@brainpilot/skills 0.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/index.d.ts +6 -0
- package/dist/index.d.ts.map +1 -0
- package/dist/index.js +28 -0
- package/dist/index.js.map +1 -0
- package/package.json +35 -0
- package/skills/01_Meta-Skills/contribute-skill/SKILL.md +277 -0
- package/skills/01_Meta-Skills/contribute-skills-via-pr/SKILL.md +163 -0
- package/skills/01_Meta-Skills/paper-to-skill/SKILL.md +435 -0
- package/skills/01_Meta-Skills/paper-to-skill/references/extraction-guide.md +286 -0
- package/skills/01_Meta-Skills/paper-to-skill/references/skill-template.md +250 -0
- package/skills/01_Meta-Skills/repo-to-skill/SKILL.md +289 -0
- package/skills/01_Meta-Skills/share-case/SKILL.md +253 -0
- package/skills/01_Meta-Skills/share-usage/README.md +63 -0
- package/skills/01_Meta-Skills/share-usage/SKILL.md +395 -0
- package/skills/01_Meta-Skills/verify-skill/SKILL.md +331 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/SKILL.md +194 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/effect-sizes.md +352 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/sample-size-guide.md +407 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-statistics/SKILL.md +361 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-statistics/references/common-analyses.md +517 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-visualization/SKILL.md +292 -0
- package/skills/02_Cross-Domain_Foundation/cogsci-visualization/references/plot-recipes.md +709 -0
- package/skills/02_Cross-Domain_Foundation/research-literacy/SKILL.md +286 -0
- package/skills/02_Cross-Domain_Foundation/research-literacy/references/common-assumptions.md +320 -0
- package/skills/02_Cross-Domain_Foundation/research-literacy/references/planning-template.md +143 -0
- package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/SKILL.md +197 -0
- package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/references/instruction-templates.md +60 -0
- package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/SKILL.md +246 -0
- package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/classic-paradigms.md +435 -0
- package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/design-principles.md +256 -0
- package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/SKILL.md +270 -0
- package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/references/lavaan-templates.md +172 -0
- package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/SKILL.md +238 -0
- package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/references/scoring-rubric.md +143 -0
- package/skills/03_Cognitive_Psychology/drift-diffusion-model/SKILL.md +203 -0
- package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/fitting-guide.md +571 -0
- package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/model-variants.md +427 -0
- package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/SKILL.md +310 -0
- package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/references/ez-diffusion-formulas.md +137 -0
- package/skills/03_Cognitive_Psychology/signal-detection-analysis/SKILL.md +300 -0
- package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/application-guide.md +278 -0
- package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/sdt-formulas.md +318 -0
- package/skills/03_Cognitive_Psychology/visual-search-array-generator/SKILL.md +283 -0
- package/skills/03_Cognitive_Psychology/visual-search-array-generator/references/array-generation-parameters.yaml +111 -0
- package/skills/04_Psycholinguistics/reading-time-analysis/SKILL.md +301 -0
- package/skills/04_Psycholinguistics/reading-time-analysis/references/measure-computation-guide.md +195 -0
- package/skills/04_Psycholinguistics/self-paced-reading-designer/SKILL.md +257 -0
- package/skills/04_Psycholinguistics/self-paced-reading-designer/references/analysis-guide.md +356 -0
- package/skills/04_Psycholinguistics/self-paced-reading-designer/references/region-segmentation.md +266 -0
- package/skills/04_Psycholinguistics/sentence-stimulus-norming/SKILL.md +346 -0
- package/skills/04_Psycholinguistics/sentence-stimulus-norming/references/lexical-databases-guide.md +184 -0
- package/skills/05_EEG_ERP/eeg-paradigm-designer/SKILL.md +226 -0
- package/skills/05_EEG_ERP/eeg-paradigm-designer/references/component-paradigm-map.md +276 -0
- package/skills/05_EEG_ERP/eeg-paradigm-designer/references/timing-parameters.md +244 -0
- package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/SKILL.md +367 -0
- package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/references/parameter-lookup-tables.md +138 -0
- package/skills/05_EEG_ERP/erp-analysis/SKILL.md +185 -0
- package/skills/05_EEG_ERP/erp-analysis/references/erp-components.md +447 -0
- package/skills/05_EEG_ERP/erp-analysis/references/preprocessing-pipeline.md +277 -0
- package/skills/05_EEG_ERP/erp-analysis/references/statistical-approaches.md +351 -0
- package/skills/05_EEG_ERP/mne-python-guide/SKILL.md +174 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/decoding.md +178 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/io_formats.md +160 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/preprocessing.md +259 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/simulation.md +173 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/source_localization.md +234 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/statistics.md +196 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/time_frequency.md +165 -0
- package/skills/05_EEG_ERP/mne-python-guide/references/visualization.md +175 -0
- package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/SKILL.md +317 -0
- package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
- package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/SKILL.md +296 -0
- package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/design-matrix-guide.md +214 -0
- package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/statistical-inference.md +288 -0
- package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/SKILL.md +274 -0
- package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/quality-control.md +336 -0
- package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/step-by-step-pipeline.md +380 -0
- package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/SKILL.md +264 -0
- package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/references/design-optimization-examples.md +114 -0
- package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/SKILL.md +273 -0
- package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/decoding-methods.md +170 -0
- package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/rsa-guide.md +266 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/SKILL.md +123 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/database-subjects.md +179 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/dataset-types.md +208 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/freesurfer-fmriprep.md +162 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mapping-transforms.md +181 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mni-utils.md +207 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/surface-analysis.md +219 -0
- package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/visualization.md +251 -0
- package/skills/07_Computational_Modeling/act-r-model-builder/SKILL.md +297 -0
- package/skills/07_Computational_Modeling/act-r-model-builder/references/model-patterns.md +197 -0
- package/skills/07_Computational_Modeling/act-r-model-builder/references/parameter-table.yaml +204 -0
- package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/SKILL.md +294 -0
- package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/diagnostics-checklist.md +351 -0
- package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/prior-selection-guide.md +241 -0
- package/skills/07_Computational_Modeling/parameter-recovery-checker/SKILL.md +269 -0
- package/skills/07_Computational_Modeling/parameter-recovery-checker/references/recovery-diagnostics.md +207 -0
