@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.
Files changed (229) hide show
  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
  151. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/diffusion_swiss_roll.png +0 -0
  152. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.pdf +0 -0
  153. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_GeneRegulatory.png +0 -0
  154. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_Trajectory.pdf +0 -0
  155. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/fig2_comparison_Trajectory.png +0 -0
  156. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/figX_comparison_Ablation.pdf +0 -0
  157. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Cflows/figures/figX_comparison_Ablation.png +0 -0
  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
  161. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/figures/idea.png +0 -0
  162. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/figures/illustration.png +0 -0
  163. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/plot_idea.py +76 -0
  164. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_Dispersion/plot_illustration.py +404 -0
  165. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_FPGM/figures/freq_prior.png +0 -0
  166. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_FPGM/plot_freq_prior.py +146 -0
  167. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_ablation_Cancer.png +0 -0
  168. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_ablation_IEDB.png +0 -0
  169. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_comparison_Cancer.png +0 -0
  170. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/figures/bars_comparison_IEDB.png +0 -0
  171. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/plot_bars.py +216 -0
  172. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ImmunoStruct/raw_data.py +125 -0
  173. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/figures/manifold.png +0 -0
  174. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/figures/manifold_holes.png +0 -0
  175. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/figures/results_comparison_optimization.png +0 -0
  176. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/figures/results_comparison_speed.png +0 -0
  177. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/figures/results_sweep.png +0 -0
  178. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_comparison.py +228 -0
  179. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_hole_manifold.py +82 -0
  180. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_manifold.py +61 -0
  181. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_RNAGenScape/plot_sweep.py +77 -0
  182. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_VIGIL/figures/comparison_posttraining.png +0 -0
  183. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_VIGIL/figures/comparison_radar.png +0 -0
  184. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_VIGIL/plot_comparison_radar.py +173 -0
  185. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_VIGIL/plot_posttraining.py +82 -0
  186. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/figures/brute_force.png +0 -0
  187. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/figures/correctness_by_category.png +0 -0
  188. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/figures/correctness_by_subcategory.png +0 -0
  189. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/figures/rewriting.png +0 -0
  190. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/figures/selfcorrection_math.png +0 -0
  191. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/plot_brute_force.py +248 -0
  192. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/plot_correctness_by_category.py +132 -0
  193. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/plot_correctness_by_subcategory.py +131 -0
  194. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/plot_rewriting.py +105 -0
  195. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_brainteaser/plot_selfcorrection_math.py +99 -0
  196. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ophthal_review/figures/composition_heatmap.png +0 -0
  197. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ophthal_review/figures/trend_by_month.png +0 -0
  198. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ophthal_review/plot_composition.py +81 -0
  199. package/skills/13_Visualization/nature-figure/assets/figures4papers/figure_ophthal_review/plot_trend.py +125 -0
  200. package/skills/13_Visualization/nature-figure/assets/gallery/fig1-material-mechanism-rich.png +0 -0
  201. package/skills/13_Visualization/nature-figure/assets/gallery/fig2-spatial-imaging-rich.png +0 -0
  202. package/skills/13_Visualization/nature-figure/assets/gallery/fig3-in-vivo-efficacy-rich.png +0 -0
  203. package/skills/13_Visualization/nature-figure/assets/gallery/fig4-single-cell-systems-rich.png +0 -0
  204. package/skills/13_Visualization/nature-figure/assets/gallery/fig5-validation-perturbation-rich.png +0 -0
  205. package/skills/13_Visualization/nature-figure/evals/evals.json +37 -0
