Import, Inspect, Analyse, and Report Gazepoint GP3 Exports

Documentation for package ‘gp3tools’ version 1.0.1

Help Pages

-- A --

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_window_denominators	Audit AOI window denominators before binomial modelling
audit_gazepoint_condition_quality_imbalance	Audit condition-level quality imbalance
audit_gazepoint_design_balance	Audit Gazepoint experimental design balance
audit_gazepoint_event_sync	Audit Gazepoint event and timing synchronisation
audit_gazepoint_exclusion_flow	Audit Gazepoint exclusion and retention flow
audit_gazepoint_gaze_signal_quality	Audit Gazepoint gaze-signal quality
audit_gazepoint_master	Audit a Gazepoint master sample table
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_stimulus_luminance	Audit stimulus luminance and brightness for Gazepoint studies

-- B --

baseline_correct_gazepoint_pupil

Baseline-correct Gazepoint pupil data

-- C --

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_real_data_readiness	Check real-data readiness before Gazepoint analysis
check_sampling_rate	Check sampling rate by group
classify_gazepoint_export	Classify a Gazepoint export
compare_gazepoint_nested_models	Compare nested Gazepoint models
compute_gazepoint_aoi_transition_matrix	Compute Gazepoint AOI transition matrices
compute_gazepoint_time_varying_transition_matrix	Compute time-varying Gazepoint transition matrices
compute_transition_matrix	Compute an AOI transition matrix
create_gazepoint_analysis_decision_audit	Create a final Gazepoint analysis-decision audit
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 --

diagnose_gazepoint_gamm	Diagnose GAM and BAM models
diagnose_gazepoint_glmm	Diagnose GLMM, LMM, and GLM models

-- E --

estimate_gazepoint_divergence_point	Estimate a bootstrapped divergence point between two Gazepoint time courses
export_gazepoint_master_audit	Export a Gazepoint master table, audit tables, and validation tables
export_gazepoint_model_tables	Export manuscript-ready model tables
export_gazepoint_tables	Export Gazepoint analysis tables to CSV files

-- F --

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_gca	Fit a Gazepoint Growth Curve Analysis mixed 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_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

-- I --

inspect_gazepoint_columns	Inspect Gazepoint columns
interpolate_gazepoint_pupil	Interpolate short missing gaps in Gazepoint pupil data
interpolate_gazepoint_pupil_pchip	Interpolate Gazepoint pupil data using PCHIP

-- P --

plot_gazepoint_aoi_gamm	Plot AOI time-course GAMM results
plot_gazepoint_aoi_transition_matrix	Plot Gazepoint AOI transition matrix
plot_gazepoint_aoi_verification	Plot AOI geometry for visual verification
plot_gazepoint_cluster_results	Plot cluster-based permutation results
plot_gazepoint_gca	Plot observed and fitted Growth Curve Analysis trajectories
plot_gazepoint_model_predictions	Plot observed summaries and model-implied predictions
plot_gazepoint_multiverse_results	Plot Gazepoint preprocessing multiverse results
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_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_hmm_data	Prepare Gazepoint AOI/state sequences for HMM-style workflows
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

-- R --

read_gazepoint	Read a Gazepoint all-gaze or fixation CSV export
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
run_gazepoint_aoi_multiverse	Run a Gazepoint AOI preprocessing multiverse
run_gazepoint_cluster_permutation	Run paired cluster-based permutation tests
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_model_leave_one_out	Run leave-one-unit model sensitivity analysis
run_gazepoint_pupil_multiverse	Run a Gazepoint pupil preprocessing multiverse
run_gazepoint_workflow	Run a complete Gazepoint analysis workflow

-- S --

save_gazepoint_plots	Save standard Gazepoint diagnostic plots
smooth_gazepoint_pupil	Smooth Gazepoint pupil data
standardise_gazepoint_names	Standardise Gazepoint column names
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_clusters	Summarise cluster-based permutation results
summarise_gazepoint_emmeans	Summarise estimated marginal means and contrasts
summarise_gazepoint_fixation_trials	Summarise Gazepoint fixation trial features
summarise_gazepoint_fixed_effects	Summarise fixed effects from fitted models
summarise_gazepoint_multiverse_results	Summarise Gazepoint preprocessing multiverse results
summarise_gazepoint_pupil	Summarise Gazepoint pupil data
summarise_gazepoint_pupil_trial_features	Summarise Gazepoint pupil trial-level features
summarise_gazepoint_pupil_windows	Summarise Gazepoint pupil responses within time windows
summarise_gazepoint_workflow	Summarise a Gazepoint workflow result
summarise_tracking_quality	Summarise Gazepoint tracking quality

-- 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_master

Validate a Gazepoint master sample table

-- W --

write_gazepoint_outputs

Write standard Gazepoint analysis outputs