- package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/SKILL.md +317 -0
- package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
- package/skills/08_Computational_Neuroscience/neural-decoding-analysis/SKILL.md +273 -0
- package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/decoding-methods.md +170 -0
- package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/rsa-guide.md +266 -0
- package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/SKILL.md +305 -0
- package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/data-requirements.md +60 -0
- package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/method-comparison.md +151 -0
- package/skills/08_Computational_Neuroscience/spiking-network-model-builder/SKILL.md +376 -0
- package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/hh-parameters.md +117 -0
- package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/network-regimes.md +130 -0
- package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/SKILL.md +258 -0
- package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/indicator-parameters.md +242 -0
- package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/pipeline-details.md +211 -0
- package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/SKILL.md +261 -0
- package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/opsin-catalog.md +124 -0
- package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/stimulation-parameters.md +304 -0
- package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/SKILL.md +367 -0
- package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/disconnection-guide.md +152 -0
- package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/vlsm-pipeline.md +182 -0
- package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/SKILL.md +250 -0
- package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/deficit-profiles.md +302 -0
- package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/test-catalog.md +304 -0
- package/skills/11_Developmental_Cognition/infant-looking-time-designer/SKILL.md +345 -0
- package/skills/11_Developmental_Cognition/infant-looking-time-designer/references/age-parameters.yaml +186 -0
- package/skills/12_Social_Cognition/tom-task-selector/SKILL.md +379 -0
- package/skills/12_Social_Cognition/tom-task-selector/references/task-database.md +317 -0
- package/skills/13_Visualization/nature-figure/README.md +442 -0
- package/skills/13_Visualization/nature-figure/SKILL.md +60 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-01-bar-charts.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-02-line-trends.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-03-heatmaps.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-04-scatter-bubble.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-05-radar-polar.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-06-distributions.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-07-forest-interval.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-08-area-stacked.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-09-image-plates.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-10-network-matrix.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_motivation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation_distillation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_contrastive.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_CEDAR.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_IEDB.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_schematic.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/RNAGenScape_schematic.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/ablation.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/comparison.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_ablation.py +86 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_comparison.py +109 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/diffusion_swiss_roll.py +97 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/diffusion_swiss_roll.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.pdf +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_Trajectory.pdf +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_Trajectory.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/figX_comparison_Ablation.pdf +0 -0
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- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Ablation.py +64 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_GeneRegulatory.py +74 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Trajectory.py +74 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/figures/idea.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/figures/illustration.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/plot_idea.py +76 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/plot_illustration.py +404 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_FPGM/figures/freq_prior.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_FPGM/plot_freq_prior.py +146 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_ablation_Cancer.png +0 -0
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- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/plot_bars.py +216 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/raw_data.py +125 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/figures/manifold.png +0 -0
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- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_comparison.py +228 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_hole_manifold.py +82 -0
- package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_manifold.py +61 -0
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- package/skills/13_Visualization/nature-figure/assets/gallery/fig4-single-cell-systems-rich.png +0 -0
- package/skills/13_Visualization/nature-figure/assets/gallery/fig5-validation-perturbation-rich.png +0 -0
- package/skills/13_Visualization/nature-figure/evals/evals.json +37 -0
- package/skills/13_Visualization/nature-figure/manifest.yaml +57 -0
- package/skills/13_Visualization/nature-figure/references/api.md +428 -0
- package/skills/13_Visualization/nature-figure/references/backend-selection.md +100 -0
- package/skills/13_Visualization/nature-figure/references/chart-types.md +281 -0
- package/skills/13_Visualization/nature-figure/references/common-patterns.md +350 -0
- package/skills/13_Visualization/nature-figure/references/demos.md +65 -0
- package/skills/13_Visualization/nature-figure/references/design-theory.md +436 -0
- package/skills/13_Visualization/nature-figure/references/figure-contract.md +93 -0
- package/skills/13_Visualization/nature-figure/references/nature-2026-observations.md +112 -0
- package/skills/13_Visualization/nature-figure/references/qa-contract.md +119 -0
- package/skills/13_Visualization/nature-figure/references/r-template-index.md +66 -0
- package/skills/13_Visualization/nature-figure/references/r-workflow.md +161 -0
- package/skills/13_Visualization/nature-figure/references/tutorials.md +251 -0
- package/skills/13_Visualization/nature-figure/static/core/contract.md +29 -0
- package/skills/13_Visualization/nature-figure/static/core/stance.md +37 -0
- package/skills/13_Visualization/nature-figure/static/fragments/backend/python.md +37 -0
- package/skills/13_Visualization/nature-figure/static/fragments/backend/r.md +44 -0
- package/skills/14_Writing/markdown-report-writing/SKILL.md +306 -0
- package/skills/14_Writing/markdown-report-writing/references/compatibility-matrix.md +72 -0
- package/skills/14_Writing/markdown-report-writing/references/templates.md +299 -0
- package/skills/15_Others/neuroimaging-power-guide/SKILL.md +324 -0
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# DDM Model Variants
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A comprehensive reference for the drift-diffusion model family, covering model specifications, parameter details, applicability, and trade-offs. All numerical parameter ranges cite their authoritative sources.
