Man pages for PennStateDEPENdLab/experiment_pipeline
Generates data markdown for NeuroMap Task
| acq2hdf5 | Calls the acq2hdf5 command (python bioread package) to... |
| acq2txt | Calls the acq2txt command (python bioread package) to convert... |
| augment_ttl_details | Recode TTL code vector to reflect changes in the value,... |
| biopac_hdf5_to_dataframe | Read a BIOPAC hdf5 file as a data.frame |
| Block-class | Class Block |
| block.validity | Checks validity of block object |
| boxcar_smooth | Apply a moving average filter to a time series by convolution |
| connect.blocks | Connects blocks |
| correct_peaks | Adjust a set of detected peaks to coincide with local signal... |
| create.block | Create a block object |
| create.log | Creates a log object that outputs to the console. |
| downsample_digital_timeseries | This function downsamples a vector of integers by keeping the... |
| downsample_digital_timeseries_r | here's a pure R version of downsampling a categorical/digital... |
| downsample_physio | downsample_physio |
| ecg_detect_beats | This function accepts a single ecg trace already scaled to... |
| ecg_stripplot | A convenience function for plotting ECG time series and QRS... |
| edf2asc | Call SRR "edf2asc" command line utility to do some work. |
| ep.eye_add_aois | Add AOI information to gaze data |
| ep.eye_build_msg_seq | Build out expected message sequences within config file. |
| ep.eye_check_msg_order | Check ordering of messages |
| ep.eye_check_requested_msg | Compare requested (from config) and extracted (from... |
| ep.eye_cleanup | Eye Data Preprocessing and Cleanup |
| ep.eye_collapse_time | Collapse timing to one row per time (paste multiple messages... |
| ep.eye_default_options | Get Default Eye-Tracking Processing Options |
| ep.eye_display_steps | Display Steps for Eye-Tracking Data Processing |
| ep.eye_downsample | Downsample gaze and/or pupil data |
| ep.eye_gen_aoi_look | Attaches AOI information to gaze data |
| ep.eye_gen_aoi_ref | Generate AOI-reference object |
| ep.eye_get_session_length | Tag ep.eye metadata with the length of the recording session |
| ep.eye_inherit_btw_ev | Interface with messages passed with not recording |
| ep.eye_initialize | Initialize an ep.eye object |
| ep.eye_interp_pupil | Interpolate over missing pupil data |
| ep.eye_meta_check | Check ep.eye metadata |
| ep.eye_msg_report | Generate a report of all eyetracker messages for user review. |
| ep.eye_parse_event_info | Extract descriptive information about events based on... |
| ep.eye_parse_events | Parse task config file, extracting essential task information |
| ep.eye_preprocess_gaze | Preprocess gaze data |
| ep.eye_preprocess_pupil | Preprocess Pupil Data |
| ep.eye_process_subject | Read and process a single .edf file. |
| ep.eye_raw_sample_continuity_check | Tag ep.eye metadata with the length of the recording session |
| ep.eye_rm_crinfo | Remove useless cr.info column. |
| ep.eye_rm_impossible | Remove values outside of screen dimensions |
| ep.eye_setup_proc_config | Read and setup processing configuration |
| ep.eye_setup_structure | Setup ep.eye structure |
| ep.eye_shift_timing | Shift timing of ep.eye object to 0 start point |
| ep.eye_store_between_event_messages | Extract messages that are passed between recording events. |
| ep.eye_tag_event_time | Tag Event Time for Eye Data |
| ep.eye_unify_gaze_events | Unify gaze events with raw data |
| ep.eye_unify_raw_msg | Add et.msg column to raw data |
| ep.eye_validate_msg_seq | Validate the presence of task-general messages by event |
| experiment.pipeline | R package for processing multi-modal experiment data |
| find.unprocessed | Finds Unprocessed files based on file names |
| get.block.name | Get name of block object |
| get.callback | Get callback function of block object |
| get.input.blocks | Get input of block object |
| get.output.blocks | Get output of block object |
| get.system | Get System Info |
| ibi_qa | Conduct basic QA checks on IBI time series of ecg signal. |
| import.all | Pipeline Block Function |
| import.dtk | Imports Defend the Kingdom data |
| import.mat | Imports MAT files |
| import.neighborhood | Imports Neighborhood data |
| import.shrooms | Imports shrooms data |
| import_subject | function for reading multimodal data files for a subject... |
| import_wfdb_annotations | Helper function to read single-channel WFDB annotations into... |
| import.yaml | Read YAML Config File |
| init.clusters | Initialize clusters |
| init_eyelog | Initializes .elog |
| log_chunk_header | Print a standardized chunk header |
| log.debug | Logs message as a debug using log object |
| log.error | Logs message as a error using log object |
| log.info | Logs message as an info using log object |
| log.warn | Logs message as a warning using log object |
| read_acq | Import Acqknowledge ACQ files into data.frames |
| read_acq_txt | Read a text file generated by acq2txt |
| read_behav | general wrapper for reading behavioral files into the package |
| read_behav_vending | Import Quail, Morris, Balleine Vending Machine task data |
| read_edf | Import EDF File |
| read_physio | general wrapper for reading physio data into the package |
| read_physio_neighborhood | Read physiology from neighborhood task |
| run.block | Runs a block and follows the output until completion |
| set.block.name | Set name of block object |
| set.callback | Set callback function of block object |
| set.input.block | Set input of block object |
| set.output.blocks | Set output of block object |
| shift_peaks | Helper function for correct_peaks. Return the shifted peaks... |
| splice_physio | Function to splice an ep.physio object to a section... |
| terminate.clusters | Terminates clusters |
| tryCatch.ep | TryCatch function to run subroutines with ease and... |
| validate_exp_yaml | Validate experimental config file |