  206. package/skills/13_Visualization/nature-figure/manifest.yaml +57 -0
  207. package/skills/13_Visualization/nature-figure/references/api.md +428 -0
  208. package/skills/13_Visualization/nature-figure/references/backend-selection.md +100 -0
  209. package/skills/13_Visualization/nature-figure/references/chart-types.md +281 -0
  210. package/skills/13_Visualization/nature-figure/references/common-patterns.md +350 -0
  211. package/skills/13_Visualization/nature-figure/references/demos.md +65 -0
  212. package/skills/13_Visualization/nature-figure/references/design-theory.md +436 -0
  213. package/skills/13_Visualization/nature-figure/references/figure-contract.md +93 -0
  214. package/skills/13_Visualization/nature-figure/references/nature-2026-observations.md +112 -0
  215. package/skills/13_Visualization/nature-figure/references/qa-contract.md +119 -0
  216. package/skills/13_Visualization/nature-figure/references/r-template-index.md +66 -0
  217. package/skills/13_Visualization/nature-figure/references/r-workflow.md +161 -0
  218. package/skills/13_Visualization/nature-figure/references/tutorials.md +251 -0
  219. package/skills/13_Visualization/nature-figure/static/core/contract.md +29 -0
  220. package/skills/13_Visualization/nature-figure/static/core/stance.md +37 -0
  221. package/skills/13_Visualization/nature-figure/static/fragments/backend/python.md +37 -0
  222. package/skills/13_Visualization/nature-figure/static/fragments/backend/r.md +44 -0
  223. package/skills/14_Writing/markdown-report-writing/SKILL.md +306 -0
  224. package/skills/14_Writing/markdown-report-writing/references/compatibility-matrix.md +72 -0
  225. package/skills/14_Writing/markdown-report-writing/references/templates.md +299 -0
  226. package/skills/15_Others/neuroimaging-power-guide/SKILL.md +324 -0
  227. package/skills/15_Others/neuroimaging-power-guide/references/effect-size-lookup-tables.md +102 -0
  228. package/skills/15_Others/neuroimaging-sample-size-calculator/SKILL.md +330 -0
  229. package/skills/15_Others/neuroimaging-sample-size-calculator/references/worked-examples.md +220 -0
@@ -0,0 +1,310 @@
1
+ ---
2
+ name: "evidence-accumulation-selector"
3
+ description: "Advises on when to use DDM vs. LBA vs. race models for choice-RT data based on experimental design and research goals"
4
+ domain: "cognitive-psychology"
5
+ version: "1.0.0"
6
+ authors:
7
+ - "Claude (AI-assisted)"
8
+ papers:
9
+ - "Ratcliff, 1978"
10
+ - "Ratcliff & McKoon, 2008"
11
+ - "Brown & Heathcote, 2008"
12
+ - "Wagenmakers et al., 2007"
13
+ - "Donkin et al., 2011"
14
+ dependencies:
15
+ required:
16
+ - research-literacy
17
+ review_status: "ai-generated"
18
+ ---
19
+
20
+ # Evidence Accumulation Model Selector
21
+
22
+ ## Purpose
23
+
24
+ This skill encodes expert knowledge for selecting among evidence accumulation models (EAMs) when analyzing choice response-time (RT) data. A competent programmer without cognitive science training would typically analyze only mean RT and accuracy separately, missing the critical insight that RT distributions and speed-accuracy tradeoffs carry rich information about latent cognitive processes. Selecting the wrong EAM -- or applying one when the data violate its assumptions -- leads to uninterpretable or misleading parameter estimates.
25
+
26
+ ## When to Use
27
+
28
+ Use this skill when:
29
+
30
+ - You have choice-time data (both accuracy and full RT distributions, not just means)
31
+ - You want to decompose observed performance into latent cognitive processes (evidence quality, response caution, non-decision time)
32
+ - You need to distinguish speed-accuracy tradeoff effects from genuine sensitivity changes
33
+ - You are deciding which model class (DDM, LBA, EZ-diffusion, race model) is appropriate for your experimental design
34
+
35
+ Do **not** use this skill when:
36
+
37
+ - You only have accuracy data without RTs (use signal detection theory instead)
38
+ - RTs are from simple detection (single response option) rather than choice tasks
39
+ - The task involves continuous tracking or free response without discrete choice points
40
+
41
+ ## Research Planning Protocol
42
+
43
+ Before executing the domain-specific steps below, you MUST:
44
+
45
+ 1. **State the research question** -- What specific question is this analysis/paradigm addressing?
46
+ 2. **Justify the method choice** -- Why is this approach appropriate? What alternatives were considered?
47
+ 3. **Declare expected outcomes** -- What results would support vs. refute the hypothesis?
48
+ 4. **Note assumptions and limitations** -- What does this method assume? Where could it mislead?
49
+ 5. **Present the plan to the user and WAIT for confirmation** before proceeding.
50
+
51
+ For detailed methodology guidance, see the `research-literacy` skill.
52
+
53
+
54
+ ## ⚠️ Verification Notice
55
+
56
+ This skill was generated by AI from academic literature. All parameters, thresholds, and citations require independent verification before use in research. If you find errors, please [open an issue](https://github.com/HaoxuanLiTHUAI/awesome_cognitive_and_neuroscience_skills/issues).