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---
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## Table of Contents
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1. [Classic DDM (Ratcliff, 1978)](#1-classic-ddm-ratcliff-1978)
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2. [Full DDM with Trial-to-Trial Variability](#2-full-ddm-with-trial-to-trial-variability)
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3. [EZ-Diffusion Model](#3-ez-diffusion-model)
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4. [Hierarchical DDM (HDDM)](#4-hierarchical-ddm-hddm)
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5. [Linear Ballistic Accumulator (LBA)](#5-linear-ballistic-accumulator-lba)
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6. [Racing Diffusion Model (RDM)](#6-racing-diffusion-model-rdm)
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7. [Collapsing Bounds DDM](#7-collapsing-bounds-ddm)
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8. [Variant Comparison Summary](#8-variant-comparison-summary)
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---
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## 1. Classic DDM (Ratcliff, 1978)
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### Model Description
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The classic drift-diffusion model posits that evidence accumulates continuously over time as a Wiener diffusion process, starting from point z and drifting toward one of two absorbing boundaries separated by distance a. The drift rate v captures the average rate of evidence accumulation, and noise is modeled as a Gaussian diffusion process with diffusion coefficient s (typically fixed to **0.1** as a scaling parameter; Ratcliff, 1978; or to **1.0** in some implementations, Ratcliff & McKoon, 2008, footnote 2).
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### Mathematical Formulation
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The evidence variable x(t) evolves according to:
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```
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dx = v dt + s dW
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```
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where v is the drift rate, s is the diffusion coefficient (noise), and dW is a Wiener process increment. A decision is made when x(t) reaches the upper boundary (a) or the lower boundary (0). The observed RT = decision time + non-decision time (t0).
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### Parameters
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| Parameter | Symbol | Description | Typical Range | Source |
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|-----------|--------|-------------|---------------|--------|
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| Drift rate | v | Mean rate of evidence accumulation | **0.1 – 5.0** (with s=0.1); commonly **0.5 – 3.0** | Ratcliff & McKoon, 2008; Voss et al., 2004, Table 2 |
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| Boundary separation | a | Distance between decision boundaries | **0.5 – 2.5** (with s=0.1); commonly **0.8 – 2.0** | Ratcliff & McKoon, 2008; Voss et al., 2004, Table 2 |
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| Non-decision time | t0 (Ter) | Time for stimulus encoding + motor response | **0.1 – 0.6 s**; commonly **0.2 – 0.5 s** | Ratcliff & McKoon, 2008; Matzke & Wagenmakers, 2009, Table 1 |
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| Starting point | z | Starting point of evidence accumulation | **0 – a**; unbiased = **a/2** | Ratcliff & McKoon, 2008; Voss et al., 2013 |
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| Diffusion coefficient | s | Within-trial noise (scaling parameter) | Fixed to **0.1** (Ratcliff convention) or **1.0** | Ratcliff, 1978; Ratcliff & McKoon, 2008 |
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**Note on scaling**: s is a scaling parameter — it determines the scale of v and a. Fixing s=0.1 (Ratcliff convention) or s=1.0 (some Bayesian implementations) yields different numerical ranges for v and a, but the model is mathematically equivalent (Donkin et al., 2009).
