Import, Inspect, Analyse, and Report Gazepoint GP3 Exports

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Documentation for package ‘gp3tools’ version 2.3.0

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A B C D E F G H I L M P R S T V W

-- A --

add_gazepoint_aoi Add rectangular AOI membership to gaze data
add_gazepoint_dynamic_aoi Add time-varying AOI membership to Gazepoint data
add_gazepoint_polygon_aoi Add polygon AOI membership to Gazepoint data
analyse_gazepoint_binocular_sensitivity Compare pupil-construction policies as a sensitivity analysis
analyze_gazepoint_window Summarise gaze or pupil measures in sliding time windows
as_gazepoint_master Convert Gazepoint all-gaze data to a master sample table
audit_gazepoint_aoi_coding_matrix Audit AOI coding against geometry
audit_gazepoint_aoi_geometry Audit AOI geometry definitions
audit_gazepoint_aoi_margin_sensitivity Audit AOI margin sensitivity
audit_gazepoint_aoi_overlap Audit AOI overlap
audit_gazepoint_aoi_screen_coverage Audit AOI coverage against screen bounds
audit_gazepoint_aoi_window_denominators Audit AOI window denominators before binomial modelling
audit_gazepoint_binocular_reconstruction Audit binocular reconstruction burden and imbalance
audit_gazepoint_condition_quality_imbalance Audit condition-level quality imbalance
audit_gazepoint_design_balance Audit Gazepoint experimental design balance
audit_gazepoint_dynamic_aoi_coverage Audit time-varying AOI coverage
audit_gazepoint_event_sync Audit Gazepoint event and timing synchronisation
audit_gazepoint_exclusion_flow Audit Gazepoint exclusion and retention flow
audit_gazepoint_face_quality Audit external facial-behaviour data quality
audit_gazepoint_face_sync Audit synchronisation between Gazepoint and external facial-behaviour data
audit_gazepoint_fixation_reliability Audit split-half reliability of fixation or AOI metrics
audit_gazepoint_gaze_signal_quality Audit Gazepoint gaze-signal quality
audit_gazepoint_master Audit a Gazepoint master sample table
audit_gazepoint_naming_consistency Audit British and American summary-function spellings
audit_gazepoint_post_exclusion_balance Audit post-exclusion condition balance
audit_gazepoint_pupil_baseline Audit Gazepoint pupil baseline quality
audit_gazepoint_pupil_drift Audit Gazepoint pupil drift
audit_gazepoint_pupil_gaps Audit Gazepoint pupil interpolation gaps
audit_gazepoint_pupil_imbalance Audit Gazepoint pupil preprocessing imbalance
audit_gazepoint_pupil_overlap_risk Audit Gazepoint pupil-response overlap risk
audit_gazepoint_pupil_reliability Audit split-half reliability for Gazepoint pupil outcomes
audit_gazepoint_screen_bounds Audit Gazepoint gaze coordinates against screen bounds
audit_gazepoint_stimulus_luminance Audit stimulus luminance and brightness for Gazepoint studies
audit_gazepoint_timecourse_grid Audit a Gazepoint time-course grid for cluster-permutation readiness

-- B --

baseline_correct_gazepoint_pupil Baseline-correct Gazepoint pupil data
benchmark_gazepoint_event_detectors Benchmark Gazepoint event detectors against reviewed events
benchmark_gazepoint_export_performance Benchmark gp3tools on increasingly large Gazepoint exports
bootstrap_gazepoint_scanpath_clusters Bootstrap scanpath-cluster stability
bootstrap_gazepoint_timecourse Bootstrap time-course summaries