57
+
58
+ ## Core Concepts: What EAMs Do
59
+
60
+ All evidence accumulation models share a common framework: on each trial, noisy evidence is accumulated over time until a decision boundary is reached, triggering a response. The models differ in their assumptions about accumulation architecture.
61
+
62
+ ### Key Parameters Across Models
63
+
64
+ | Parameter | Cognitive Interpretation | Typical Manipulation |
65
+ |-----------|------------------------|---------------------|
66
+ | **Drift rate (v)** | Quality/rate of evidence extraction | Stimulus difficulty, S/N ratio (Ratcliff & McKoon, 2008) |
67
+ | **Boundary separation (a)** | Speed-accuracy tradeoff / response caution | Speed vs. accuracy instructions (Ratcliff & Rouder, 1998) |
68
+ | **Non-decision time (Ter / t0)** | Encoding + motor execution time | Response modality, stimulus quality (Ratcliff & McKoon, 2008) |
69
+ | **Starting point (z)** | Prior bias toward one response | Prior probability, payoff asymmetry (Ratcliff, 1985) |
70
+ | **Drift rate variability (eta/sv)** | Across-trial variability in evidence quality | Individual or item differences (Ratcliff, 1978) |
71
+ | **Non-decision time variability (st0)** | Variability in encoding/motor processes | (Ratcliff & Tuerlinckx, 2002) |
72
+
73
+ ## Decision Tree: Selecting a Model
74
+
75
+ ```
76
+ How many response alternatives does the task have?
77
+ |
78
+ +-- TWO alternatives
79
+ | |
80
+ | +-- Do you need full distributional analysis?
81
+ | | |
82
+ | | +-- YES --> Do you have sufficient trial counts (>50/condition)?
83
+ | | | |
84
+ | | | +-- YES --> Use the FULL DIFFUSION MODEL (DDM)
85
+ | | | | (Ratcliff, 1978; Ratcliff & McKoon, 2008)
86
+ | | | |
87
+ | | | +-- NO (fewer trials) --> Use EZ-DIFFUSION
88
+ | | | (Wagenmakers et al., 2007)
89
+ | | |
90
+ | | +-- NO (means/summaries sufficient)
91
+ | | --> Use EZ-DIFFUSION for simplicity
92
+ | | (Wagenmakers et al., 2007)
93
+ | |
94
+ | +-- Is response bias (starting point) a key research question?
95
+ | |
96
+ | +-- YES --> Use FULL DDM with z parameter free
97
+ | | (Ratcliff, 1985; White & Poldrack, 2014)
98
+ | |
99
+ | +-- NO --> DDM with z fixed at a/2 (unbiased)
100
+ |
101
+ +-- MORE THAN TWO alternatives
102
+ | |
103
+ | +-- Use the LINEAR BALLISTIC ACCUMULATOR (LBA)
104
+ | | (Brown & Heathcote, 2008)
105
+ | | or RACING DIFFUSION MODEL
106
+ | | (Tillman et al., 2020)
107
+ | |
108
+ | +-- Do accumulators need to be independent?
109
+ | |
110
+ | +-- YES --> LBA (independent accumulators by design)
111
+ | |
112
+ | +-- NO (competition matters) --> Racing diffusion
113
+ | or leaky competing accumulator (LCA; Usher & McClelland, 2001)
114
+ |
115
+ +-- SPECIAL CASES
116
+ |
117
+ +-- Extremely fast RTs (<200 ms median)?
118
+ | --> EAMs are likely inappropriate; these may be anticipatory
119
+ | responses (Luce, 1986)
120
+ |
121
+ +-- No speed pressure at all (untimed)?
122
+ | --> EAMs are inappropriate; use accuracy-based models
123
+ |
124
+ +-- Go/no-go task?
125
+ --> Use the DDM with absorbing boundary modifications
126
+ or the SSRT framework (Verbruggen & Logan, 2008)
127
+ ```
128
+
129
+ ## Model Descriptions
130
+
131
+ ### Drift Diffusion Model (DDM)
132
+
133
+ The canonical EAM for two-choice tasks (Ratcliff, 1978; Ratcliff & McKoon, 2008).
134
+
135
+ **Architecture**: A single accumulator drifts between two absorbing boundaries. Evidence for option A moves the process toward the upper boundary; evidence for option B moves it toward the lower boundary.