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### When to Use
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- Two-choice RT tasks with sufficient trials (> **40 per condition**; Ratcliff & Childers, 2015)
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- When you want to decompose RT and accuracy into process-level components
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- When trial-to-trial variability is not of primary theoretical interest (or when trial counts are insufficient to estimate it)
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- When the research question focuses on how experimental manipulations selectively affect drift, boundary, or non-decision time
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### Strengths
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- Parsimonious: 4 free parameters capture RT distributions for both correct and error responses
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- Well-validated across many cognitive domains (Ratcliff & McKoon, 2008)
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- Closed-form expressions for first-passage time distribution exist (Navarro & Fuss, 2009)
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- Efficient to fit with moderate trial counts
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### Limitations
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- Cannot account for certain phenomena without trial-to-trial variability (e.g., slow errors require sv > 0; Ratcliff & Rouder, 1998)
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- Assumes constant drift rate within a trial
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- Limited to two-choice decisions
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---
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## 2. Full DDM with Trial-to-Trial Variability
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### Model Description
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The full DDM extends the classic model by allowing three parameters to vary across trials according to specified distributions (Ratcliff & Tuerlinckx, 2002):
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- Drift rate varies normally: v ~ N(v, sv)
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- Starting point varies uniformly: z ~ U(z - sz/2, z + sz/2)
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- Non-decision time varies uniformly: t0 ~ U(t0 - st0/2, t0 + st0/2)
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### Additional Parameters
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| Parameter | Symbol | Description | Typical Range | Source |
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|-----------|--------|-------------|---------------|--------|
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| Drift rate variability | sv | SD of cross-trial drift rate distribution | **0 – 2.0** (with s=0.1) | Ratcliff & McKoon, 2008 |
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| Starting point variability | sz | Range of cross-trial starting point distribution | **0 – 0.3 × a** | Ratcliff & McKoon, 2008 |
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| Non-decision time variability | st0 | Range of cross-trial non-decision time distribution | **0 – 0.3 s** | Ratcliff & McKoon, 2008 |
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### Why Trial-to-Trial Variability Matters
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- **sv > 0** produces **slow errors**: When drift rate varies across trials, low-drift trials produce both more errors and slower RTs, matching empirical data where errors are often slower than correct responses (Ratcliff & Rouder, 1998; Ratcliff, 1978)
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- **sz > 0** produces **fast errors**: Starting point variability means some trials start closer to the wrong boundary, producing fast errors (Laming, 1968; Ratcliff & Rouder, 1998)
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- **st0 > 0** accounts for the leading edge of the RT distribution being variable across trials
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### When to Use
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- When error RTs are systematically faster or slower than correct RTs (requires sv or sz to capture this pattern)
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- When you have **> 200 trials per condition** for stable estimation of all 7 parameters (Ratcliff & Childers, 2015)
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- When the goal is the most complete characterization of the decision process
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- In domains where the full model is standard (e.g., recognition memory, lexical decision; Ratcliff et al., 2004)
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### Strengths
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- Captures nuanced RT distribution features (e.g., relative speed of correct vs. error responses)
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- Most complete account of 2AFC RT data
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- Well-established fitting tools available (fast-dm, DMAT)
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### Limitations
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- 7 free parameters require substantial data (> **200 trials per condition** recommended; Ratcliff & Childers, 2015)
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- sv and sz are often poorly identifiable with limited data (Boehm et al., 2018)
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- Longer fitting times due to numerical integration (no closed-form solution with variability parameters)
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- Risk of overfitting with small datasets
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### Identifiability Guidance
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When trial counts are moderate (**100-200 per condition**), consider fixing one or more variability parameters:
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1. Fix sz = 0 first (least impact on model fits in most domains; Ratcliff & Childers, 2015)
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2. Fix st0 = 0 next if needed
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3. sv is typically the most important variability parameter to retain (captures slow-error phenomenon)
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---
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## 3. EZ-Diffusion Model
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### Model Description
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The EZ-diffusion model (Wagenmakers et al., 2007) provides closed-form equations that map three summary statistics — mean RT for correct responses (MRT), RT variance for correct responses (VRT), and accuracy (Pc) — directly to three DDM parameters (v, a, t0). No iterative fitting is required.
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### Parameters Estimated
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| Parameter | Symbol | Estimated From | Typical Range | Source |
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|-----------|--------|----------------|---------------|--------|
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| Drift rate | v | Pc, MRT, VRT | Same as classic DDM | Wagenmakers et al., 2007, Equations 1-3 |
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| Boundary separation | a | Pc, VRT | Same as classic DDM | Wagenmakers et al., 2007, Equations 1-3 |
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| Non-decision time | t0 | MRT, v, a | Same as classic DDM | Wagenmakers et al., 2007, Equations 1-3 |
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### Assumptions
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- Starting point is unbiased: z = a/2 (not estimable)
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- No trial-to-trial variability: sv = sz = st0 = 0
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- Diffusion coefficient s is fixed (default **0.1**; Wagenmakers et al., 2007)
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### Edge Correction
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When accuracy is exactly 0, 0.5, or 1.0, the EZ equations are undefined. Apply the edge correction: replace extreme accuracy values by shifting them **half a trial** toward 0.5 (Wagenmakers et al., 2007):
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```
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If Pc = 1: Pc_corrected = 1 - 1/(2N)
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If Pc = 0: Pc_corrected = 1/(2N)
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If Pc = 0.5: Pc_corrected = 0.5 + 1/(2N)
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```
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where N is the number of trials.
