@brainpilot/skills 0.0.6

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  1. package/dist/index.d.ts +6 -0
  2. package/dist/index.d.ts.map +1 -0
  3. package/dist/index.js +28 -0
  4. package/dist/index.js.map +1 -0
  5. package/package.json +35 -0
  6. package/skills/01_Meta-Skills/contribute-skill/SKILL.md +277 -0
  7. package/skills/01_Meta-Skills/contribute-skills-via-pr/SKILL.md +163 -0
  8. package/skills/01_Meta-Skills/paper-to-skill/SKILL.md +435 -0
  9. package/skills/01_Meta-Skills/paper-to-skill/references/extraction-guide.md +286 -0
  10. package/skills/01_Meta-Skills/paper-to-skill/references/skill-template.md +250 -0
  11. package/skills/01_Meta-Skills/repo-to-skill/SKILL.md +289 -0
  12. package/skills/01_Meta-Skills/share-case/SKILL.md +253 -0
  13. package/skills/01_Meta-Skills/share-usage/README.md +63 -0
  14. package/skills/01_Meta-Skills/share-usage/SKILL.md +395 -0
  15. package/skills/01_Meta-Skills/verify-skill/SKILL.md +331 -0
  16. package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/SKILL.md +194 -0
  17. package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/effect-sizes.md +352 -0
  18. package/skills/02_Cross-Domain_Foundation/cogsci-power-analysis/references/sample-size-guide.md +407 -0
  19. package/skills/02_Cross-Domain_Foundation/cogsci-statistics/SKILL.md +361 -0
  20. package/skills/02_Cross-Domain_Foundation/cogsci-statistics/references/common-analyses.md +517 -0
  21. package/skills/02_Cross-Domain_Foundation/cogsci-visualization/SKILL.md +292 -0
  22. package/skills/02_Cross-Domain_Foundation/cogsci-visualization/references/plot-recipes.md +709 -0
  23. package/skills/02_Cross-Domain_Foundation/research-literacy/SKILL.md +286 -0
  24. package/skills/02_Cross-Domain_Foundation/research-literacy/references/common-assumptions.md +320 -0
  25. package/skills/02_Cross-Domain_Foundation/research-literacy/references/planning-template.md +143 -0
  26. package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/SKILL.md +197 -0
  27. package/skills/03_Cognitive_Psychology/alternative-uses-task-designer/references/instruction-templates.md +60 -0
  28. package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/SKILL.md +246 -0
  29. package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/classic-paradigms.md +435 -0
  30. package/skills/03_Cognitive_Psychology/cognitive-paradigm-design/references/design-principles.md +256 -0
  31. package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/SKILL.md +270 -0
  32. package/skills/03_Cognitive_Psychology/creativity-self-efficacy-mediation/references/lavaan-templates.md +172 -0
  33. package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/SKILL.md +238 -0
  34. package/skills/03_Cognitive_Psychology/divergent-thinking-scoring/references/scoring-rubric.md +143 -0
  35. package/skills/03_Cognitive_Psychology/drift-diffusion-model/SKILL.md +203 -0
  36. package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/fitting-guide.md +571 -0
  37. package/skills/03_Cognitive_Psychology/drift-diffusion-model/references/model-variants.md +427 -0
  38. package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/SKILL.md +310 -0
  39. package/skills/03_Cognitive_Psychology/evidence-accumulation-selector/references/ez-diffusion-formulas.md +137 -0
  40. package/skills/03_Cognitive_Psychology/signal-detection-analysis/SKILL.md +300 -0
  41. package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/application-guide.md +278 -0
  42. package/skills/03_Cognitive_Psychology/signal-detection-analysis/references/sdt-formulas.md +318 -0
  43. package/skills/03_Cognitive_Psychology/visual-search-array-generator/SKILL.md +283 -0
  44. package/skills/03_Cognitive_Psychology/visual-search-array-generator/references/array-generation-parameters.yaml +111 -0
  45. package/skills/04_Psycholinguistics/reading-time-analysis/SKILL.md +301 -0
  46. package/skills/04_Psycholinguistics/reading-time-analysis/references/measure-computation-guide.md +195 -0
  47. package/skills/04_Psycholinguistics/self-paced-reading-designer/SKILL.md +257 -0
  48. package/skills/04_Psycholinguistics/self-paced-reading-designer/references/analysis-guide.md +356 -0
  49. package/skills/04_Psycholinguistics/self-paced-reading-designer/references/region-segmentation.md +266 -0
  50. package/skills/04_Psycholinguistics/sentence-stimulus-norming/SKILL.md +346 -0
  51. package/skills/04_Psycholinguistics/sentence-stimulus-norming/references/lexical-databases-guide.md +184 -0
  52. package/skills/05_EEG_ERP/eeg-paradigm-designer/SKILL.md +226 -0
  53. package/skills/05_EEG_ERP/eeg-paradigm-designer/references/component-paradigm-map.md +276 -0
  54. package/skills/05_EEG_ERP/eeg-paradigm-designer/references/timing-parameters.md +244 -0
  55. package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/SKILL.md +367 -0
  56. package/skills/05_EEG_ERP/eeg-preprocessing-pipeline-guide/references/parameter-lookup-tables.md +138 -0
