Man pages for PennStateDEPENdLab/experiment.pipeline
Generates data markdown for NeuroMap Task

acq2hdf5Calls the acq2hdf5 command (python bioread package) to...
acq2txtCalls the acq2txt command (python bioread package) to convert...
augment_ttl_detailsRecode TTL code vector to reflect changes in the value,...
biopac_hdf5_to_dataframeRead a BIOPAC hdf5 file as a data.frame
Block-classClass Block
block.validityChecks validity of block object
boxcar_smoothApply a moving average filter to a time series by convolution
connect.blocksConnects blocks
correct_peaksAdjust a set of detected peaks to coincide with local signal...
create.blockCreate a block object
create.logCreates a log object that outputs to the console.
downsample_digital_timeseriesThis function downsamples a vector of integers by keeping the...
downsample_digital_timeseries_rhere's a pure R version of downsampling a categorical/digital...
downsample_physiodownsample_physio
ecg_detect_beatsThis function accepts a single ecg trace already scaled to...
ecg_stripplotA convenience function for plotting ECG time series and QRS...
edf2ascCall SRR "edf2asc" command line utility to do some work.
ep.eye_add_aoisAdd AOI information to gaze data
ep.eye_build_msg_seqBuild out expected message sequences within config file.
ep.eye_check_msg_orderCheck ordering of messages
ep.eye_check_requested_msgCompare requested (from config) and extracted (from...
ep.eye_cleanupEye Data Preprocessing and Cleanup
ep.eye_collapse_timeCollapse timing to one row per time (paste multiple messages...
ep.eye_default_optionsGet Default Eye-Tracking Processing Options
ep.eye_display_stepsDisplay Steps for Eye-Tracking Data Processing
ep.eye_downsampleDownsample gaze and/or pupil data
ep.eye_gen_aoi_lookAttaches AOI information to gaze data
ep.eye_gen_aoi_refGenerate AOI-reference object
ep.eye_get_session_lengthTag ep.eye metadata with the length of the recording session
ep.eye_inherit_btw_evInterface with messages passed with not recording
ep.eye_initializeInitialize an ep.eye object
ep.eye_interp_pupilInterpolate over missing pupil data
ep.eye_meta_checkCheck ep.eye metadata
ep.eye_msg_reportGenerate a report of all eyetracker messages for user review.
ep.eye_parse_event_infoExtract descriptive information about events based on...
ep.eye_parse_eventsParse task config file, extracting essential task information
ep.eye_preprocess_gazePreprocess gaze data
ep.eye_preprocess_pupilPreprocess Pupil Data
ep.eye_process_subjectRead and process a single .edf file.
ep.eye_raw_sample_continuity_checkTag ep.eye metadata with the length of the recording session
ep.eye_rm_crinfoRemove useless cr.info column.
ep.eye_rm_impossibleRemove values outside of screen dimensions
ep.eye_setup_proc_configRead and setup processing configuration
ep.eye_setup_structureSetup ep.eye structure
ep.eye_shift_timingShift timing of ep.eye object to 0 start point
ep.eye_store_between_event_messagesExtract messages that are passed between recording events.
ep.eye_tag_event_timeTag Event Time for Eye Data
ep.eye_unify_gaze_eventsUnify gaze events with raw data
ep.eye_unify_raw_msgAdd et.msg column to raw data
ep.eye_validate_msg_seqValidate the presence of task-general messages by event
experiment.pipelineR package for processing multi-modal experiment data
find.unprocessedFinds Unprocessed files based on file names
get.block.nameGet name of block object
get.callbackGet callback function of block object
get.input.blocksGet input of block object
get.output.blocksGet output of block object
get.systemGet System Info
ibi_qaConduct basic QA checks on IBI time series of ecg signal.
import.allPipeline Block Function
import.dtkImports Defend the Kingdom data
import.matImports MAT files
import.neighborhoodImports Neighborhood data
import.shroomsImports shrooms data
import_subjectfunction for reading multimodal data files for a subject...
import_wfdb_annotationsHelper function to read single-channel WFDB annotations into...
import.yamlRead YAML Config File
init.clustersInitialize clusters
init_eyelogInitializes .elog
log_chunk_headerPrint a standardized chunk header
log.debugLogs message as a debug using log object
log.errorLogs message as a error using log object
log.infoLogs message as an info using log object
log.warnLogs message as a warning using log object
read_acqImport Acqknowledge ACQ files into data.frames
read_acq_txtRead a text file generated by acq2txt
read_behavgeneral wrapper for reading behavioral files into the package
read_behav_vendingImport Quail, Morris, Balleine Vending Machine task data
read_edfImport EDF File
read_physiogeneral wrapper for reading physio data into the package
read_physio_neighborhoodRead physiology from neighborhood task
run.blockRuns a block and follows the output until completion
set.block.nameSet name of block object
set.callbackSet callback function of block object
set.input.blockSet input of block object
set.output.blocksSet output of block object
shift_peaksHelper function for correct_peaks. Return the shifted peaks...
splice_physioFunction to splice an ep.physio object to a section...
terminate.clustersTerminates clusters
tryCatch.epTryCatch function to run subroutines with ease and...
validate_exp_yamlValidate experimental config file
PennStateDEPENdLab/experiment.pipeline documentation built on Sept. 4, 2024, 10:55 a.m.