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### When to Use
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- Quick exploratory analysis before committing to full model fitting
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- Datasets with few trials per condition (**20-40**; Wagenmakers et al., 2007)
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- Large-scale individual differences studies where computational efficiency matters
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- When response bias is not of theoretical interest (z cannot be estimated)
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- As a sanity check: EZ estimates should roughly agree with full DDM estimates
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### Strengths
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- No iterative fitting: closed-form, instantaneous computation
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- Requires very few trials (as few as **20 per condition**; Wagenmakers et al., 2007, simulation results)
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- Excellent parameter recovery in simulation studies (Wagenmakers et al., 2007, Table 1)
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- Transparent: easy to implement and check
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### Limitations
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- Cannot estimate starting point bias (z) or trial-to-trial variability parameters
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- Assumes no response bias — inappropriate if bias is expected (e.g., cue validity manipulations)
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- Does not use error RT information (only uses accuracy and correct RT statistics)
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- May not capture all features of the RT distribution
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### Extensions
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- **EZ2-diffusion** (Grasman et al., 2009): Extends EZ to estimate starting point z using accuracy and error RT statistics in addition to correct RT statistics. Requires error trials to be available.
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- **Robust EZ** (Wagenmakers et al., 2007): Applies the model to individual participant data with bootstrapped confidence intervals.
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---
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## 4. Hierarchical DDM (HDDM)
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### Model Description
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The Hierarchical DDM (Wiecki et al., 2013) implements the DDM within a hierarchical Bayesian framework. Individual-level parameters are assumed to be drawn from group-level distributions, providing regularization (shrinkage toward group means) and enabling principled individual differences analysis.
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### Hierarchical Structure
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```
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Group level: v_group ~ prior, a_group ~ prior, ...
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↓
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Individual: v_i ~ N(v_group, sigma_v), a_i ~ N(a_group, sigma_a), ...
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↓
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Trial level: RT_ij, accuracy_ij ~ DDM(v_i, a_i, t0_i, z_i)
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```
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### Default Priors (HDDM Python package)
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| Parameter | Prior Distribution | Source |
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|-----------|-------------------|--------|
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| v (drift rate) | N(2, 3) | Wiecki et al., 2013, Table 1 |
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| a (boundary) | Gamma(1.5, 0.75) | Wiecki et al., 2013, Table 1 |
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| t0 (non-decision) | N(0.3, 0.5), truncated at 0 | Wiecki et al., 2013, Table 1 |
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| z (starting point) | Beta(1, 1) — i.e., Uniform(0,1) as proportion of a | Wiecki et al., 2013, Table 1 |
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| sv | Half-Normal | Wiecki et al., 2013 |
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**Note**: These are the defaults in the HDDM package (v0.9+). Researchers should perform prior sensitivity analysis, especially for informative priors.
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### When to Use
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- Group comparisons (patients vs. controls, conditions) where you want to borrow strength across participants
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- Moderate per-participant trial counts (**40-100 per condition**) where individual-level fitting is noisy — hierarchical shrinkage improves estimates (Wiecki et al., 2013)
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- Individual differences research where you need reliable person-level parameter estimates
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- When principled model comparison is needed (DIC, WAIC, Bayes factors)
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- When you want full posterior distributions rather than point estimates
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### Strengths
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- Handles moderate trial counts better than individual-level fitting via hierarchical shrinkage (Wiecki et al., 2013)
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- Provides full posterior distributions — natural uncertainty quantification
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- Model comparison via DIC/WAIC (Spiegelhalter et al., 2002; Watanabe, 2010)
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- Can include regression models on DDM parameters (e.g., linking neural data to drift rate)
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- Well-maintained Python package with good documentation
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### Limitations
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- Computationally intensive: MCMC sampling can take hours for large datasets
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- Requires convergence diagnostics (R-hat < **1.1**, effective sample size > **200**; Gelman & Rubin, 1992; Wiecki et al., 2013)
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- Prior sensitivity: results can depend on prior choices, especially with small samples
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- Group-level normality assumption may not hold for all parameters
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### MCMC Diagnostics Checklist
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1. **R-hat (Gelman-Rubin statistic)**: Should be < **1.1** for all parameters (Gelman & Rubin, 1992)
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2. **Effective sample size**: Should be > **200** for reliable posterior summaries (Wiecki et al., 2013)
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3. **Visual trace inspection**: Chains should show good mixing (no trends, no stuck periods)
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4. **Posterior predictive checks**: Simulated data from the posterior should match observed RT distributions
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---
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## 5. Linear Ballistic Accumulator (LBA)
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### Model Description
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The LBA (Brown & Heathcote, 2008) is an alternative evidence accumulation model where evidence accumulates linearly (no within-trial noise) and deterministically on each trial, but with trial-to-trial variability in both drift rate and starting point. Each response option has its own accumulator racing toward a common threshold.