-- C --

check_gazepoint_bayesian_readiness Check readiness of a Gazepoint-derived dataset for Bayesian or advanced models
check_gazepoint_file_pairs Check Gazepoint all-gaze and fixation file pairs
check_gazepoint_model_convergence Check model convergence
check_gazepoint_model_overdispersion Check model overdispersion
check_gazepoint_model_singularity Check model singularity
check_gazepoint_performance_regression Check gp3tools performance results against regression limits
check_gazepoint_real_data_readiness Check real-data readiness before Gazepoint analysis
check_sampling_rate Check sampling rate by group
classify_gazepoint_events_hmm Classify gaze events with a lightweight unsupervised HMM
classify_gazepoint_export Classify a Gazepoint export
clean_gazepoint_by_trackloss Flag or filter Gazepoint data by trackloss
cluster_gazepoint_scanpaths Cluster Gazepoint AOI scanpaths
collect_gazepoint_qc_summaries Collect Gazepoint QC summaries
combine_gazepoint_eyes Combine left and right Gazepoint eye channels
compare_gazepoint_event_detectors Compare Gazepoint event-detection workflows
compare_gazepoint_nested_models Compare nested Gazepoint models
compute_gazepoint_aoi_entropy Compute AOI entropy metrics
compute_gazepoint_aoi_sequence_metrics Compute AOI sequence metrics
compute_gazepoint_aoi_transition_matrix Compute Gazepoint AOI transition matrices
compute_gazepoint_saccade_metrics Compute basic saccade metrics from fixation coordinates
compute_gazepoint_scanpath_geometry Compute scanpath geometry features by subject and trial
compute_gazepoint_scanpath_similarity Compute AOI scanpath similarity
compute_gazepoint_sequence_complexity Compute AOI sequence complexity metrics
compute_gazepoint_sequence_distance Compute AOI sequence distance
compute_gazepoint_sequence_recurrence Compute simple categorical sequence recurrence metrics
compute_gazepoint_time_varying_transition_matrix Compute time-varying Gazepoint transition matrices
compute_gazepoint_transition_network_metrics Compute lightweight AOI transition-network metrics
compute_transition_matrix Compute an AOI transition matrix
construct_gazepoint_combined_pupil Construct an explicitly governed combined pupil signal
create_gazepoint_analysis_decision_audit Create a final Gazepoint analysis-decision audit
create_gazepoint_bayesian_sap Create a Bayesian ocular Statistical Analysis Plan checklist
create_gazepoint_brms_template Create brms formula and prior templates for Gazepoint-derived metrics
create_gazepoint_cross_package_report Create a combined gp3tools-gpbiometrics workflow report
create_gazepoint_event_review_template Create a manual event-review template
create_gazepoint_face_reporting_checklist Create a reporting checklist for external facial-behaviour workflows
create_gazepoint_hddm_fit_script Create a Python HDDM fitting script from a Gazepoint HDDM export
create_gazepoint_markovchain_object Create a Gazepoint AOI Markov-chain object
create_gazepoint_master Create a master long-format dataset from Gazepoint all-gaze data
create_gazepoint_preprocessing_multiverse Create a Gazepoint preprocessing multiverse
create_gazepoint_preprocessing_registry Create a Gazepoint pupil-preprocessing registry
create_gazepoint_report Create a Gazepoint HTML diagnostic report
create_gazepoint_reporting_checklist Create a Gazepoint reporting checklist

-- D --

detect_gazepoint_blinks Detect blink intervals from pupil measurements
detect_gazepoint_fixations_ivt Detect simple I-VT fixations from gaze samples
detect_gazepoint_fixations_velocity Detect fixations with a velocity-threshold algorithm
diagnose_gazepoint_binocular_pupil Diagnose binocular pupil quality and agreement
diagnose_gazepoint_cluster_design Diagnose the design assumptions of a Gazepoint cluster-permutation workflow
diagnose_gazepoint_gamm Diagnose GAM and BAM models
diagnose_gazepoint_glmm Diagnose GLMM, LMM, and GLM models
downsample_gazepoint_pupil Downsample pupil data by integer-factor aggregation