  57. package/skills/05_EEG_ERP/erp-analysis/SKILL.md +185 -0
  58. package/skills/05_EEG_ERP/erp-analysis/references/erp-components.md +447 -0
  59. package/skills/05_EEG_ERP/erp-analysis/references/preprocessing-pipeline.md +277 -0
  60. package/skills/05_EEG_ERP/erp-analysis/references/statistical-approaches.md +351 -0
  61. package/skills/05_EEG_ERP/mne-python-guide/SKILL.md +174 -0
  62. package/skills/05_EEG_ERP/mne-python-guide/references/decoding.md +178 -0
  63. package/skills/05_EEG_ERP/mne-python-guide/references/io_formats.md +160 -0
  64. package/skills/05_EEG_ERP/mne-python-guide/references/preprocessing.md +259 -0
  65. package/skills/05_EEG_ERP/mne-python-guide/references/simulation.md +173 -0
  66. package/skills/05_EEG_ERP/mne-python-guide/references/source_localization.md +234 -0
  67. package/skills/05_EEG_ERP/mne-python-guide/references/statistics.md +196 -0
  68. package/skills/05_EEG_ERP/mne-python-guide/references/time_frequency.md +165 -0
  69. package/skills/05_EEG_ERP/mne-python-guide/references/visualization.md +175 -0
  70. package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/SKILL.md +317 -0
  71. package/skills/06_fMRI_Neuroimaging/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
  72. package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/SKILL.md +296 -0
  73. package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/design-matrix-guide.md +214 -0
  74. package/skills/06_fMRI_Neuroimaging/fmri-glm-analysis-guide/references/statistical-inference.md +288 -0
  75. package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/SKILL.md +274 -0
  76. package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/quality-control.md +336 -0
  77. package/skills/06_fMRI_Neuroimaging/fmri-preprocessing-pipeline-guide/references/step-by-step-pipeline.md +380 -0
  78. package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/SKILL.md +264 -0
  79. package/skills/06_fMRI_Neuroimaging/fmri-task-design-guide/references/design-optimization-examples.md +114 -0
  80. package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/SKILL.md +273 -0
  81. package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/decoding-methods.md +170 -0
  82. package/skills/06_fMRI_Neuroimaging/neural-decoding-analysis/references/rsa-guide.md +266 -0
  83. package/skills/06_fMRI_Neuroimaging/pycortex-guide/SKILL.md +123 -0
  84. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/database-subjects.md +179 -0
  85. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/dataset-types.md +208 -0
  86. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/freesurfer-fmriprep.md +162 -0
  87. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mapping-transforms.md +181 -0
  88. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/mni-utils.md +207 -0
  89. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/surface-analysis.md +219 -0
  90. package/skills/06_fMRI_Neuroimaging/pycortex-guide/references/visualization.md +251 -0
  91. package/skills/07_Computational_Modeling/act-r-model-builder/SKILL.md +297 -0
  92. package/skills/07_Computational_Modeling/act-r-model-builder/references/model-patterns.md +197 -0
  93. package/skills/07_Computational_Modeling/act-r-model-builder/references/parameter-table.yaml +204 -0
  94. package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/SKILL.md +294 -0
  95. package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/diagnostics-checklist.md +351 -0
  96. package/skills/07_Computational_Modeling/bayesian-cognitive-model-builder/references/prior-selection-guide.md +241 -0
  97. package/skills/07_Computational_Modeling/parameter-recovery-checker/SKILL.md +269 -0
  98. package/skills/07_Computational_Modeling/parameter-recovery-checker/references/recovery-diagnostics.md +207 -0
  99. package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/SKILL.md +317 -0
  100. package/skills/08_Computational_Neuroscience/brain-connectivity-modeler/references/method-implementation-guide.md +116 -0
  101. package/skills/08_Computational_Neuroscience/neural-decoding-analysis/SKILL.md +273 -0
  102. package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/decoding-methods.md +170 -0
  103. package/skills/08_Computational_Neuroscience/neural-decoding-analysis/references/rsa-guide.md +266 -0
  104. package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/SKILL.md +305 -0
  105. package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/data-requirements.md +60 -0
  106. package/skills/08_Computational_Neuroscience/neural-population-analysis-guide/references/method-comparison.md +151 -0
  107. package/skills/08_Computational_Neuroscience/spiking-network-model-builder/SKILL.md +376 -0
  108. package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/hh-parameters.md +117 -0