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### Key Difference from DDM
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| Feature | DDM | LBA |
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|---------|-----|-----|
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| Number of accumulators | 1 (single process, two boundaries) | N (one per response option) |
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| Within-trial noise | Yes (Wiener diffusion) | No (ballistic/deterministic) |
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| Between-trial variability | Source of stochasticity | Primary source of stochasticity |
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| Response alternatives | 2 only | 2 or more (natural extension) |
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### Parameters
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| Parameter | Symbol | Description | Typical Range | Source |
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|-----------|--------|-------------|---------------|--------|
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| Mean drift rate | v_i | Mean drift for accumulator i | **0 – 5.0** | Brown & Heathcote, 2008, Table 1 |
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| Drift rate variability | s_i | SD of drift for accumulator i (across trials) | **0.5 – 2.0** (often fixed to **1.0** for scaling) | Brown & Heathcote, 2008 |
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| Response threshold | b | Common threshold for all accumulators | **1.0 – 5.0** | Brown & Heathcote, 2008, Table 1 |
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| Starting point range | A | Upper bound of uniform starting point U(0, A) | **0 – b** | Brown & Heathcote, 2008 |
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| Non-decision time | t0 | Encoding + motor execution time | **0.1 – 0.5 s** | Brown & Heathcote, 2008, Table 1 |
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**Scaling convention**: One s_i (or the drift difference) is typically fixed for identification. Common choice: fix s = 1 for one accumulator (Donkin et al., 2011).
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271
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+
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272
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+
### When to Use
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273
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+
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274
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- Tasks with **more than 2 response alternatives** (natural multi-accumulator extension; Brown & Heathcote, 2008)
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275
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+
- When mathematical tractability is important: LBA has closed-form likelihood (Brown & Heathcote, 2008, Equation 1-3), making it fast to fit
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276
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+
- When within-trial noise is not theoretically important for your research question
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277
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+
- As a comparison model to DDM for model selection (Donkin et al., 2011)
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278
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+
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279
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+
### Strengths
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280
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+
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281
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+
- Natural extension to N > 2 alternatives without additional assumptions
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282
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+
- Closed-form likelihood — very fast fitting
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283
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+
- Mathematically simpler than DDM
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284
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+
- Good empirical fits across many paradigms (Donkin et al., 2011)
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285
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+
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286
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+
### Limitations
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287
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+
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288
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+
- No within-trial noise: cannot capture some phenomena that arise from noisy accumulation
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289
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+
- Different cognitive interpretation: stochasticity comes from trial-to-trial variability, not moment-to-moment noise
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290
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+
- Cannot distinguish between some mechanisms that DDM can (e.g., within-trial evidence fluctuations)
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291
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+
- May overfit with too many free parameters in multi-alternative tasks
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292
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+
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293
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+
---
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294
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+
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295
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+
## 6. Racing Diffusion Model (RDM)
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296
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+
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297
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+
### Model Description
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298
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+
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299
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+
The Racing Diffusion Model (Tillman et al., 2020) combines features of the DDM and LBA: multiple accumulators (one per response option) race toward a common boundary, but each accumulator is a diffusion process with within-trial noise (unlike LBA's ballistic accumulation).
|
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300
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+
|
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301
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+
### Parameters
|
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302
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+
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303
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+
| Parameter | Symbol | Description | Typical Range | Source |
|
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304
|
+
|-----------|--------|-------------|---------------|--------|
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305
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+
| Drift rate per accumulator | v_i | Mean drift for accumulator i | **0.5 – 5.0** | Tillman et al., 2020, Table 1 |
|
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306
|
+
| Boundary | a | Common threshold | **0.5 – 3.0** | Tillman et al., 2020, Table 1 |
|
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307
|
+
| Non-decision time | t0 | Encoding + motor time | **0.1 – 0.5 s** | Tillman et al., 2020 |
|
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308
|
+
| Within-trial noise | s | Diffusion coefficient (often fixed to **1.0**) | Fixed as scaling parameter | Tillman et al., 2020 |
|
|
309
|
+
|
|
310
|
+
### When to Use
|
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311
|
+
|
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312
|
+
- Multi-alternative tasks (> 2 choices) where within-trial noise is theoretically important
|
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313
|
+
- When you believe that momentary evidence fluctuations matter (not just trial-to-trial variability)
|
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314
|
+
- Model comparison studies: RDM vs. LBA to test whether within-trial noise improves fit (Tillman et al., 2020)
|
|
315
|
+
|
|
316
|
+
### Strengths
|
|
317
|
+
|
|
318
|
+
- Combines DDM's within-trial noise with multi-accumulator architecture
|
|
319
|
+
- More psychologically plausible than LBA for tasks involving noisy sensory evidence
|
|
320
|
+
- Can be fit using likelihood-free methods or analytical approximations
|
|
321
|
+
|
|
322
|
+
### Limitations
|
|
323
|
+
|
|
324
|
+
- More parameters than LBA for multi-alternative tasks
|
|
325
|
+
- No universally available software (though implementations exist in Julia and R)
|
|
326
|
+
- Relatively newer model; less empirical validation than DDM or LBA
|
|
327
|
+
|
|
328
|
+
---
|
|
329
|
+
|
|
330
|
+
## 7. Collapsing Bounds DDM
|
|
331
|
+
|
|
332
|
+
### Model Description
|
|
333
|
+
|
|
334
|
+
In the standard DDM, boundaries are fixed over time. The collapsing bounds variant allows the decision boundary to decrease as a function of time, implementing urgency — the idea that decision-makers become less cautious as time elapses (Hawkins et al., 2015; Palestro et al., 2018).
