Package: gp3tools 1.0.1

Stefanos Balaskas

gp3tools: Import, Inspect, Analyse, and Report Gazepoint GP3 Exports

Imports, inspects, cleans, summarises, models, and reports Gazepoint GP3 and Gazepoint Analysis CSV exports. Supports offline workflows for all-gaze, fixation, pupil, area-of-interest, transition, time-course, quality-audit, and manuscript-reporting analyses.

Authors:Stefanos Balaskas [aut, cre]

gp3tools_1.0.1.tar.gz
gp3tools_1.0.1.tar.gz(r-4.7-any)gp3tools_1.0.1.tar.gz(r-4.6-any)
gp3tools_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gp3tools/json (API)

# Install 'gp3tools' in R:
install.packages('gp3tools', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stefanosbalaskas/gp3tools/issues

Datasets:

On CRAN:

Conda:

3.00 score 124 exports 39 dependencies

Last updated from:9e62e21e96. Checks:4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK363
source / vignettesOK248
linux-release-x86_64OK360
wasm-releaseOK191

Exports:as_gazepoint_masteraudit_gazepoint_aoi_coding_matrixaudit_gazepoint_aoi_geometryaudit_gazepoint_aoi_margin_sensitivityaudit_gazepoint_aoi_overlapaudit_gazepoint_aoi_window_denominatorsaudit_gazepoint_condition_quality_imbalanceaudit_gazepoint_design_balanceaudit_gazepoint_event_syncaudit_gazepoint_exclusion_flowaudit_gazepoint_gaze_signal_qualityaudit_gazepoint_masteraudit_gazepoint_post_exclusion_balanceaudit_gazepoint_pupil_baselineaudit_gazepoint_pupil_driftaudit_gazepoint_pupil_gapsaudit_gazepoint_pupil_imbalanceaudit_gazepoint_pupil_overlap_riskaudit_gazepoint_pupil_reliabilityaudit_gazepoint_stimulus_luminancebaseline_correct_gazepoint_pupilcheck_gazepoint_file_pairscheck_gazepoint_model_convergencecheck_gazepoint_model_overdispersioncheck_gazepoint_model_singularitycheck_gazepoint_real_data_readinesscheck_sampling_rateclassify_gazepoint_exportcompare_gazepoint_nested_modelscompute_gazepoint_aoi_transition_matrixcompute_gazepoint_time_varying_transition_matrixcompute_transition_matrixcreate_gazepoint_analysis_decision_auditcreate_gazepoint_markovchain_objectcreate_gazepoint_mastercreate_gazepoint_preprocessing_multiversecreate_gazepoint_preprocessing_registrycreate_gazepoint_reportcreate_gazepoint_reporting_checklistdiagnose_gazepoint_gammdiagnose_gazepoint_glmmestimate_gazepoint_divergence_pointexport_gazepoint_master_auditexport_gazepoint_model_tablesexport_gazepoint_tablesfit_gazepoint_aoi_gammfit_gazepoint_aoi_model_sensitivityfit_gazepoint_aoi_window_glmmfit_gazepoint_gcafit_gazepoint_pupil_gammfit_gazepoint_pupil_pfe_gammfit_gazepoint_pupil_window_lmmfit_gazepoint_pupil_window_sensitivityfit_gazepoint_transition_count_nb_sensitivityflag_gazepoint_pupilflag_gazepoint_pupil_artifactsflag_gazepoint_pupil_hampelflag_tracking_qualityinspect_gazepoint_columnsinterpolate_gazepoint_pupilinterpolate_gazepoint_pupil_pchipplot_gazepoint_aoi_gammplot_gazepoint_aoi_transition_matrixplot_gazepoint_aoi_verificationplot_gazepoint_cluster_resultsplot_gazepoint_gcaplot_gazepoint_model_predictionsplot_gazepoint_multiverse_resultsplot_gazepoint_pupil_preprocessingplot_gazepoint_pupil_statusplot_gazepoint_pupil_timecourseplot_sampling_rateplot_tracking_qualityplot_transition_heatmapprepare_gazepoint_aoi_gamm_dataprepare_gazepoint_aoi_glmm_dataprepare_gazepoint_aoi_sequencesprepare_gazepoint_cluster_dataprepare_gazepoint_eyetools_dataprepare_gazepoint_eyetrackingr_dataprepare_gazepoint_fixation_aligned_dataprepare_gazepoint_gazer_dataprepare_gazepoint_gca_dataprepare_gazepoint_hmm_dataprepare_gazepoint_pupil_gamm_dataprepare_gazepoint_pupil_window_model_dataprepare_gazepoint_pupillometryr_dataprepare_gazepoint_semimarkov_dataread_gazepointread_gazepoint_folderread_gazepoint_summaryrecalibrate_gazepoint_gazerecommend_gazepoint_exclusionsrun_gazepoint_aoi_multiverserun_gazepoint_cluster_permutationrun_gazepoint_eyetools_fixation_detectionrun_gazepoint_gazer_crosscheckrun_gazepoint_model_leave_one_outrun_gazepoint_pupil_multiverserun_gazepoint_workflowsave_gazepoint_plotssmooth_gazepoint_pupilstandardise_gazepoint_namessummarise_aoi_samplessummarise_fixationssummarise_gazepoint_aoisummarise_gazepoint_aoi_entriessummarise_gazepoint_aoi_transitionssummarise_gazepoint_aoi_trial_featuressummarise_gazepoint_aoi_windowssummarise_gazepoint_clusterssummarise_gazepoint_emmeanssummarise_gazepoint_fixation_trialssummarise_gazepoint_fixed_effectssummarise_gazepoint_multiverse_resultssummarise_gazepoint_pupilsummarise_gazepoint_pupil_trial_featuressummarise_gazepoint_pupil_windowssummarise_gazepoint_workflowsummarise_tracking_qualitytidy_gazepoint_model_summarytransform_gazepoint_aoi_empirical_logitvalidate_gazepoint_masterwrite_gazepoint_outputs

