Name		Name	Last commit message	Last commit date
eda_glm_analysis		eda_glm_analysis
results		results
.gitignore		.gitignore
89540A Mouse PD ABET Cog Manual v.1.1.pdf		89540A Mouse PD ABET Cog Manual v.1.1.pdf
ANALYSIS_GUIDE.md		ANALYSIS_GUIDE.md
ANALYSIS_STATUS_AND_RECOMMENDATIONS.md		ANALYSIS_STATUS_AND_RECOMMENDATIONS.md
ANALYSIS_SUMMARY.md		ANALYSIS_SUMMARY.md
COMPLETE_FIGURES_MANIFEST.md		COMPLETE_FIGURES_MANIFEST.md
COMPREHENSIVE_ANALYSIS_PLAN.md		COMPREHENSIVE_ANALYSIS_PLAN.md
CROSS_VALIDATION_INSTRUCTIONS.md		CROSS_VALIDATION_INSTRUCTIONS.md
F LD Data 11.08 All_processed.csv		F LD Data 11.08 All_processed.csv
FIGURE_REGENERATION_SUMMARY.md		FIGURE_REGENERATION_SUMMARY.md
F_LD_LDR_triallevel.csv		F_LD_LDR_triallevel.csv
F_cohort_validation.py		F_cohort_validation.py
Fall 25 TSC Processing.py		Fall 25 TSC Processing.py
GLM_HMM_Analysis_Ashwood.ipynb		GLM_HMM_Analysis_Ashwood.ipynb
HYPOTHESIS_TESTING_GUIDE.md		HYPOTHESIS_TESTING_GUIDE.md
IMPLEMENTATION_PLAN.md		IMPLEMENTATION_PLAN.md
LDR 2025 data1_processed_withSecondCriterion.csv		LDR 2025 data1_processed_withSecondCriterion.csv
Mouse Touch LD ABET II Manual V2 _2x6.pdf		Mouse Touch LD ABET II Manual V2 _2x6.pdf
README.md		README.md
REASONING.md		REASONING.md
REGENERATE_FIGURES_README.md		REGENERATE_FIGURES_README.md
RESOLUTION_accuracy_discrepancy.md		RESOLUTION_accuracy_discrepancy.md
TASK_UNDERSTANDING_AND_CORRECTIONS.md		TASK_UNDERSTANDING_AND_CORRECTIONS.md
TSC GLM HMM 2025.ipynb		TSC GLM HMM 2025.ipynb
TSC LDR crit.py		TSC LDR crit.py
W LD Data 11.08 All_processed.csv		W LD Data 11.08 All_processed.csv
W LD Data 11.08 PD_processed.csv		W LD Data 11.08 PD_processed.csv
additional_visualizations.py		additional_visualizations.py
advanced_analysis.py		advanced_analysis.py
advanced_visualization.py		advanced_visualization.py
analysis_output.log		analysis_output.log
complete_F_cohort_phase1.py		complete_F_cohort_phase1.py
comprehensive_genotype_analysis.py		comprehensive_genotype_analysis.py
comprehensive_individual_analysis.py		comprehensive_individual_analysis.py
comprehensive_statistical_analysis.py		comprehensive_statistical_analysis.py
create_ambiguity_removal_figures.py		create_ambiguity_removal_figures.py
create_cohort_summaries.py		create_cohort_summaries.py
create_enhanced_state_visualizations.py		create_enhanced_state_visualizations.py
create_interpretation_guide.py		create_interpretation_guide.py
create_labeled_transition_matrices.py		create_labeled_transition_matrices.py
create_methods_figure.py		create_methods_figure.py
create_phase2_detailed_analyses.py		create_phase2_detailed_analyses.py
create_phase2_individual_learning_curves.py		create_phase2_individual_learning_curves.py
create_phase2_psychometric_curves.py		create_phase2_psychometric_curves.py
create_phase2_visualizations.py		create_phase2_visualizations.py
create_rt_analysis.py		create_rt_analysis.py
create_state_psychometric_functions.py		create_state_psychometric_functions.py
critical_task_validation.py		critical_task_validation.py
enhanced_phase2_visualization.py		enhanced_phase2_visualization.py
enhanced_poster_visualizations.py		enhanced_poster_visualizations.py
generate_F_cohort_summary.py		generate_F_cohort_summary.py
generate_F_summaries_from_results.py		generate_F_summaries_from_results.py
generate_additional_figures.py		generate_additional_figures.py
genotype_labels.py		genotype_labels.py
genotype_sex_comparisons.py		genotype_sex_comparisons.py
glmhmm_ashwood.py		glmhmm_ashwood.py
glmhmm_utils.py		glmhmm_utils.py
investigate_accuracy_mismatches.py		investigate_accuracy_mismatches.py
late_lapser_analysis.py		late_lapser_analysis.py
master_figure_regenerator.py		master_figure_regenerator.py
monitor_progress.py		monitor_progress.py
phase2_combined_cohort_analysis.py		phase2_combined_cohort_analysis.py
phase2_state_dynamics_regression.py		phase2_state_dynamics_regression.py
priority1_complete.py		priority1_complete.py
priority1_fix.py		priority1_fix.py
priority1_visualizations.py		priority1_visualizations.py
priority2_detailed_state_analysis.py		priority2_detailed_state_analysis.py
priority2_fixes_and_additions.py		priority2_fixes_and_additions.py
priority2_model_validation.py		priority2_model_validation.py
priority2_state_dynamics.py		priority2_state_dynamics.py
regenerate_all_figures_locally.py		regenerate_all_figures_locally.py
regenerate_all_figures_with_new_labels.py		regenerate_all_figures_with_new_labels.py
regenerate_cohort_pickles.py		regenerate_cohort_pickles.py
reversal_detection.py		reversal_detection.py
run_complete_analysis.py		run_complete_analysis.py
run_cross_validation.py		run_cross_validation.py
run_cross_validation_comprehensive.py		run_cross_validation_comprehensive.py
run_cross_validation_local.py		run_cross_validation_local.py
run_phase1_analysis.py		run_phase1_analysis.py
run_phase2_analysis.py		run_phase2_analysis.py
run_phase2_reversal_analysis.py		run_phase2_reversal_analysis.py
simple_figure_regenerator.py		simple_figure_regenerator.py
state_transitions.py		state_transitions.py
state_validation.py		state_validation.py
task_progression_evidence.py		task_progression_evidence.py
test_both_cohorts.py		test_both_cohorts.py
test_multiple_animals.py		test_multiple_animals.py
test_phase1_single.py		test_phase1_single.py
traditional_statistical_analyses.py		traditional_statistical_analyses.py
verify_accuracy_match.py		verify_accuracy_match.py

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GLMHMM

GLMHMM analysis for touchscreen data

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GLMHMM analysis for touchscreen data

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