|
|
335
|
+
|
|
336
|
+
### Common Boundary Functions
|
|
337
|
+
|
|
338
|
+
| Function | Formula | Parameters | Source |
|
|
339
|
+
|----------|---------|------------|--------|
|
|
340
|
+
| Linear collapse | a(t) = a_0 - k × t | a_0 (initial), k (collapse rate) | Hawkins et al., 2015 |
|
|
341
|
+
| Exponential collapse | a(t) = a_0 × exp(-k × t) | a_0 (initial), k (collapse rate) | Palestro et al., 2018 |
|
|
342
|
+
| Weibull collapse | a(t) = a_0 × (1 - (t/lambda)^k) | a_0, lambda (scale), k (shape) | Hawkins et al., 2015 |
|
|
343
|
+
|
|
344
|
+
### When to Use
|
|
345
|
+
|
|
346
|
+
- Tasks with deadlines or response pressure where urgency is expected
|
|
347
|
+
- When standard DDM with fixed bounds provides poor fits to slow RT quantiles
|
|
348
|
+
- When testing theoretical claims about urgency signals (e.g., Cisek et al., 2009)
|
|
349
|
+
- Model comparison: test whether collapsing bounds improve fit over fixed bounds
|
|
350
|
+
|
|
351
|
+
### Strengths
|
|
352
|
+
|
|
353
|
+
- Captures urgency and deadline effects
|
|
354
|
+
- Can explain certain RT distribution shapes that fixed-bound DDM cannot
|
|
355
|
+
- Theoretically motivated by neural urgency signals (Churchland et al., 2008; Cisek et al., 2009)
|
|
356
|
+
|
|
357
|
+
### Limitations
|
|
358
|
+
|
|
359
|
+
- Adds at least 1-2 parameters for the boundary function
|
|
360
|
+
- Empirical evidence for collapsing bounds vs. fixed bounds is mixed (Hawkins et al., 2015; Palestro et al., 2018 — found limited evidence for collapsing bounds in standard tasks)
|
|
361
|
+
- May trade off with trial-to-trial variability parameters (identifiability concern)
|
|
362
|
+
|
|
363
|
+
---
|
|
364
|
+
|
|
365
|
+
## 8. Variant Comparison Summary
|
|
366
|
+
|
|
367
|
+
### Decision Matrix
|
|
368
|
+
|
|
369
|
+
| Variant | Free Parameters | Min Trials per Condition | Fitting Complexity | Multi-Alternative | Key Use Case |
|
|
370
|
+
|---------|-----------------|--------------------------|-------------------|-------------------|--------------|
|
|
371
|
+
| Classic DDM | 4 | **40+** (Ratcliff & Childers, 2015) | Moderate | No (2 only) | Standard decomposition |
|
|
372
|
+
| Full DDM | 7 | **200+** (Ratcliff & Childers, 2015) | High | No (2 only) | Complete characterization |
|
|
373
|
+
| EZ-diffusion | 3 | **20+** (Wagenmakers et al., 2007) | None (closed-form) | No (2 only) | Quick estimation |
|
|
374
|
+
| HDDM | 4-7 per person | **40+** per person (Wiecki et al., 2013) | High (MCMC) | No (2 only) | Group studies, individual differences |
|
|
375
|
+
| LBA | 5+ | **40+** (Brown & Heathcote, 2008) | Low (closed-form likelihood) | Yes | Multi-alternative tasks |
|
|
376
|
+
| Racing Diffusion | 4+ per accumulator | **100+** (Tillman et al., 2020) | High | Yes | Multi-alternative with within-trial noise |
|
|
377
|
+
| Collapsing Bounds DDM | 5-6 | **200+** (Hawkins et al., 2015) | High | No (2 only) | Urgency/deadline tasks |
|
|
378
|
+
|
|
379
|
+
### Quick Selection Guide
|
|
380
|
+
|
|
381
|
+
```
|
|
382
|
+
Start here:
|
|
383
|
+
│
|
|
384
|
+
├── 2-choice task?
|
|
385
|
+
│ ├── YES
|
|
386
|
+
│ │ ├── < 40 trials per condition → EZ-diffusion
|
|
387
|
+
│ │ ├── 40-200 trials → Classic DDM or HDDM (if group study)
|
|
388
|
+
│ │ ├── > 200 trials → Full DDM
|
|
389
|
+
│ │ └── Urgency/deadline present? → Consider collapsing bounds
|
|
390
|
+
│ │
|
|
391
|
+
│ └── NO (> 2 choices)
|
|
392
|
+
│ ├── Within-trial noise important? → Racing Diffusion Model
|
|
393
|
+
│ └── Otherwise → LBA
|
|
394
|
+
│
|
|
395
|
+
└── Group-level analysis?
|
|
396
|
+
├── YES, with moderate per-person data → HDDM
|
|
397
|
+
└── NO, or large per-person data → Fit individually with classic/full DDM
|
|
398
|
+
```
|
|
399
|
+
|
|
400
|
+
---
|
|
401
|
+
|
|
402
|
+
## References
|
|
403
|
+
|
|
404
|
+
- Brown, S. D., & Heathcote, A. (2008). The simplest complete model of choice response time: Linear ballistic accumulation. *Cognitive Psychology*, 57(3), 153–178.