  109. package/skills/08_Computational_Neuroscience/spiking-network-model-builder/references/network-regimes.md +130 -0
  110. package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/SKILL.md +258 -0
  111. package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/indicator-parameters.md +242 -0
  112. package/skills/09_Cellular_Molecular_Neuroscience/calcium-imaging-analysis-guide/references/pipeline-details.md +211 -0
  113. package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/SKILL.md +261 -0
  114. package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/opsin-catalog.md +124 -0
  115. package/skills/09_Cellular_Molecular_Neuroscience/optogenetics-protocol-designer/references/stimulation-parameters.md +304 -0
  116. package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/SKILL.md +367 -0
  117. package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/disconnection-guide.md +152 -0
  118. package/skills/10_Clinical_Neuropsychology/lesion-symptom-mapping-guide/references/vlsm-pipeline.md +182 -0
  119. package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/SKILL.md +250 -0
  120. package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/deficit-profiles.md +302 -0
  121. package/skills/10_Clinical_Neuropsychology/neuropsych-battery-selector/references/test-catalog.md +304 -0
  122. package/skills/11_Developmental_Cognition/infant-looking-time-designer/SKILL.md +345 -0
  123. package/skills/11_Developmental_Cognition/infant-looking-time-designer/references/age-parameters.yaml +186 -0
  124. package/skills/12_Social_Cognition/tom-task-selector/SKILL.md +379 -0
  125. package/skills/12_Social_Cognition/tom-task-selector/references/task-database.md +317 -0
  126. package/skills/13_Visualization/nature-figure/README.md +442 -0
  127. package/skills/13_Visualization/nature-figure/SKILL.md +60 -0
  128. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-01-bar-charts.png +0 -0
  129. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-02-line-trends.png +0 -0
  130. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-03-heatmaps.png +0 -0
  131. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-04-scatter-bubble.png +0 -0
  132. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-05-radar-polar.png +0 -0
  133. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-06-distributions.png +0 -0
  134. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-07-forest-interval.png +0 -0
  135. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-08-area-stacked.png +0 -0
  136. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-09-image-plates.png +0 -0
  137. package/skills/13_Visualization/nature-figure/assets/chart-atlas/atlas-10-network-matrix.png +0 -0
  138. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_motivation.png +0 -0
  139. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation.png +0 -0
  140. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/Dispersion_observation_distillation.png +0 -0
  141. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_contrastive.png +0 -0
  142. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_CEDAR.png +0 -0
  143. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_results_IEDB.png +0 -0
  144. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/ImmunoStruct_schematic.png +0 -0
  145. package/skills/13_Visualization/nature-figure/assets/figures4papers/assets/RNAGenScape_schematic.png +0 -0
  146. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/ablation.png +0 -0
  147. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/figures/comparison.png +0 -0
  148. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_ablation.py +86 -0
  149. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_CellSpliceNet/plot_comparison.py +109 -0
  150. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/diffusion_swiss_roll.py +97 -0
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  152. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.pdf +0 -0
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  158. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Ablation.py +64 -0
  159. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_GeneRegulatory.py +74 -0
  160. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/plot_comparison_Trajectory.py +74 -0
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  167. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_ablation_Cancer.png +0 -0
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  172. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/raw_data.py +125 -0
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  179. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_hole_manifold.py +82 -0
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1
+ # DDM Model Variants
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+
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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.