Dependencies:bitbit64clicliprcpp11crayondplyrfarvergenericsggplot2gluegtablehmsisobandlabelinglifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangS7scalesstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

AOI, fixation, transition, and time-course workflow
title: "AOI, fixation, transition, and time-course workflow"output: rmarkdown::html_vignettevignette: >%\VignetteIndexEntry | Overview | 1. Load example data or import your own exports | 2. Validate the master table | 3. AOI geometry and coding checks | 4. AOI entries and AOI-window summaries | 5. AOI-window GLMM | 6. AOI, fixation, and transition features | 7. Advanced sequence-model preparation | 8. AOI time-course GAMM | 9. Diagnostics and reporting
Rendered fromaoi_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-06-29
Started: 2026-06-29

Pupil preprocessing and modelling workflow
title: "Pupil preprocessing and modelling workflow"output: rmarkdown::html_vignettevignette: >%\VignetteIndexEntry | Overview | 1. Load example data or import your own exports | 2. Validate the master table | 3. Light pupil preprocessing branch | 4. Conservative artifact-cleaned branch | 5. Pupil quality audits | 6. Reliability and sensitivity checks | 7. Confirmatory pupil-window LMM | 8. Pupil time-course models | 9. Cluster permutation and divergence point | 10. Reporting
Rendered frompupil_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-06-29
Started: 2026-06-29