|
|
405
|
+
- Boehm, U., Annis, J., Frank, M. J., Hawkins, G. E., Heathcote, A., Kellen, D., ... & Wagenmakers, E.-J. (2018). Estimating across-trial variability parameters of the diffusion decision model: Expert advice and recommendations. *Journal of Mathematical Psychology*, 87, 46–75.
|
|
406
|
+
- Churchland, A. K., Kiani, R., & Shadlen, M. N. (2008). Decision-making with multiple alternatives. *Nature Neuroscience*, 11(6), 693–702.
|
|
407
|
+
- Cisek, P., Puskas, G. A., & El-Murr, S. (2009). Decisions in changing conditions: The urgency-gating model. *Journal of Neuroscience*, 29(37), 11560–11571.
|
|
408
|
+
- Donkin, C., Averell, L., Brown, S., & Heathcote, A. (2009). Getting more from accuracy and response time data: Methods for fitting the linear ballistic accumulator. *Behavior Research Methods*, 41(4), 1095–1110.
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409
|
+
- Donkin, C., Brown, S., Heathcote, A., & Wagenmakers, E.-J. (2011). Diffusion versus linear ballistic accumulation: Different models but the same conclusions about psychological processes? *Psychonomic Bulletin & Review*, 18(1), 61–69.
|
|
410
|
+
- Grasman, R. P. P. P., Wagenmakers, E.-J., & van der Maas, H. L. J. (2009). On the mean and variance of response times under the diffusion model with an application to parameter estimation. *Journal of Mathematical Psychology*, 53(2), 55–68.
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411
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+
- Hawkins, G. E., Forstmann, B. U., Wagenmakers, E.-J., Ratcliff, R., & Brown, S. D. (2015). Revisiting the evidence for collapsing boundaries and urgency signals in perceptual decision-making. *Journal of Neuroscience*, 35(6), 2476–2484.
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412
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+
- Heathcote, A., Brown, S., & Mewhort, D. J. K. (2002). Quantile maximum probability as a method for response time distributions. *Psychonomic Bulletin & Review*, 9(2), 394–401.
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|
413
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+
- Laming, D. R. J. (1968). *Information theory of choice-reaction times*. London: Academic Press.
|
|
414
|
+
- Matzke, D., & Wagenmakers, E.-J. (2009). Psychological interpretation of the ex-Gaussian and shifted Wald parameters: A diffusion model analysis. *Psychonomic Bulletin & Review*, 16(5), 798–817.
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415
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+
- Navarro, D. J., & Fuss, I. G. (2009). Fast and accurate calculations for first-passage times in Wiener diffusion models. *Journal of Mathematical Psychology*, 53(4), 222–230.
|
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416
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+
- Palestro, J. J., Weichart, E., Sederberg, P. B., & Turner, B. M. (2018). Some task demands induce collapsing bounds: Evidence from a behavioral analysis. *Psychonomic Bulletin & Review*, 25(4), 1225–1248.
|
|
417
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- Ratcliff, R. (1978). A theory of memory retrieval. *Psychological Review*, 85(2), 59–108.
|
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418
|
+
- Ratcliff, R., & Childers, R. (2015). Individual differences and fitting methods for the two-choice diffusion model of decision making. *Decision*, 2(4), 237–279.
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419
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+
- Ratcliff, R., Gomez, P., & McKoon, G. (2004). A diffusion model account of the lexical decision task. *Psychological Review*, 111(1), 159–182.
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420
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+
- Ratcliff, R., & McKoon, G. (2008). The diffusion decision model: Theory and data for two-choice decision tasks. *Neural Computation*, 20(4), 873–922.
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- Ratcliff, R., & Rouder, J. N. (1998). Modeling response times for two-choice decisions. *Psychological Science*, 9(5), 347–356.
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- Ratcliff, R., & Tuerlinckx, F. (2002). Estimating parameters of the diffusion model: Approaches to dealing with contaminant reaction times and parameter variability. *Psychonomic Bulletin & Review*, 9(3), 438–481.
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- Tillman, G., Van Zandt, T., & Logan, G. D. (2020). Sequential sampling models without random between-trial variability: The racing diffusion model with its three-boundary extension. *Journal of Mathematical Psychology*, 96, 102368.
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- Voss, A., Nagler, M., & Lerche, V. (2013). Diffusion models in experimental psychology: A practical introduction. *Experimental Psychology*, 60(6), 385–402.
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425
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- Voss, A., Rothermund, K., & Voss, J. (2004). Interpreting the parameters of the diffusion model: An empirical validation. *Memory & Cognition*, 32(7), 1206–1220.
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- Wagenmakers, E.-J., van der Maas, H. L. J., & Grasman, R. P. P. P. (2007). An EZ-diffusion model for response time and accuracy. *Psychonomic Bulletin & Review*, 14(1), 3–22.
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- Wiecki, T. V., Sofer, I., & Frank, M. J. (2013). HDDM: Hierarchical Bayesian estimation of the drift-diffusion model in Python. *Frontiers in Neuroinformatics*, 7, 14.
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