136
+
137
+ **Full DDM parameters** (7 parameters; Ratcliff & Tuerlinckx, 2002):
138
+
139
+ | Parameter | Symbol | Typical Range | Role |
140
+ |-----------|--------|---------------|------|
141
+ | Drift rate | v | -5 to 5 (Ratcliff & McKoon, 2008) | Evidence quality |
142
+ | Boundary separation | a | 0.5 to 2.5 (Ratcliff & McKoon, 2008) | Response caution |
143
+ | Non-decision time | Ter | 0.1 to 0.5 s (Ratcliff & McKoon, 2008) | Encoding + motor |
144
+ | Starting point | z | 0 to a (typically a/2) | Prior bias |
145
+ | Drift variability | eta (sv) | 0 to 2 (Ratcliff, 1978) | Cross-trial drift noise |
146
+ | Starting point variability | sz | 0 to a | Cross-trial bias noise |
147
+ | Non-decision variability | st0 | 0 to 0.3 s | Cross-trial Ter noise |
148
+
149
+ **When to use DDM**:
150
+ - Two-choice tasks with speed-accuracy tradeoff
151
+ - At least **40-50 trials per condition** for the full model (Ratcliff & Childers, 2015), though **200+ recommended** for stable individual parameter estimates (Lerche et al., 2017)
152
+ - RTs in the typical range: **200 ms to 2000 ms** (Ratcliff & McKoon, 2008)
153
+
154
+ **Key assumption**: Only two response options. The DDM cannot natively handle >2 choices.
155
+
156
+ ### EZ-Diffusion
157
+
158
+ A simplified closed-form estimator for three DDM parameters (Wagenmakers et al., 2007).
159
+
160
+ **Estimated parameters**: v (drift rate), a (boundary separation), Ter (non-decision time).
161
+
162
+ **Input**: Only three summary statistics per condition -- mean RT for correct responses (MRT), variance of RT for correct responses (VRT), and accuracy (Pc).
163
+
164
+ **Closed-form equations** (Wagenmakers et al., 2007, Eq. 1-3; see `references/ez-diffusion-formulas.md`):
165
+
166
+ **When to use EZ-diffusion**:
167
+ - Quick exploration before committing to full DDM fitting
168
+ - Low trial counts where full DDM is unstable (as few as **~10 trials per condition**; Wagenmakers et al., 2007)
169
+ - When only summary-level data are available (e.g., published means and variances)
170
+ - When the research question does not require starting point bias or cross-trial variability parameters
171
+
172
+ **Limitations**:
173
+ - Assumes no starting point variability (sz = 0) and no cross-trial drift variability (sv = 0)
174
+ - Cannot estimate response bias
175
+ - The "edge correction" is needed when accuracy is 0.5 or 1.0 (Wagenmakers et al., 2007)
176
+
177
+ ### Linear Ballistic Accumulator (LBA)
178
+
179
+ A multi-alternative accumulator model (Brown & Heathcote, 2008).
180
+
181
+ **Architecture**: N independent linear accumulators (one per response option) race to a common threshold. The first accumulator to reach threshold triggers the corresponding response. Accumulation is ballistic (no within-trial noise) -- all variability comes from across-trial variation in drift rates and starting points.
182
+
183
+ **Parameters per accumulator** (Brown & Heathcote, 2008):
184
+
185
+ | Parameter | Symbol | Role |
186
+ |-----------|--------|------|
187
+ | Mean drift rate | vi | Evidence accumulation rate for option i |
188
+ | Drift rate variability | s | Across-trial standard deviation of drift (often fixed to 1 for scaling) |
189
+ | Response threshold | b | Evidence needed to trigger response |
190
+ | Maximum starting point | A | Upper bound of uniform start-point distribution [0, A] |
191
+ | Non-decision time | t0 | Encoding + motor time |
192
+
193
+ **When to use LBA**:
194
+ - Tasks with **2 or more** response alternatives (Brown & Heathcote, 2008)
195
+ - When you need a mathematically tractable multi-choice model
196
+ - When accumulators can be assumed independent (no lateral inhibition)
197
+ - Minimum **~100 trials per condition** recommended (Donkin et al., 2011)
198
+
199
+ ### Race Models
200
+
201
+ **Classical race model** (Pike, 1966; Townsend & Ashby, 1983): Multiple accumulators race independently; first to finish wins. Unlike DDM, there is no competition between accumulators.