-- E --

estimate_gazepoint_cluster_offset Guardrail for exact cluster-offset estimation
estimate_gazepoint_cluster_onset Guardrail for exact cluster-onset estimation
estimate_gazepoint_divergence_point Estimate a bootstrapped divergence point between two Gazepoint time courses
export_gazepoint_cluster_results Export Gazepoint cluster-permutation results
export_gazepoint_heatmap_png Export a Gazepoint heatmap plot to PNG
export_gazepoint_master_audit Export a Gazepoint master table, audit tables, and validation tables
export_gazepoint_mne_cluster_input Export Gazepoint time-course data for MNE-style cluster workflows
export_gazepoint_model_tables Export manuscript-ready model tables
export_gazepoint_permuco_cluster_input Export Gazepoint time-course data for permuco-style cluster workflows
export_gazepoint_permutes_cluster_input Export Gazepoint time-course data for permutes-style cluster workflows
export_gazepoint_tables Export Gazepoint analysis tables to CSV files
export_gazepoint_to_bids Export Gazepoint data to a lightweight BIDS-style folder
extract_gazepoint_representative_scanpaths Extract representative scanpaths

-- F --

filter_gazepoint_cnn_uncertainty Apply uncertainty filtering to Bayesian CNN or webcam gaze outputs
fit_gazepoint_aoi_brms Fit an optional Bayesian AOI model with brms
fit_gazepoint_aoi_gamm Fit AOI time-course GAMMs
fit_gazepoint_aoi_model_sensitivity Fit AOI-window model-family sensitivity checks
fit_gazepoint_aoi_window_glmm Fit an AOI-window binomial GLMM
fit_gazepoint_binocular_calibration Fit audited cross-eye pupil calibration models
fit_gazepoint_brms_model Fit an optional brms model for Gazepoint-derived data
fit_gazepoint_face_window_lmm Fit a facial-behaviour window mixed or linear model
fit_gazepoint_gca Fit a Gazepoint Growth Curve Analysis mixed model
fit_gazepoint_multimodal_response_model Fit a multimodal response model
fit_gazepoint_pupil_gamm Fit a Gazepoint pupil GAMM
fit_gazepoint_pupil_pfe_gamm Fit a gaze-position-adjusted pupil GAMM sensitivity model
fit_gazepoint_pupil_window_lmm Fit confirmatory pupil-window linear mixed models
fit_gazepoint_pupil_window_sensitivity Run sensitivity models for confirmatory pupil-window analyses
fit_gazepoint_transition_count_nb_sensitivity Fit optional negative-binomial transition-count sensitivity models
flag_gazepoint_pupil Flag invalid, missing, implausible, and outlying Gazepoint pupil samples
flag_gazepoint_pupil_artifacts Flag Gazepoint pupil artifacts before interpolation
flag_gazepoint_pupil_hampel Flag pupil artifacts with a Hampel filter
flag_gazepoint_sequence_anomalies Flag unusual AOI sequences
flag_tracking_quality Flag low-quality Gazepoint recordings

-- G --

gazepoint_example_aoi_geometry Example AOI geometry table
gazepoint_example_aoi_windows Example AOI-window summary table
gazepoint_example_fixations Example Gazepoint fixation table
gazepoint_example_master Example Gazepoint master table
gazepoint_example_pupil_windows Example pupil-window summary table
gp3tools_naming_policy gp3tools user-facing naming policy
gp3tools_performance_limits Default performance limits for gp3tools export workflows

-- H --

harmonize_gazepoint_screen_coordinates Harmonize Gazepoint screen coordinates across resolutions

-- I --

impute_gazepoint_pupil_gp Impute missing pupil samples with a lightweight Gaussian-process smoother
inspect_gazepoint_columns Inspect Gazepoint columns
interpolate_gazepoint_blinks Interpolate pupil values across detected blink intervals
interpolate_gazepoint_pupil Interpolate short missing gaps in Gazepoint pupil data
interpolate_gazepoint_pupil_pchip Interpolate Gazepoint pupil data using PCHIP

