarize_confounds | Extract confounding variables calculated separately for each... |
| tag_blinks | Tag blinks in pupil data |
| tag_gaze_coords | Tag gaze coordinates as on/off screen |
| tick | Tick a progress bar |
| trim_pre_decimation_cols | Retain only the columns needed to plot pre-decimation... |
| write_csv_and_db | Write data to CSV and/or database (helper function) |
| write_eyeris_data_to_db | Write eyeris data to database |
| zip_and_cleanup_source_figures | Zip and cleanup source figure files |
| zscore | Z-score pupil time series data |
| zscore_pupil | Internal function to z-score pupil data |