202
+
203
+ **When to use**:
204
+ - As a baseline/null model to test against more complex models
205
+ - When inhibitory competition between responses is not theoretically expected
206
+
207
+ **Limitation**: The standard race model cannot account for speed-accuracy tradeoff without additional assumptions (Ratcliff & McKoon, 2008).
208
+
209
+ ## Model Comparison Methods
210
+
211
+ When comparing model fits, use information criteria that penalize complexity:
212
+
213
+ | Method | When to Use | Citation |
214
+ |--------|-------------|----------|
215
+ | **BIC** | Frequentist model comparison; favors parsimony; appropriate for large N | Schwarz, 1978 |
216
+ | **AIC** | Less conservative than BIC; better for prediction | Akaike, 1974 |
217
+ | **DIC** | Bayesian hierarchical models (e.g., HDDM) | Spiegelhalter et al., 2002 |
218
+ | **WAIC** | Bayesian; more stable than DIC for hierarchical models | Watanabe, 2010 |
219
+ | **Bayes factor** | Direct comparison of model evidence; interpretable strength | Kass & Raftery, 1995 |
220
+
221
+ **Preferred approach**: Fit competing models and compare using WAIC or Bayes factors in a Bayesian framework (Annis et al., 2017). Lower WAIC = better fit.
222
+
223
+ ## Parameter Recovery Check
224
+
225
+ Before interpreting fitted parameters, **always** conduct a parameter recovery study (Heathcote et al., 2015):
226
+
227
+ 1. Simulate data from known parameter values matching your design
228
+ 2. Fit the model to simulated data
229
+ 3. Check that recovered parameters correlate highly (r > 0.90) with generating parameters
230
+ 4. If recovery fails, the model is too complex for your data or trial counts are insufficient
231
+
232
+ ## Software Recommendations
233
+
234
+ | Software | Model | Language | Citation |
235
+ |----------|-------|----------|----------|
236
+ | **HDDM** | DDM (hierarchical Bayesian) | Python | Wiecki et al., 2013 |
237
+ | **fast-dm** | DDM (frequentist, fast) | C / R wrapper | Voss & Voss, 2007 |
238
+ | **EZ-diffusion** | EZ | R / any | Wagenmakers et al., 2007 |
239
+ | **rtdists** | DDM, LBA | R | Singmann et al., 2016 |
240
+ | **PyDDM** | DDM (flexible extensions) | Python | Shinn et al., 2020 |
241
+ | **DMC** | LBA, DDM, racing diffusion | R | Heathcote et al., 2019 |
242
+
243
+ ## Common Pitfalls
244
+
245
+ 1. **Analyzing mean RT only**: Mean RT conflates drift rate, boundary separation, and non-decision time. Two conditions with identical mean RTs can have very different latent processes (Ratcliff & McKoon, 2008).
246
+
247
+ 2. **Applying DDM to >2-choice tasks**: The standard DDM is defined for two-choice tasks only. For 3+ alternatives, use LBA, racing diffusion, or the multi-alternative DDM extension (Ratcliff & Starns, 2013).
248
+
249
+ 3. **Insufficient trial counts**: The full DDM requires at least **40-50 trials per condition** for group-level estimates and **200+ for stable individual estimates** (Ratcliff & Childers, 2015; Lerche et al., 2017). With fewer trials, use EZ-diffusion or hierarchical Bayesian fitting.
250
+
251
+ 4. **Ignoring RT distribution shape**: EAMs predict specific distributional forms (right-skewed). If your RT distribution is bimodal or has a long left tail, check for contaminant processes (e.g., fast guesses) before fitting (Ratcliff & Tuerlinckx, 2002).
252
+
253
+ 5. **Not trimming outlier RTs**: Extremely fast (<200 ms) or slow (>3000 ms for speeded tasks) RTs likely reflect processes outside the model. Standard practice: trim RTs below **200 ms** and above a task-appropriate upper bound (Ratcliff & McKoon, 2008).
254
+
255
+ 6. **Fitting too many free parameters**: The full 7-parameter DDM is often overparameterized. Fix parameters that are not theoretically relevant (e.g., fix sz = 0 and st0 = 0 as a starting point; Ratcliff & Childers, 2015).
256
+
257
+ 7. **Confusing EZ-diffusion limitations**: EZ-diffusion assumes no across-trial variability in drift or starting point. If your design manipulates prior probability (affecting starting point bias), EZ cannot capture this (Wagenmakers et al., 2007).
258
+
259
+ 8. **Skipping parameter recovery**: Without recovery checks, you cannot know whether your data are informative for the parameters you want to interpret (Heathcote et al., 2015).