-- L --

launch_gazepoint_qc_dashboard Launch or describe a lightweight QC dashboard

-- M --

mean_gazepoint_pupil Calculate mean binocular pupil size

-- P --

plot_gazepoint_aoi_gamm Plot AOI time-course GAMM results
plot_gazepoint_aoi_timeline Plot an AOI timeline
plot_gazepoint_aoi_transition_matrix Plot Gazepoint AOI transition matrix
plot_gazepoint_aoi_verification Plot AOI geometry for visual verification
plot_gazepoint_binocular_diagnostics Plot binocular pupil diagnostics, reconstruction, and sensitivity
plot_gazepoint_cluster_null_distribution Plot the cluster-permutation null distribution
plot_gazepoint_cluster_permutation Plot a Gazepoint cluster-permutation result
plot_gazepoint_cluster_results Plot cluster-based permutation results
plot_gazepoint_event_detector_agreement Plot event-detector comparison diagnostics
plot_gazepoint_event_detector_benchmark Plot event-detector benchmark diagnostics
plot_gazepoint_face_quality Plot external facial-behaviour data quality
plot_gazepoint_gca Plot observed and fitted Growth Curve Analysis trajectories
plot_gazepoint_heatmap Plot a Gazepoint gaze or fixation heatmap
plot_gazepoint_heatmap_overlay Plot a Gazepoint heatmap over a background image
plot_gazepoint_missingness_profile Plot a Gazepoint missingness profile
plot_gazepoint_model_predictions Plot observed summaries and model-implied predictions
plot_gazepoint_model_residuals Plot model residual diagnostics
plot_gazepoint_multiverse_results Plot Gazepoint preprocessing multiverse results
plot_gazepoint_phase_timeline Plot a Gazepoint task-phase timeline
plot_gazepoint_pupil_preprocessing Plot Gazepoint pupil preprocessing for one trial
plot_gazepoint_pupil_status Plot Gazepoint pupil preprocessing status
plot_gazepoint_pupil_timecourse Plot Gazepoint pupil time course
plot_gazepoint_qc_overview Plot a Gazepoint QC overview
plot_gazepoint_scanpath Plot a fixation scanpath
plot_gazepoint_scanpaths Plot multiple Gazepoint scanpaths
plot_gazepoint_scanpath_clusters Plot fitted scanpath clusters
plot_gazepoint_scanpath_cluster_stability Plot scanpath-cluster stability
plot_gazepoint_stimulus_layout_qc Plot stimulus-layout quality control
plot_gazepoint_time_series Plot a Gazepoint-style time series
plot_gazepoint_time_varying_effect Plot a time-varying effect curve
plot_sampling_rate Plot Gazepoint sampling-rate diagnostics
plot_tracking_quality Plot Gazepoint tracking-quality diagnostics
plot_transition_heatmap Plot an AOI transition heatmap
prepare_gazepoint_aoi_gamm_data Prepare AOI time-course data for GAMM analysis
prepare_gazepoint_aoi_glmm_data Prepare AOI-window data for binomial GLMMs
prepare_gazepoint_aoi_sequences Prepare Gazepoint AOI sequences
prepare_gazepoint_cluster_data Prepare time-course data for cluster-based permutation tests
prepare_gazepoint_eyetools_data Prepare Gazepoint master data for eyetools-style workflows
prepare_gazepoint_eyetrackingr_data Prepare Gazepoint master data for eyetrackingR-style workflows
prepare_gazepoint_fixation_aligned_data Prepare fixation- or saccade-contingent aligned Gazepoint data
prepare_gazepoint_gazer_data Prepare Gazepoint master data for gazer-style workflows
prepare_gazepoint_gca_data Prepare Gazepoint Growth Curve Analysis data
prepare_gazepoint_gpbiometrics_bridge Prepare gp3tools gaze output for a gpbiometrics workflow
prepare_gazepoint_hddm_export Prepare a trial-level export for Python HDDM
prepare_gazepoint_heatmap_data Prepare gaze or fixation coordinates for heatmap plotting
prepare_gazepoint_hmm_data Prepare Gazepoint AOI/state sequences for HMM-style workflows
prepare_gazepoint_multimodal_data Prepare multimodal Gazepoint and external face-window data
prepare_gazepoint_pupillometryr_data Prepare Gazepoint master data for pupillometryR-style workflows
prepare_gazepoint_pupil_gamm_data Prepare Gazepoint pupil GAMM data
prepare_gazepoint_pupil_window_model_data Prepare pupil-window data for confirmatory mixed models
prepare_gazepoint_semimarkov_data Prepare Gazepoint AOI sequences for semi-Markov modelling
prepare_gazepoint_timecourse_test_data Prepare time-course data for Gazepoint cluster-permutation testing
prepare_gazepoint_traminer_data Prepare AOI sequences for TraMineR-style workflows
preprocess_gazepoint_signals Run an integrated Gazepoint signal-preprocessing workflow