Readme and manuals

Help Manual

Help pageTopics
Convert Gazepoint all-gaze data to a master sample tableas_gazepoint_master
Audit AOI coding against geometryaudit_gazepoint_aoi_coding_matrix
Audit AOI geometry definitionsaudit_gazepoint_aoi_geometry
Audit AOI margin sensitivityaudit_gazepoint_aoi_margin_sensitivity
Audit AOI overlapaudit_gazepoint_aoi_overlap
Audit AOI window denominators before binomial modellingaudit_gazepoint_aoi_window_denominators
Audit condition-level quality imbalanceaudit_gazepoint_condition_quality_imbalance
Audit Gazepoint experimental design balanceaudit_gazepoint_design_balance
Audit Gazepoint event and timing synchronisationaudit_gazepoint_event_sync
Audit Gazepoint exclusion and retention flowaudit_gazepoint_exclusion_flow
Audit Gazepoint gaze-signal qualityaudit_gazepoint_gaze_signal_quality
Audit a Gazepoint master sample tableaudit_gazepoint_master
Audit post-exclusion condition balanceaudit_gazepoint_post_exclusion_balance
Audit Gazepoint pupil baseline qualityaudit_gazepoint_pupil_baseline
Audit Gazepoint pupil driftaudit_gazepoint_pupil_drift
Audit Gazepoint pupil interpolation gapsaudit_gazepoint_pupil_gaps
Audit Gazepoint pupil preprocessing imbalanceaudit_gazepoint_pupil_imbalance
Audit Gazepoint pupil-response overlap riskaudit_gazepoint_pupil_overlap_risk
Audit split-half reliability for Gazepoint pupil outcomesaudit_gazepoint_pupil_reliability
Audit stimulus luminance and brightness for Gazepoint studiesaudit_gazepoint_stimulus_luminance
Baseline-correct Gazepoint pupil databaseline_correct_gazepoint_pupil
Check Gazepoint all-gaze and fixation file pairscheck_gazepoint_file_pairs
Check model convergencecheck_gazepoint_model_convergence
Check model overdispersioncheck_gazepoint_model_overdispersion
Check model singularitycheck_gazepoint_model_singularity
Check real-data readiness before Gazepoint analysischeck_gazepoint_real_data_readiness
Check sampling rate by groupcheck_sampling_rate
Classify a Gazepoint exportclassify_gazepoint_export
Compare nested Gazepoint modelscompare_gazepoint_nested_models
Compute Gazepoint AOI transition matricescompute_gazepoint_aoi_transition_matrix
Compute time-varying Gazepoint transition matricescompute_gazepoint_time_varying_transition_matrix
Compute an AOI transition matrixcompute_transition_matrix
Create a final Gazepoint analysis-decision auditcreate_gazepoint_analysis_decision_audit
Create a Gazepoint AOI Markov-chain objectcreate_gazepoint_markovchain_object
Create a master long-format dataset from Gazepoint all-gaze datacreate_gazepoint_master
Create a Gazepoint preprocessing multiversecreate_gazepoint_preprocessing_multiverse
Create a Gazepoint pupil-preprocessing registrycreate_gazepoint_preprocessing_registry
Create a Gazepoint HTML diagnostic reportcreate_gazepoint_report
Create a Gazepoint reporting checklistcreate_gazepoint_reporting_checklist
Diagnose GAM and BAM modelsdiagnose_gazepoint_gamm
Diagnose GLMM, LMM, and GLM modelsdiagnose_gazepoint_glmm
Estimate a bootstrapped divergence point between two Gazepoint time coursesestimate_gazepoint_divergence_point
Export a Gazepoint master table, audit tables, and validation tablesexport_gazepoint_master_audit
Export manuscript-ready model tablesexport_gazepoint_model_tables
Export Gazepoint analysis tables to CSV filesexport_gazepoint_tables
Fit AOI time-course GAMMsfit_gazepoint_aoi_gamm
Fit AOI-window model-family sensitivity checksfit_gazepoint_aoi_model_sensitivity
Fit an AOI-window binomial GLMMfit_gazepoint_aoi_window_glmm
Fit a Gazepoint Growth Curve Analysis mixed modelfit_gazepoint_gca
Fit a Gazepoint pupil GAMMfit_gazepoint_pupil_gamm
Fit a gaze-position-adjusted pupil GAMM sensitivity modelfit_gazepoint_pupil_pfe_gamm
Fit confirmatory pupil-window linear mixed modelsfit_gazepoint_pupil_window_lmm
Run sensitivity models for confirmatory pupil-window analysesfit_gazepoint_pupil_window_sensitivity
Fit optional negative-binomial transition-count sensitivity modelsfit_gazepoint_transition_count_nb_sensitivity
Flag invalid, missing, implausible, and outlying Gazepoint pupil samplesflag_gazepoint_pupil
Flag Gazepoint pupil artifacts before interpolationflag_gazepoint_pupil_artifacts
Flag pupil artifacts with a Hampel filterflag_gazepoint_pupil_hampel
Flag low-quality Gazepoint recordingsflag_tracking_quality
Example AOI geometry tablegazepoint_example_aoi_geometry
Example AOI-window summary tablegazepoint_example_aoi_windows
Example Gazepoint fixation tablegazepoint_example_fixations
Example Gazepoint master tablegazepoint_example_master
Example pupil-window summary tablegazepoint_example_pupil_windows
Inspect Gazepoint columnsinspect_gazepoint_columns
Interpolate short missing gaps in Gazepoint pupil datainterpolate_gazepoint_pupil
