├── LICENSE.md ├── README.md ├── analyticalDDM ├── DDM │ ├── .DS_Store │ ├── FIT_regular_DDM_PSO.m │ ├── ML_from_fpts_regularDDM.m │ ├── ReadMe.txt │ ├── add_contaminants.m │ ├── fpt_regular_DDM.m │ ├── lgwt.m │ ├── particle_swarm │ │ ├── A Particle Swarm Optimization (PSO) Primer.pdf │ │ ├── DemoPSOBehavior.m │ │ ├── ReadME.txt │ │ ├── goplotpso.m │ │ ├── goplotpso4demo.m │ │ ├── hiddenutils │ │ │ ├── forcecol.m │ │ │ ├── forcerow.m │ │ │ ├── linear_dyn.m │ │ │ ├── normmat.m │ │ │ └── spiral_dyn.m │ │ ├── license.txt │ │ ├── nnet │ │ │ ├── demoPSOnet.m │ │ │ ├── goplotpso4net.m │ │ │ ├── pso_neteval.m │ │ │ └── trainpso.m │ │ ├── pso_Trelea_vectorized.m │ │ ├── pso_Trelea_vectorized.m~ │ │ └── testfunctions │ │ │ ├── DeJong_f2.m │ │ │ ├── DeJong_f3.m │ │ │ ├── DeJong_f4.m │ │ │ ├── Foxhole.m │ │ │ ├── Griewank.m │ │ │ ├── NDparabola.m │ │ │ ├── Rastrigin.m │ │ │ ├── Rosenbrock.m │ │ │ ├── ackley.m │ │ │ ├── alpine.m │ │ │ ├── f6.m │ │ │ ├── f6_bubbles_dyn.m │ │ │ ├── f6_linear_dyn.m │ │ │ ├── f6_spiral_dyn.m │ │ │ ├── f6mod.m │ │ │ └── tripod.m │ ├── sim_G.m │ └── sim_Pe.m ├── LeakyAccumulator │ ├── FIT_2acc.m │ ├── L2acc.m │ ├── ML_2acc.m │ ├── ReadMe.txt │ ├── get_grid_min.m │ ├── get_param_mat.m │ ├── get_param_order.m │ ├── sim2acc.m │ └── sim2acc_no_bound.m └── README.md ├── barplots_BIC.m ├── barplots_DIC_stcoh.m ├── barplots_modelcomparison.m ├── barplots_modelcomparison_regression.m ├── compare_correlations_correct_error.m ├── conditional_bias_functions_collapsed.m ├── conditional_bias_functions_collapsed_summary.m ├── corrcoef2.m ├── correlate_z_vbias.m ├── correlations_regression_lags.m ├── define_behavioral_metrics.m ├── dprime_driftrate_correlation.m ├── extended_models ├── .DS_Store ├── README.md ├── data_processing │ ├── descriptives.mat │ ├── descriptives_script.m │ ├── motionEnergyData_AnkeMEG.mat │ └── motionEnergyData_AnkeMEG_Dynamic.mat ├── default_protocol │ ├── .DS_Store │ ├── Drift_Bias │ │ ├── cost_fit.m │ │ ├── diffusion_custom2.m │ │ ├── superScript_Step1.m │ │ └── superScript_Step2.m │ ├── Hybrid │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ ├── Hybrid_Ramping │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ ├── Naive │ │ ├── Bridge_Fits.m │ │ ├── cost_fit.m │ │ ├── diffusion_custom2.m │ │ ├── superScript_Step1.m │ │ └── superScript_Step2.m │ ├── Simple_Ramping │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ └── Starting_Point │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m └── dynamic_protocol │ ├── .DS_Store │ ├── collapsing_bounds │ ├── .DS_Store │ ├── Drift_Bias │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ ├── Hybrid │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ ├── Leaky_Input_Bias │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ ├── Leaky_Starting_Point │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ ├── Leaky_lambda_Bias │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ └── Starting_Point │ │ ├── cost_fit.m │ │ └── diffusion_custom2.m │ └── static_bounds │ ├── .DS_Store │ ├── Drift_Bias │ ├── cost_fit.m │ └── diffusion_custom2.m │ ├── Hybrid_Ramping │ ├── cost_fit.m │ └── diffusion_custom2.m │ ├── Leaky_Input_Bias │ ├── cost_fit.m │ └── diffusion_custom2.m │ ├── Leaky_Starting_Point │ ├── cost_fit.m │ └── diffusion_custom2.m │ ├── Leaky_lambda_Bias │ ├── cost_fit.m │ └── diffusion_custom2.m │ ├── Naive │ ├── cost_fit.m │ ├── diffusion_custom2.m │ ├── superScript_Step1.m │ └── superScript_Step2.m │ └── Simple_Ramping │ ├── cost_fit.m │ └── diffusion_custom2.m ├── fitHDDM.py ├── fitLogistic.m ├── forestPlot.m ├── gelman_rubin.m ├── graphicalModels ├── HDDM.pdf ├── HISTORY.rst ├── LICENSE.rst ├── MANIFEST.in ├── MCMC.dot ├── README.rst ├── daft.py ├── daft.pyc ├── docs │ ├── .gitignore │ ├── Makefile │ ├── _static │ │ ├── d3.v2.min.js │ │ ├── examples.js │ │ ├── examples.json │ │ ├── favicon.png │ │ └── logo.png │ ├── _themes │ │ └── daft │ │ │ ├── layout.html │ │ │ ├── relations.html │ │ │ ├── search.html │ │ │ ├── searchbox.html │ │ │ ├── static │ │ │ ├── code.css │ │ │ ├── daft.css │ │ │ └── normalize.css │ │ │ └── theme.conf │ ├── api.rst │ ├── conf.py │ ├── examples │ │ ├── badfont.rst │ │ ├── classic.rst │ │ ├── exoplanets.rst │ │ ├── index.rst │ │ ├── mrf.rst │ │ ├── nocircles.rst │ │ ├── nogray.rst │ │ ├── recursive.rst │ │ ├── weaklensing.rst │ │ └── wordy.rst │ ├── gen_example.py │ └── index.rst ├── example1_graph.png ├── examples │ ├── astronomy.py │ ├── badfont.py │ ├── bca.py │ ├── classic.py │ ├── exoplanets.py │ ├── fixed.py │ ├── gaia.py │ ├── galex.py │ ├── huey_p_newton.py │ ├── logo.py │ ├── mrf.py │ ├── nocircles.py │ ├── nogray.py │ ├── recursive.py │ ├── thicklines.py │ ├── weaklensing.py │ ├── wordy.py │ └── yike.py ├── graph.dotfile ├── graph1.gv ├── hddm_graph.png ├── images │ ├── classic.pdf │ ├── classic.png │ ├── logo.png │ ├── nocircles.pdf │ ├── nocircles.png │ ├── nogray.pdf │ ├── nogray.png │ ├── weaklensing.pdf │ ├── weaklensing.png │ ├── wordy.pdf │ └── wordy.png ├── lda_graph.png ├── manualGraphical.py ├── plotHDDMgraphical.py └── setup.py ├── hddm_models.py ├── hddm_models.pyc ├── hddmparams ├── hddmparams_PPC ├── history_kernels.m ├── individual_correlation_PES.m ├── individual_correlation_main.m ├── individual_correlation_pharma.m ├── individual_correlation_prevcorrect.m ├── individual_correlation_repeaters_vs_alternators.m ├── individual_correlation_tcoh.m ├── kernels_lags_bestmodel.m ├── kostis_all_AICs.m ├── kostis_all_correlations_selected.m ├── kostis_makeTable_v2.m ├── make_dataframe.m ├── make_stopos_file.m ├── meg_regression_dic.m ├── meg_regression_posteriors.m ├── motionEnergy_check.m ├── motionEnergy_filterDots.m ├── motionEnergy_kernels.m ├── nondecisiontime_coherence.m ├── old_code ├── ._HDDM_concat.py ├── A5b_FruendModel.m ├── B4_HDDMfits.m ├── Elisa │ ├── MergeFiles.m │ └── PupilAnalysisMain_Elisa.m ├── HDDM_RunStopos.py ├── HDDM_assessFit.py ├── HDDM_concat.py ├── HDDM_joblib.py ├── HDDM_plotOutput.py ├── HDDM_plotOutput.pyc ├── HDDMstoposJob ├── a1_PupilAnalysis_RT.m ├── a2_writeData2CSV.m ├── barplots_DIC_previousresponse_outcome.m ├── bernouilli_process.m ├── bias_by_congruency.m ├── c1_basicBehaviour.m ├── c3_modelfreeplots.m ├── c4_mulderetalplots.m ├── c5_repetition_betalateralisation.m ├── c6_Anke_HDDM.m ├── compare_stimcoding_regression.m ├── compare_svgroups.m ├── conditionalAccuracyFunctions.m ├── conditional_bias_functions.m ├── count_subjects_trials.m ├── cumulative_prepeat.m ├── d1_PL_SfN.m ├── e10_serialBias_SfN_personality.m ├── e11_serialBias_MEGregression_DIC.m ├── e11_serialBias_MEGregression_posteriors.m ├── e1_serialBias_SfN_BIC.m ├── e1b_serialBias_SfN_ModelFreeCorrelation.m ├── e1b_serialBias_SfN_ModelFreeCorrelation_chiSquare.m ├── e1b_serialBias_SfN_StartingPointTest.m ├── e3_serialBias_SfN_Posteriors.m ├── e3_serialBias_SfN_RTmodulation.m ├── e4_serialBias_SfN_RTmodulation_correlation.m ├── e5_serialBias_SfN_Stability.m ├── e6_serialBias_CBFs_perCoherence.m ├── e6_serialBias_SfN_modelFree.m ├── e6_serialBias_SfN_modelFree_CRF.m ├── e6_serialBias_SfN_modelFree_CRF_PPC_median.m ├── e6_serialBias_SfN_modelFree_Reciprobit.m ├── e6_serialBias_SfN_modelFree_fromPython.m ├── e7_serialBias_SfN_biased.m ├── e9_prevCorrect.m ├── evidencegraphic.m ├── hddmparams ├── hddmparams_concat ├── individual_correlation_congruency.m ├── individual_correlation_fastslow.m ├── individual_correlation_independentfits.m ├── kostis_all_BICs.m ├── kostis_all_correlations.m ├── kostis_makeTable.m ├── kostis_plainDDM.m ├── kostis_plotDDM.m ├── kostis_plotDDMCol_BIC.m ├── kostis_plotDDMCol_correlation.m ├── kostis_plotDDMDCol_correlation.m ├── kostis_plotDDM_BIC.m ├── kostis_plotDDM_correlation.m ├── kostis_plotOUD_BIC.m ├── kostis_plotOUD_correlation.m ├── kostis_plotOU_BIC.m ├── kostis_plotOU_correlation.m ├── kostis_plotRamp_BIC.m ├── kostis_plotRamp_CBFs.m ├── kostis_plotRamp_correlation.m ├── kostis_summary.m ├── make_parameter_tables.m ├── multiplicative_vbias.m ├── multiplicative_vbias_DIC.m ├── multiplicative_vbias_psychfuncs.m ├── multiplicative_vbias_psychfuncs_ppc.m ├── multiplicative_vbias_residuals.m ├── multiplicative_vbias_residuals_scatter.m ├── old-hddm │ ├── JW_runHDDM.py │ ├── hddm_collect.py │ ├── hddm_run.py │ ├── ipp_HDDM_Anne.py │ ├── joblib_HDDM_Anne.py │ ├── notes │ ├── runHDDM_parallel.py │ └── submitJoblibModels.sh~ ├── pharmaPosteriors.m ├── plotRepetitionByPreviousConfidence.m ├── plot_TORC.m ├── plot_dynamic_bias_signal.m ├── psychfuncs_vbias_split.m ├── regression_models.py ├── s1_PupilAnalysis_PeterMurphy.m ├── s1_PupilAnalysis_RT_forGLM.m ├── s1b_GLMbased_PupilSplit.m ├── s2_writeData4JW_PeterMurphy.m ├── s9a_Pupil_RTvariability.m ├── s9b_Behaviour_PeterMurphy.m ├── s9c_pupilAutoCorrelation.m ├── simulate_correlations.m ├── sv_comparison.m ├── test_regression_recoding.m ├── trialfun_EL_PeterMurphy.m └── trivial_repetition.png ├── plotScatter.m ├── plot_HDDM_priors.py ├── plot_all.m ├── plot_all_MEG.m ├── plot_dynamic_bias_signal_hanks.m ├── plot_posteriors.m ├── post_error_slowing.m ├── posterior_predictive_checks.m ├── posteriorpval.m ├── read_into_Matlab.m ├── read_into_Matlab_gSquare.m ├── rename_PPC_files.m ├── repetition_range.m ├── repetition_withintrial.m ├── schematic.m ├── simulate_correlations.m ├── simulations ├── .DS_Store ├── .idea │ ├── encodings.xml │ ├── misc.xml │ ├── modules.xml │ ├── simulations.iml │ ├── vcs.xml │ └── workspace.xml ├── 1_ddm_rts.py ├── 2_ou_rts.py ├── 3_lca_rts.py ├── 4_ddm_autocorrelation.py ├── DDM_fits.py ├── __pycache__ │ ├── sim_tools.cpython-36.pyc │ └── sim_tools.cpython-37.pyc ├── boundaries.ipynb ├── sim_tools.py └── sim_tools.pyc ├── spearmans.m ├── stoposJob_HDDM ├── stoposJob_HDDM_PPC ├── stoposJob_HDDM_gSquare ├── stoposJob_short ├── strategy_plot.m ├── strategy_plot_2to7.m ├── subjectspecifics.m └── tableSubjectData.csv /LICENSE.md: -------------------------------------------------------------------------------- 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