-- R --

read_gazepoint Read a Gazepoint all-gaze or fixation CSV export
read_gazepoint_face_export Read external facial-analysis exports
read_gazepoint_folder Read multiple Gazepoint CSV exports from a folder
read_gazepoint_summary Read a Gazepoint Analysis Data Summary export
recalibrate_gazepoint_gaze Offline gaze recalibration using known target coordinates
recommend_gazepoint_exclusions Recommend trial and participant exclusions
recommend_gazepoint_model_family Recommend model families for Gazepoint-derived metrics
reconstruct_gazepoint_binocular_pupil Reconstruct temporarily unavailable binocular pupil channels
regress_gazepoint_pupils Fuse binocular pupil traces using cross-eye regression
report_gazepoint_cluster_permutation Report a Gazepoint cluster-permutation result
report_gazepoint_face_qc Report external facial-behaviour QC and reporting readiness
report_gazepoint_missingness Report Gazepoint missingness
report_gazepoint_multiverse Report multiverse-analysis results
report_gazepoint_phase_coverage Report task-phase coverage
report_gazepoint_qc_overview Report Gazepoint QC overview
run_gazepoint_aoi_multiverse Run a Gazepoint AOI preprocessing multiverse
run_gazepoint_cluster_permutation Run paired cluster-based permutation tests
run_gazepoint_cluster_permutation_anova Guardrail for cluster-permutation ANOVA
run_gazepoint_cluster_permutation_covariate_adjusted Guardrail for covariate-adjusted cluster permutation
run_gazepoint_cluster_permutation_lmer Guardrail for mixed-model cluster permutation
run_gazepoint_cluster_permutation_parallel Guardrail for parallel cluster permutation
run_gazepoint_cluster_threshold_sensitivity Run threshold-sensitivity checks for Gazepoint cluster permutation
run_gazepoint_eyetools_fixation_detection Run optional eyetools fixation and saccade detection
run_gazepoint_gazer_crosscheck Run an optional gazeR pupil-preprocessing cross-check
run_gazepoint_gpbiometrics_workflow Run a tested gp3tools-to-gpbiometrics integration workflow
run_gazepoint_model_leave_one_out Run leave-one-unit model sensitivity analysis
run_gazepoint_multidimensional_cluster_permutation Guardrail for multidimensional cluster permutation
run_gazepoint_pupil_multiverse Run a Gazepoint pupil preprocessing multiverse
run_gazepoint_tfce Guardrail for threshold-free cluster enhancement
run_gazepoint_workflow Run a complete Gazepoint analysis workflow