4
+
5
+ ---
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+
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+ ## Table of Contents
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+
9
+ 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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+
18
+ ---
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+
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+ ## 1. Classic DDM (Ratcliff, 1978)
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+
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+ ### Model Description
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+
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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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+
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+ ### Mathematical Formulation
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+
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+ The evidence variable x(t) evolves according to:
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+
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+ ```
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+ dx = v dt + s dW
32
+ ```
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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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+
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+ ### Parameters
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+
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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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+
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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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+
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+ ### When to Use
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+
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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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+
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+ ### Strengths
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+
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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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+
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+ ### Limitations
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+
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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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+
68
+ ---
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+
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+ ## 2. Full DDM with Trial-to-Trial Variability
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+
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+ ### Model Description
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+
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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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+
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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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+
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+ ### Additional Parameters
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+
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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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+
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+ ### Why Trial-to-Trial Variability Matters
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+
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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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+
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+ ### When to Use
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+
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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
99
+ - In domains where the full model is standard (e.g., recognition memory, lexical decision; Ratcliff et al., 2004)
100
+
101
+ ### Strengths
102
+
103
+ - Captures nuanced RT distribution features (e.g., relative speed of correct vs. error responses)
104
+ - Most complete account of 2AFC RT data
105
+ - Well-established fitting tools available (fast-dm, DMAT)
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+
107
+ ### Limitations
108
+
109
+ - 7 free parameters require substantial data (> **200 trials per condition** recommended; Ratcliff & Childers, 2015)
110
+ - sv and sz are often poorly identifiable with limited data (Boehm et al., 2018)
111
+ - Longer fitting times due to numerical integration (no closed-form solution with variability parameters)
112
+ - Risk of overfitting with small datasets
113
+
114
+ ### Identifiability Guidance
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+
116
+ When trial counts are moderate (**100-200 per condition**), consider fixing one or more variability parameters:
117
+
118
+ 1. Fix sz = 0 first (least impact on model fits in most domains; Ratcliff & Childers, 2015)
119
+ 2. Fix st0 = 0 next if needed
120
+ 3. sv is typically the most important variability parameter to retain (captures slow-error phenomenon)
121
+
122
+ ---
123
+
124
+ ## 3. EZ-Diffusion Model
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+
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+ ### Model Description
127
+
128
+ 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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+
130
+ ### Parameters Estimated
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+
132
+ | 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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+
138
+ ### Assumptions
139
+
140
+ - Starting point is unbiased: z = a/2 (not estimable)
141
+ - 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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+
144
+ ### Edge Correction
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+
146
+ 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):
147
+
148
+ ```
149
+ If Pc = 1: Pc_corrected = 1 - 1/(2N)
150
+ If Pc = 0: Pc_corrected = 1/(2N)
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+ If Pc = 0.5: Pc_corrected = 0.5 + 1/(2N)
152
+ ```
153
+
154
+ where N is the number of trials.
155
+
156
+ ### When to Use
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+
158
+ - 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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+
164
+ ### Strengths
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+
166
+ - 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)
169
+ - Transparent: easy to implement and check
170
+
171
+ ### Limitations
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+
173
+ - 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
177
+
178
+ ### Extensions
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+
180
+ - **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.
182
+
183
+ ---
184
+
185
+ ## 4. Hierarchical DDM (HDDM)
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+
187
+ ### Model Description
188
+
189
+ 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.
190
+
191
+ ### Hierarchical Structure
192
+
193
+ ```
194
+ Group level: v_group ~ prior, a_group ~ prior, ...
195
+
196
+ Individual: v_i ~ N(v_group, sigma_v), a_i ~ N(a_group, sigma_a), ...
197
+
198
+ Trial level: RT_ij, accuracy_ij ~ DDM(v_i, a_i, t0_i, z_i)
199
+ ```
200
+
201
+ ### Default Priors (HDDM Python package)
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+
203
+ | Parameter | Prior Distribution | Source |
204
+ |-----------|-------------------|--------|
205
+ | v (drift rate) | N(2, 3) | Wiecki et al., 2013, Table 1 |
206
+ | 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 |
209
+ | sv | Half-Normal | Wiecki et al., 2013 |
210
+
211
+ **Note**: These are the defaults in the HDDM package (v0.9+). Researchers should perform prior sensitivity analysis, especially for informative priors.
212
+
213
+ ### When to Use
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+
215
+ - 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)
217
+ - Individual differences research where you need reliable person-level parameter estimates
218
+ - When principled model comparison is needed (DIC, WAIC, Bayes factors)
219
+ - When you want full posterior distributions rather than point estimates
220
+
221
+ ### Strengths
222
+
223
+ - Handles moderate trial counts better than individual-level fitting via hierarchical shrinkage (Wiecki et al., 2013)
224
+ - Provides full posterior distributions — natural uncertainty quantification
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+ - Model comparison via DIC/WAIC (Spiegelhalter et al., 2002; Watanabe, 2010)
226
+ - Can include regression models on DDM parameters (e.g., linking neural data to drift rate)
227
+ - Well-maintained Python package with good documentation
228
+
229
+ ### Limitations
230
+
231
+ - Computationally intensive: MCMC sampling can take hours for large datasets
232
+ - Requires convergence diagnostics (R-hat < **1.1**, effective sample size > **200**; Gelman & Rubin, 1992; Wiecki et al., 2013)
233
+ - Prior sensitivity: results can depend on prior choices, especially with small samples
234
+ - Group-level normality assumption may not hold for all parameters
235
+
236
+ ### MCMC Diagnostics Checklist
237
+
238
+ 1. **R-hat (Gelman-Rubin statistic)**: Should be < **1.1** for all parameters (Gelman & Rubin, 1992)
239
+ 2. **Effective sample size**: Should be > **200** for reliable posterior summaries (Wiecki et al., 2013)
240
+ 3. **Visual trace inspection**: Chains should show good mixing (no trends, no stuck periods)
241
+ 4. **Posterior predictive checks**: Simulated data from the posterior should match observed RT distributions
242
+
243
+ ---
244
+
245
+ ## 5. Linear Ballistic Accumulator (LBA)
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+
247
+ ### Model Description
248
+
249
+ 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.