Interpolate Gazepoint pupil data using PCHIPinterpolate_gazepoint_pupil_pchip
Plot AOI time-course GAMM resultsplot_gazepoint_aoi_gamm
Plot Gazepoint AOI transition matrixplot_gazepoint_aoi_transition_matrix
Plot AOI geometry for visual verificationplot_gazepoint_aoi_verification
Plot cluster-based permutation resultsplot_gazepoint_cluster_results
Plot observed and fitted Growth Curve Analysis trajectoriesplot_gazepoint_gca
Plot observed summaries and model-implied predictionsplot_gazepoint_model_predictions
Plot Gazepoint preprocessing multiverse resultsplot_gazepoint_multiverse_results
Plot Gazepoint pupil preprocessing for one trialplot_gazepoint_pupil_preprocessing
Plot Gazepoint pupil preprocessing statusplot_gazepoint_pupil_status
Plot Gazepoint pupil time courseplot_gazepoint_pupil_timecourse
Plot Gazepoint sampling-rate diagnosticsplot_sampling_rate
Plot Gazepoint tracking-quality diagnosticsplot_tracking_quality
Plot an AOI transition heatmapplot_transition_heatmap
Prepare AOI time-course data for GAMM analysisprepare_gazepoint_aoi_gamm_data
Prepare AOI-window data for binomial GLMMsprepare_gazepoint_aoi_glmm_data
Prepare Gazepoint AOI sequencesprepare_gazepoint_aoi_sequences
Prepare time-course data for cluster-based permutation testsprepare_gazepoint_cluster_data
Prepare Gazepoint master data for eyetools-style workflowsprepare_gazepoint_eyetools_data
Prepare Gazepoint master data for eyetrackingR-style workflowsprepare_gazepoint_eyetrackingr_data
Prepare fixation- or saccade-contingent aligned Gazepoint dataprepare_gazepoint_fixation_aligned_data
Prepare Gazepoint master data for gazer-style workflowsprepare_gazepoint_gazer_data
Prepare Gazepoint Growth Curve Analysis dataprepare_gazepoint_gca_data
Prepare Gazepoint AOI/state sequences for HMM-style workflowsprepare_gazepoint_hmm_data
Prepare Gazepoint pupil GAMM dataprepare_gazepoint_pupil_gamm_data
Prepare pupil-window data for confirmatory mixed modelsprepare_gazepoint_pupil_window_model_data
Prepare Gazepoint master data for pupillometryR-style workflowsprepare_gazepoint_pupillometryr_data
Prepare Gazepoint AOI sequences for semi-Markov modellingprepare_gazepoint_semimarkov_data
Read a Gazepoint all-gaze or fixation CSV exportread_gazepoint
Read multiple Gazepoint CSV exports from a folderread_gazepoint_folder
Read a Gazepoint Analysis Data Summary exportread_gazepoint_summary
Offline gaze recalibration using known target coordinatesrecalibrate_gazepoint_gaze
Recommend trial and participant exclusionsrecommend_gazepoint_exclusions
Run a Gazepoint AOI preprocessing multiverserun_gazepoint_aoi_multiverse
Run paired cluster-based permutation testsrun_gazepoint_cluster_permutation
Run optional eyetools fixation and saccade detectionrun_gazepoint_eyetools_fixation_detection
Run an optional gazeR pupil-preprocessing cross-checkrun_gazepoint_gazer_crosscheck
Run leave-one-unit model sensitivity analysisrun_gazepoint_model_leave_one_out
Run a Gazepoint pupil preprocessing multiverserun_gazepoint_pupil_multiverse
Run a complete Gazepoint analysis workflowrun_gazepoint_workflow
Save standard Gazepoint diagnostic plotssave_gazepoint_plots
Smooth Gazepoint pupil datasmooth_gazepoint_pupil
Standardise Gazepoint column namesstandardise_gazepoint_names
Summarise sample-level AOI viewingsummarise_aoi_samples
Summarise fixation-level AOI metricssummarise_fixations
Summarise Gazepoint AOI metrics from gaze and fixation exportssummarise_gazepoint_aoi
Summarise Gazepoint AOI entry episodessummarise_gazepoint_aoi_entries
Summarise Gazepoint AOI transition featuressummarise_gazepoint_aoi_transitions
Summarise Gazepoint AOI trial featuressummarise_gazepoint_aoi_trial_features
Summarise Gazepoint AOI samples within predefined time windowssummarise_gazepoint_aoi_windows
Summarise cluster-based permutation resultssummarise_gazepoint_clusters
Summarise estimated marginal means and contrastssummarise_gazepoint_emmeans
Summarise Gazepoint fixation trial featuressummarise_gazepoint_fixation_trials
Summarise fixed effects from fitted modelssummarise_gazepoint_fixed_effects
Summarise Gazepoint preprocessing multiverse resultssummarise_gazepoint_multiverse_results
Summarise Gazepoint pupil datasummarise_gazepoint_pupil
Summarise Gazepoint pupil trial-level featuressummarise_gazepoint_pupil_trial_features
Summarise Gazepoint pupil responses within time windowssummarise_gazepoint_pupil_windows
Summarise a Gazepoint workflow resultsummarise_gazepoint_workflow
Summarise Gazepoint tracking qualitysummarise_tracking_quality
Create a tidy model summary for manuscript tablestidy_gazepoint_model_summary
Transform AOI proportions to empirical logitstransform_gazepoint_aoi_empirical_logit
Validate a Gazepoint master sample tablevalidate_gazepoint_master
Write standard Gazepoint analysis outputswrite_gazepoint_outputs