-- S --

save_gazepoint_plots Save standard Gazepoint diagnostic plots
segment_gazepoint_task_phases Segment Gazepoint-style data into task phases
select_gazepoint_adaptive_trial Select the next adaptive trial from candidate stimuli
select_gazepoint_scanpath_clusters Select the number of scanpath clusters
simulate_gazepoint_cluster_timecourse_data Simulate simple Gazepoint cluster time-course data
simulate_gazepoint_data Simulate simple Gazepoint-style gaze data
simulate_gazepoint_fixations Simulate Gazepoint-like fixation events
simulate_gazepoint_pupil_data Simulate Gazepoint-like pupil data
smooth_gazepoint_coordinate Smooth gaze coordinates within independent sequences
smooth_gazepoint_pupil Smooth Gazepoint pupil data
standardise_gazepoint_names Standardise Gazepoint column names
standardize_gazepoint_face_columns Standardise external facial-analysis columns
stress_test_gazepoint_binocular_reconstruction Stress-test binocular reconstruction across missingness levels
summarise_aoi_samples Summarise sample-level AOI viewing
summarise_fixations Summarise fixation-level AOI metrics
summarise_gazepoint_aoi Summarise Gazepoint AOI metrics from gaze and fixation exports
summarise_gazepoint_aoi_entries Summarise Gazepoint AOI entry episodes
summarise_gazepoint_aoi_transitions Summarise Gazepoint AOI transition features
summarise_gazepoint_aoi_trial_features Summarise Gazepoint AOI trial features
summarise_gazepoint_aoi_windows Summarise Gazepoint AOI samples within predefined time windows
summarise_gazepoint_binocular_reporting Create manuscript-ready binocular reconstruction reporting
summarise_gazepoint_clusters Summarise cluster-based permutation results
summarise_gazepoint_coordinate_coverage British-spelling alias for 'summarize_gazepoint_coordinate_coverage()'
summarise_gazepoint_emmeans Summarise estimated marginal means and contrasts
summarise_gazepoint_event_detector_agreement Summarise agreement between event detectors
summarise_gazepoint_event_detector_benchmark Summarise an event-detector benchmark
summarise_gazepoint_face_quality Summarise external facial-behaviour data quality
summarise_gazepoint_face_reactivity British-spelling alias for 'summarize_gazepoint_face_reactivity()'
summarise_gazepoint_face_windows British-spelling alias for 'summarize_gazepoint_face_windows()'
summarise_gazepoint_fixation_trials Summarise Gazepoint fixation trial features
summarise_gazepoint_fixed_effects Summarise fixed effects from fitted models
summarise_gazepoint_markovchain Summarise a Gazepoint Markov-chain object
summarise_gazepoint_missingness Summarize missingness in Gazepoint-style data
summarise_gazepoint_multiverse_results Summarise Gazepoint preprocessing multiverse results
summarise_gazepoint_phase_coverage Summarize task-phase coverage
summarise_gazepoint_pupil Summarise Gazepoint pupil data
summarise_gazepoint_pupil_response_features British-spelling alias for 'summarize_gazepoint_pupil_response_features()'
summarise_gazepoint_pupil_trial_features Summarise Gazepoint pupil trial-level features
summarise_gazepoint_pupil_windows Summarise Gazepoint pupil responses within time windows
summarise_gazepoint_qc_status Summarize Gazepoint QC status
summarise_gazepoint_scanpath_cluster_stability Summarise scanpath-cluster stability
summarise_gazepoint_semimarkov Summarise Gazepoint semi-Markov data
summarise_gazepoint_time_clusters British-spelling alias for 'summarize_gazepoint_time_clusters()'
summarise_gazepoint_workflow Summarise a Gazepoint workflow result
summarise_tracking_quality Summarise Gazepoint tracking quality
summarize_gazepoint_coordinate_coverage Summarize gaze-coordinate coverage over a screen grid
summarize_gazepoint_face_quality Summarise external facial-behaviour data quality
summarize_gazepoint_face_reactivity Summarise facial-behaviour reactivity between two windows
summarize_gazepoint_face_windows Summarise external facial-behaviour data within analysis windows
summarize_gazepoint_missingness Summarize missingness in Gazepoint-style data
summarize_gazepoint_phase_coverage Summarize task-phase coverage
summarize_gazepoint_pupil_response_features Summarize pupil response features by subject and trial
summarize_gazepoint_qc_status Summarize Gazepoint QC status
summarize_gazepoint_time_clusters Summarize Gazepoint time clusters
sync_gazepoint_face_data Synchronise external facial-behaviour data with Gazepoint data

-- T --

tidy_gazepoint_model_summary Create a tidy model summary for manuscript tables
transform_gazepoint_aoi_empirical_logit Transform AOI proportions to empirical logits

-- V --

validate_gazepoint_binocular_reconstruction Validate binocular reconstruction using artificial monocular loss
validate_gazepoint_master Validate a Gazepoint master sample table

-- W --

write_gazepoint_naming_audit Write a gp3tools naming-consistency audit
write_gazepoint_outputs Write standard Gazepoint analysis outputs
write_gazepoint_performance_benchmark Write gp3tools performance benchmark tables