260
+
261
+ ## Minimum Reporting Checklist
262
+
263
+ Based on Dutilh et al. (2019) and current best practices:
264
+
265
+ - [ ] Model selected and justification (why DDM vs. LBA vs. EZ)
266
+ - [ ] Number of trials per condition per participant
267
+ - [ ] RT trimming criteria and percentage of data excluded
268
+ - [ ] Complete list of free vs. fixed parameters with rationale
269
+ - [ ] Fitting method (MLE, chi-square, Bayesian) and software (with version)
270
+ - [ ] Model fit assessment (quantile probability plots, AIC/BIC/WAIC)
271
+ - [ ] Parameter recovery results (simulated data check)
272
+ - [ ] All parameter estimates with uncertainty (SE or credible intervals)
273
+ - [ ] Model comparison results if multiple models were fit
274
+ - [ ] Diagnostic plots: observed vs. predicted RT quantiles (0.1, 0.3, 0.5, 0.7, 0.9) for correct and error responses
275
+
276
+ ## References
277
+
278
+ - Akaike, H. (1974). A new look at the statistical model identification. *IEEE Transactions on Automatic Control*, 19, 716-723.
279
+ - Annis, J., Miller, B. J., & Palmeri, T. J. (2017). Bayesian inference with Stan: A tutorial on adding custom distributions. *Behavior Research Methods*, 49, 863-886.
280
+ - Brown, S. D., & Heathcote, A. (2008). The simplest complete model of choice response time: Linear ballistic accumulation. *Cognitive Psychology*, 57, 153-178.
281
+ - Donkin, C., Averell, L., Brown, S., & Heathcote, A. (2011). Getting more from accuracy and response time data: Methods for fitting the linear ballistic accumulator. *Behavior Research Methods*, 43, 332-343.
282
+ - Dutilh, G., et al. (2019). The quality of response time data inference: A blinded, collaborative assessment of the validity of cognitive models. *Psychonomic Bulletin & Review*, 26, 1051-1069.
283
+ - Heathcote, A., Brown, S. D., & Wagenmakers, E.-J. (2015). An introduction to good practices in cognitive modeling. In B. U. Forstmann & E.-J. Wagenmakers (Eds.), *An introduction to model-based cognitive neuroscience*. New York: Springer.
284
+ - Heathcote, A., Lin, Y.-S., Reynolds, A., Strickland, L., Gretton, M., & Matzke, D. (2019). Dynamic models of choice. *Behavior Research Methods*, 51, 961-985.
285
+ - Kass, R. E., & Raftery, A. E. (1995). Bayes factors. *Journal of the American Statistical Association*, 90, 773-795.
286
+ - Lerche, V., Voss, A., & Nagler, M. (2017). How many trials are required for parameter estimation in diffusion modeling? *Behavior Research Methods*, 49, 513-537.
287
+ - Luce, R. D. (1986). *Response times: Their role in inferring elementary mental organization*. New York: Oxford University Press.
288
+ - Pike, R. (1966). Stochastic models of choice behaviour: Response probabilities and latencies of finite Markov chain systems. *British Journal of Mathematical and Statistical Psychology*, 19, 15-32.
289
+ - Ratcliff, R. (1978). A theory of memory retrieval. *Psychological Review*, 85, 59-108.
290
+ - Ratcliff, R. (1985). Theoretical interpretations of the speed and accuracy of positive and negative responses. *Psychological Review*, 92, 212-225.
291
+ - Ratcliff, R., & Childers, R. (2015). Individual differences and fitting methods for the two-choice diffusion model of decision making. *Decision*, 2, 237-279.
292
+ - Ratcliff, R., & McKoon, G. (2008). The diffusion decision model: Theory and data for two-choice decision tasks. *Neural Computation*, 20, 873-922.
293
+ - Ratcliff, R., & Rouder, J. N. (1998). Modeling response times for two-choice decisions. *Psychological Science*, 9, 347-356.
294
+ - Ratcliff, R., & Starns, J. J. (2013). Modeling response times, accuracy, and confidence in two-choice tasks. *Psychological Review*, 120, 510-560.
295
+ - Ratcliff, R., & Tuerlinckx, F. (2002). Estimating parameters of the diffusion model. *Psychonomic Bulletin & Review*, 9, 438-481.
296
+ - Schwarz, G. (1978). Estimating the dimension of a model. *Annals of Statistics*, 6, 461-464.