250
+
251
+ ### Key Difference from DDM
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+
253
+ | Feature | DDM | LBA |
254
+ |---------|-----|-----|
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+ | Number of accumulators | 1 (single process, two boundaries) | N (one per response option) |
256
+ | 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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+
260
+ ### Parameters
261
+
262
+ | 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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+
270
+ **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).
271
+
272
+ ### When to Use
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+
274
+ - Tasks with **more than 2 response alternatives** (natural multi-accumulator extension; Brown & Heathcote, 2008)
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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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+ - When within-trial noise is not theoretically important for your research question
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+ - As a comparison model to DDM for model selection (Donkin et al., 2011)
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+
279
+ ### Strengths
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+
281
+ - Natural extension to N > 2 alternatives without additional assumptions
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+ - Closed-form likelihood — very fast fitting
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+ - Mathematically simpler than DDM
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+ - Good empirical fits across many paradigms (Donkin et al., 2011)
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+
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+ ### Limitations
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+
288
+ - No within-trial noise: cannot capture some phenomena that arise from noisy accumulation
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+ - Different cognitive interpretation: stochasticity comes from trial-to-trial variability, not moment-to-moment noise
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+ - Cannot distinguish between some mechanisms that DDM can (e.g., within-trial evidence fluctuations)
291
+ - May overfit with too many free parameters in multi-alternative tasks
292
+
293
+ ---
294
+
295
+ ## 6. Racing Diffusion Model (RDM)
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+
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+ ### Model Description
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+
299
+ 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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+
301
+ ### Parameters
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+
303
+ | Parameter | Symbol | Description | Typical Range | Source |
304
+ |-----------|--------|-------------|---------------|--------|
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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 |
306
+ | Boundary | a | Common threshold | **0.5 – 3.0** | Tillman et al., 2020, Table 1 |
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+ | Non-decision time | t0 | Encoding + motor time | **0.1 – 0.5 s** | Tillman et al., 2020 |
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+ | Within-trial noise | s | Diffusion coefficient (often fixed to **1.0**) | Fixed as scaling parameter | Tillman et al., 2020 |
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+
310
+ ### When to Use
311
+
312
+ - Multi-alternative tasks (> 2 choices) where within-trial noise is theoretically important
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+ - When you believe that momentary evidence fluctuations matter (not just trial-to-trial variability)
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+ - Model comparison studies: RDM vs. LBA to test whether within-trial noise improves fit (Tillman et al., 2020)
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+
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.
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.
411
+ - 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.
412
+ - 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.
413
+ - 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.
415
+ - 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.
416
+ - 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
+ - Ratcliff, R. (1978). A theory of memory retrieval. *Psychological Review*, 85(2), 59–108.
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.
419
+ - Ratcliff, R., Gomez, P., & McKoon, G. (2004). A diffusion model account of the lexical decision task. *Psychological Review*, 111(1), 159–182.
420
+ - Ratcliff, R., & McKoon, G. (2008). The diffusion decision model: Theory and data for two-choice decision tasks. *Neural Computation*, 20(4), 873–922.
421
+ - Ratcliff, R., & Rouder, J. N. (1998). Modeling response times for two-choice decisions. *Psychological Science*, 9(5), 347–356.
422
+ - 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.
423
+ - 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.
424
+ - Voss, A., Nagler, M., & Lerche, V. (2013). Diffusion models in experimental psychology: A practical introduction. *Experimental Psychology*, 60(6), 385–402.
425
+ - Voss, A., Rothermund, K., & Voss, J. (2004). Interpreting the parameters of the diffusion model: An empirical validation. *Memory & Cognition*, 32(7), 1206–1220.
426
+ - 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.
427
+ - 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.