# Import, Inspect, Analyse, and Report Gazepoint GP3 Exports

## Documentation for package ‘gp3tools’ version 1.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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

## -- 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