297
+ - Shinn, M., Lam, N. H., & Murray, J. D. (2020). A flexible framework for simulating and fitting generalized drift-diffusion models. *eLife*, 9, e56938.
298
+ - Singmann, H., Brown, S., Gretton, M., & Heathcote, A. (2016). rtdists: Response time distributions. R package.
299
+ - Spiegelhalter, D. J., Best, N. G., Carlin, B. P., & van der Linde, A. (2002). Bayesian measures of model complexity and fit. *Journal of the Royal Statistical Society B*, 64, 583-639.
300
+ - Tillman, G., Van Zandt, T., & Logan, G. D. (2020). Sequential sampling models without random between-trial variability: The racing diffusion model with its competing risks. *Psychonomic Bulletin & Review*, 27, 1170-1190.
301
+ - Townsend, J. T., & Ashby, F. G. (1983). *Stochastic modeling of elementary psychological processes*. Cambridge University Press.
302
+ - Usher, M., & McClelland, J. L. (2001). The time course of perceptual choice: The leaky, competing accumulator model. *Psychological Review*, 108, 550-592.
303
+ - Verbruggen, F., & Logan, G. D. (2008). Response inhibition in the stop-signal paradigm. *Trends in Cognitive Sciences*, 12, 418-424.
304
+ - Voss, A., & Voss, J. (2007). Fast-dm: A free program for efficient diffusion model analysis. *Behavior Research Methods*, 39, 767-775.
305
+ - 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, 3-22.
306
+ - Watanabe, S. (2010). Asymptotic equivalence of Bayes cross validation and widely applicable information criterion in singular learning theory. *Journal of Machine Learning Research*, 11, 3571-3594.
307
+ - White, C. N., & Poldrack, R. A. (2014). Decomposing bias in different types of simple decisions. *Journal of Experimental Psychology: Learning, Memory, and Cognition*, 40, 385-398.
308
+ - 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.
309
+
310
+ See `references/ez-diffusion-formulas.md` for EZ-diffusion closed-form equations and worked examples.
@@ -0,0 +1,137 @@
1
+ # EZ-Diffusion Formulas and Worked Examples
2
+
3
+ This reference file supplements the main `SKILL.md` with the closed-form equations for EZ-diffusion (Wagenmakers et al., 2007) and worked examples.
4
+
5
+ ## 1. Input Requirements
6
+
7
+ EZ-diffusion requires three summary statistics per experimental condition:
8
+
9
+ - **Pc**: Proportion correct (accuracy), where 0.5 < Pc <= 1.0
10
+ - **MRT**: Mean response time for correct responses (in seconds)
11
+ - **VRT**: Variance of response times for correct responses (in seconds squared)
12
+
13
+ ## 2. Closed-Form Equations
14
+
15
+ The following equations yield the three EZ-diffusion parameters from the summary statistics (Wagenmakers et al., 2007, Eq. 1-3).
16
+
17
+ ### Step 1: Compute drift rate (v)
18
+
19
+ ```
20
+ Define: s = constant scaling parameter (typically s = 0.1; Ratcliff, 1978)
21
+
22
+ L = logit(Pc) = ln(Pc / (1 - Pc))
23
+
24
+ x = L * (L * Pc^2 - L * Pc + Pc - 0.5) / VRT
25
+
26
+ v = sign(Pc - 0.5) * s * x^(1/4)
27
+ ```
28
+
29
+ ### Step 2: Compute boundary separation (a)
30
+
31
+ ```
32
+ y = -v * L / (Pc^2 * (s^2 / (2*v^2)) * (exp(-2 * v * L * s^(-2)) - 1))
33
+
34
+ Wait -- using the cleaner formulation from Wagenmakers et al. (2007):
35
+
36
+ a = s^2 * L / v
37
+ ```
38
+
39
+ Note: The sign convention ensures a > 0 when Pc > 0.5.
40
+
41
+ ### Step 3: Compute non-decision time (Ter)
42
+
43
+ ```
44
+ Ter = MRT - (a / (2 * v)) * ((1 - exp(-v * a / s^2)) / (1 + exp(-v * a / s^2)))
45
+ ```
46
+
47
+ ## 3. Edge Correction
48
+
49
+ When Pc = 0.5 (chance) or Pc = 1.0 (perfect), the equations break down (Wagenmakers et al., 2007).
50
+
51
+ **Correction for Pc = 1.0**:
52
+ ```
53
+ Pc_corrected = 1 - 1 / (2 * N)
54
+ ```
55
+
56
+ **Correction for Pc = 0.5**:
57
+ ```
58
+ Pc_corrected = 0.5 + 1 / (2 * N)
59
+ ```
60
+
61
+ Where N = number of trials in that condition. Apply these corrections before computing EZ parameters.
62
+
63
+ ## 4. Robust EZ (REZ)
64
+
65
+ Robust EZ (Grasman et al., 2009) addresses two limitations of basic EZ:
66
+
67
+ 1. Uses **median RT** instead of mean RT (more robust to outliers)
68
+ 2. Uses a **quantile-based variance estimate** (interquartile range) instead of sample variance
69
+
70
+ Equations are similar but use robust estimators. See Grasman, Wagenmakers, & van der Maas (2009) for details.
71
+
72
+ ## 5. Worked Example
73
+
74
+ ### Example Data
75
+
76
+ A participant in a lexical decision task:
77
+ - Condition: High frequency words
78
+ - Trials: 100 correct out of 120 total
79
+ - Pc = 100/120 = 0.833
80
+ - MRT (correct) = 0.623 s
81
+ - VRT (correct) = 0.018 s^2
82
+
83
+ ### Step-by-step Computation
84
+
85
+ Using scaling parameter s = 0.1 (Ratcliff, 1978):
86
+
87
+ ```
88
+ L = ln(0.833 / 0.167) = ln(4.988) = 1.607
89
+
90
+ v = sign(0.833 - 0.5) * 0.1 * (1.607 * (1.607 * 0.833^2 - 1.607 * 0.833 + 0.833 - 0.5) / 0.018)^(1/4)
91
+ = 0.1 * (1.607 * (1.115 - 1.339 + 0.333) / 0.018)^(1/4)
92
+ = 0.1 * (1.607 * 0.109 / 0.018)^(1/4)
93
+ = 0.1 * (9.731)^(1/4)
94
+ = 0.1 * 1.766
95
+ = 0.177
96
+
97
+ a = 0.01 * 1.607 / 0.177
98
+ = 0.091
99
+
100
+ Ter = 0.623 - (0.091 / (2 * 0.177)) * ((1 - exp(-0.177 * 0.091 / 0.01)) / (1 + exp(-0.177 * 0.091 / 0.01)))
101
+ = 0.623 - 0.257 * ((1 - exp(-1.611)) / (1 + exp(-1.611)))
102
+ = 0.623 - 0.257 * ((1 - 0.200) / (1 + 0.200))
103
+ = 0.623 - 0.257 * 0.667
104
+ = 0.623 - 0.171
105
+ = 0.452 s
106
+ ```
107
+
108
+ ### Interpretation
109
+
110
+ - **v = 0.177**: Moderate drift rate, indicating reasonable evidence accumulation for high-frequency words
111
+ - **a = 0.091**: Boundary separation reflecting the speed-accuracy tradeoff setting
112
+ - **Ter = 0.452 s**: Non-decision time, encompassing stimulus encoding and motor execution
113
+
114
+ ## 6. Comparison: When EZ Diverges from Full DDM
115
+
116
+ EZ-diffusion assumes:
117
+ - No across-trial variability in drift rate (sv = 0)
118
+ - No across-trial variability in starting point (sz = 0)
119
+ - No across-trial variability in non-decision time (st0 = 0)
120
+
121
+ When these variability parameters are non-zero in reality (Ratcliff, 1978):
122
+ - EZ drift rate estimates tend to be **underestimates** of true drift rate
123
+ - EZ boundary estimates remain relatively accurate
124
+ - EZ non-decision time can be **overestimated**
125
+
126
+ The mismatch is most problematic when:
127
+ - Error RTs are substantially faster or slower than correct RTs (indicating sv > 0; Ratcliff & McKoon, 2008)
128
+ - There is strong a priori bias toward one response (indicating sz > 0)
129
+
130
+ For designs where these variabilities are theoretically important, use the full DDM instead.
131
+
132
+ ## References
133
+
134
+ - 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, 55-68.
135
+ - Ratcliff, R. (1978). A theory of memory retrieval. *Psychological Review*, 85, 59-108.
136
+ - Ratcliff, R., & McKoon, G. (2008). The diffusion decision model: Theory and data for two-choice decision tasks. *Neural Computation*, 20, 873-922.
137
+ - 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, 3-22.