From ad27b1ed98fa6cf03e86d0c0cc31563aad2a6090 Mon Sep 17 00:00:00 2001 From: Anne Urai Date: Tue, 20 Nov 2018 16:37:27 -0500 Subject: [PATCH] cleanup --- hddm_models.pyc | Bin 18112 -> 0 bytes hddmparams | 14 -- hddmparams_PPC | 14 -- kostis_driftRate.m | 21 --- motionEnergy_kernels_logistic.m | 129 ------------------ .../barplots_DIC_previousresponse_outcome.m | 0 .../compare_correlations_correct_error.m | 0 .../compare_svgroups.m | 0 .../conditional_bias_functions.m | 0 .../individual_correlation_independentfits.m | 0 .../kostis_all_correlations.m | 0 .../kostis_makeTable.m | 0 .../kostis_plainDDM.m | 0 kostis_plotDDM.m => old_code/kostis_plotDDM.m | 0 .../kostis_plotDDMCol_BIC.m | 0 .../kostis_plotDDMCol_correlation.m | 0 .../kostis_plotDDMDCol_correlation.m | 0 .../kostis_plotDDM_BIC.m | 0 .../kostis_plotDDM_correlation.m | 0 .../kostis_plotOUD_BIC.m | 0 .../kostis_plotOUD_correlation.m | 0 .../kostis_plotOU_BIC.m | 0 .../kostis_plotOU_correlation.m | 0 .../kostis_plotRamp_BIC.m | 0 .../kostis_plotRamp_CBFs.m | 0 .../kostis_plotRamp_correlation.m | 0 kostis_summary.m => old_code/kostis_summary.m | 0 .../multiplicative_vbias_DIC.m | 0 .../multiplicative_vbias_psychfuncs_ppc.m | 0 plot_TORC.m => old_code/plot_TORC.m | 0 .../plot_dynamic_bias_signal.m | 0 .../regression_models.py | 0 .../simulate_correlations.m | 0 stoposjob_matlab.sh | 11 -- 34 files changed, 189 deletions(-) delete mode 100644 hddm_models.pyc delete mode 100644 hddmparams delete mode 100644 hddmparams_PPC delete mode 100644 kostis_driftRate.m delete mode 100644 motionEnergy_kernels_logistic.m rename barplots_DIC_previousresponse_outcome.m => old_code/barplots_DIC_previousresponse_outcome.m (100%) rename compare_correlations_correct_error.m => old_code/compare_correlations_correct_error.m (100%) rename compare_svgroups.m => old_code/compare_svgroups.m (100%) rename conditional_bias_functions.m => old_code/conditional_bias_functions.m (100%) rename individual_correlation_independentfits.m => old_code/individual_correlation_independentfits.m (100%) rename kostis_all_correlations.m => old_code/kostis_all_correlations.m (100%) rename kostis_makeTable.m => old_code/kostis_makeTable.m (100%) rename kostis_plainDDM.m => old_code/kostis_plainDDM.m (100%) rename kostis_plotDDM.m => old_code/kostis_plotDDM.m (100%) rename kostis_plotDDMCol_BIC.m => old_code/kostis_plotDDMCol_BIC.m (100%) rename kostis_plotDDMCol_correlation.m => old_code/kostis_plotDDMCol_correlation.m (100%) rename kostis_plotDDMDCol_correlation.m => old_code/kostis_plotDDMDCol_correlation.m (100%) rename kostis_plotDDM_BIC.m => old_code/kostis_plotDDM_BIC.m (100%) rename kostis_plotDDM_correlation.m => old_code/kostis_plotDDM_correlation.m (100%) rename kostis_plotOUD_BIC.m => old_code/kostis_plotOUD_BIC.m (100%) rename kostis_plotOUD_correlation.m => old_code/kostis_plotOUD_correlation.m (100%) rename kostis_plotOU_BIC.m => old_code/kostis_plotOU_BIC.m (100%) rename kostis_plotOU_correlation.m => old_code/kostis_plotOU_correlation.m (100%) rename kostis_plotRamp_BIC.m => old_code/kostis_plotRamp_BIC.m (100%) rename kostis_plotRamp_CBFs.m => old_code/kostis_plotRamp_CBFs.m (100%) rename kostis_plotRamp_correlation.m => old_code/kostis_plotRamp_correlation.m (100%) rename kostis_summary.m => old_code/kostis_summary.m (100%) rename multiplicative_vbias_DIC.m => old_code/multiplicative_vbias_DIC.m (100%) rename multiplicative_vbias_psychfuncs_ppc.m => old_code/multiplicative_vbias_psychfuncs_ppc.m (100%) rename plot_TORC.m => old_code/plot_TORC.m (100%) rename plot_dynamic_bias_signal.m => old_code/plot_dynamic_bias_signal.m (100%) rename regression_models.py => old_code/regression_models.py (100%) rename simulate_correlations.m => old_code/simulate_correlations.m (100%) delete mode 100644 stoposjob_matlab.sh diff --git a/hddm_models.pyc b/hddm_models.pyc deleted file mode 100644 index bff57cb7c695047526229315753fa2c95f2712ac..0000000000000000000000000000000000000000 GIT binary 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--git a/hddmparams_PPC b/hddmparams_PPC deleted file mode 100644 index 47f996c..0000000 --- a/hddmparams_PPC +++ /dev/null @@ -1,14 +0,0 @@ -0 16 -0 17 -1 16 -1 17 -2 16 -2 17 -3 16 -3 17 -4 16 -4 17 -5 16 -5 17 -6 16 -6 17 diff --git a/kostis_driftRate.m b/kostis_driftRate.m deleted file mode 100644 index f1a0117..0000000 --- a/kostis_driftRate.m +++ /dev/null @@ -1,21 +0,0 @@ - - -%% GET ANKE'S DATA, AND DERIVE A COHERENCE BY DRIFT RATE FUNCTION -global datasets -d = 4; -load(sprintf('%s/summary/%s/stimcoding_nohist_all.mat', mypath, datasets{d})); - -dat.coherence_levels = [0 3 9 27 81]; -dat.drift_rates = [individuals.v_0_mean' ... - individuals.v_3_mean' ... - individuals.v_9_mean' ... - individuals.v_27_mean' ... - individuals.v_81_mean' ]; - -close; -plot(dat.coherence_levels, dat.drift_rates) -xlabel('% coherence'); -ylabel('Drift rate'); -print(gcf, '-dpdf', sprintf('~/Data/serialHDDM/Anke_driftrates.pdf',d)); - -save(sprintf('%s/summary/%s/driftRates.mat', mypath, datasets{d})); diff --git a/motionEnergy_kernels_logistic.m b/motionEnergy_kernels_logistic.m deleted file mode 100644 index 22701ca..0000000 --- a/motionEnergy_kernels_logistic.m +++ /dev/null @@ -1,129 +0,0 @@ - -% ================================================= % -% code from https://www.mathworks.com/matlabcentral/fileexchange/31661-fit-glm-with-quadratic-penalty?s_tid=prof_contriblnk -% ================================================= % - -clear all; close all; -addpath('/Users/urai/Documents/code/fitglmqp130'); -path = '~/Data/psychophysicalKernels'; -load(sprintf('%s/%s', path, 'motionEnergyData_AnkeMEG.mat')); - -% normalize to range of -1, 1 to be in line with the prior -scaleFactor = 0.004; % determined through trial and error... this value ensures that the fitted weights match glmfit [0.004] -data.motionenergy_normalized = data.motionenergy_normalized * scaleFactor; -data.behavior.motionenergy = mean(data.motionenergy_normalized, 2); -data.behavior.stimulus = data.behavior.stimulus .* data.behavior.coherence .* scaleFactor; - -% remove the initial filter rise time -timeStart = 5; -data.motionenergy_normalized = data.motionenergy_normalized(:, timeStart:end); -data.timeaxis = data.timeaxis(timeStart:end); - -% grab data -r = double(data.behavior.response > 0); -X = [ones(length(r), 1) data.behavior.stimulus data.behavior.motionenergy]; - -% set some default options -opts.family = 'binomlogit'; % assume logistic regression - -% first do a normal glmfit to know the range of expected weights across subjects -psychfunc = splitapply(@(r,X) {glmfit(X, r, 'binomial', 'constant', 0)}, ... - r, X, findgroups(data.behavior.subj_idx)); -results.w_psychfunc = cat(2, psychfunc{:})'; -results.w_psychfunc_fixed = glmfit(X, r, 'binomial', 'constant', 0); - -% MAKE SURE THIS CODE CAN FIT A BASIC PSYCHOMETRIC FUNCTION FOR EACH SUBJECT! -results_fit = splitapply(@(r,X) evidenceglmfitqp(r,X, ... - blkdiag( results.w_psychfunc_fixed(1), results.w_psychfunc_fixed(2), results.w_psychfunc_fixed(2)), opts), ... - r, X, findgroups(data.behavior.subj_idx)); -results.w_psychfunc_evidence = [results_fit.w]'; - -% do these two methods give the same result? -figure; -for i = 1:3, - subplot(3,3,i); scatter(results.w_psychfunc(:, i), results.w_psychfunc_evidence(:, i)); - rl = refline(1); rl.Color = 'k'; lsline; - title(sprintf('r = %.2f', corr(results.w_psychfunc(:, i), results.w_psychfunc_evidence(:, i)))); - xlabel('glmfit'); ylabel('evidence fit'); -end - -%% ================================================= % -% NOW FIT ACROSS OBSERVERS' REAL RESPONSES -% ================================================= % - -% match the prior values to the known slope -qf = blkdiag(results.w_psychfunc_fixed(3) * qfsmooth1D(size(data.motionenergy_normalized, 2)), ... - results.w_psychfunc_fixed(1)); -X = [data.motionenergy_normalized ones(length(r), 1)]; - -% confirm that the slope and bias terms estimated are similar -results_fit_fixedeffects = evidenceglmfitqp(r, X, qf, opts); -results.w_psychfunc_kernelfit_fixedeffects = results_fit_fixedeffects.w(end); -results.w_kernelfit_fixedeffects = results_fit_fixedeffects.w(1:end-1); - -% then, for each subject -results_fit = splitapply(@(r,X) evidenceglmfitqp(r,X,qf,opts), ... - r, X, findgroups(data.behavior.subj_idx)); -results.w = cat(2, results_fit.w)'; - -% compute the psychometric slope as the average of weights over time -results.w_psychfunc_kernelfit = [nanmean(results.w(:, 1:end-1), 2) results.w(:, end)]; -results.w = results.w(:, 1:end-1); - -% plot the results -clf; subplot(221); plot(data.timeaxis, results.w_kernelfit_fixedeffects, 'k'); ylabel('Fixed effects'); -hold on; yyaxis right; plot(data.timeaxis, nanmean(results.w), 'linewidth', 2); -ylabel('Average of subjects'); -axis tight; vline(data.timeaxis(13)); - -% these are the individual results -subplot(222); hold on; -plot(data.timeaxis, results.w); - -hold on; -boundedline(data.timeaxis, mean(results.w), ... - std(results.w) ./ sqrt(size(results.w, 1)), 'cmap', [0 0 0]); -%ylim([0.17 0.22]); - -subplot(223); -scatter(results.w_psychfunc_evidence(:, 3), results.w_psychfunc_kernelfit(:, 1)); -xlabel('psychfunc slope'); -ylabel('kernel slope'); -title(sprintf('r = %.3f', corr(results.w_psychfunc_evidence(:, 3), results.w_psychfunc_kernelfit(:, 1)))); -lsline; - -% check that the intercepts do match as a sanity check -assert(corr(results.w_psychfunc(:, 1), results.w_psychfunc_kernelfit(:, 2)) > 0.9, ... - 'logistic intercepts dont match'); - - - %% ================================================= % -% FIRST, CONFIRM THAT WE GET SENSIBLE WEIGHTS WHEN WE KNOW WHAT THE -% OBSERVER DOES -% ================================================= % - -% % SIMULATE A LINEARLY DECAYING WEIGHT AND AN OFFSET -% % FINDING: THE MODEL CAN RECOVER WEIGHTS BETWEEN 2-1 BEST! -% w_simul = results.w_psychfunc_fixed(2) .* ones(size(data.timeaxis))'; -% w_simul = linspace(results.w_psychfunc_fixed(2)+2, results.w_psychfunc_fixed(2)-1, ... -% numel(data.timeaxis))'; -% -% % simulate weights of the same order of magnitude, is this retrieved? -% r_simul = X*[w_simul; results.w_psychfunc_fixed(1)]; -% r_simul = binornd(1,1./(1+exp(-r_simul))); -% -% results_simulated = splitapply(@(r,X) evidenceglmfitqp(r,X, ... -% blkdiag(qfsmooth1D(size(X, 2)-1), 0.01), opts), ... -% r_simul, X, findgroups(data.behavior.prevresp)); -% sim.w = cat(2, results_simulated.w)'; -% sim.w = sim.w(:, 1:end-1); -% -% results_simulated_fixedeffects = evidenceglmfitqp(r_simul, X, ... -% blkdiag(qfsmooth1D(size(X, 2)-1), 0.01), opts); -% sim.w_fixedeffects = results_simulated_fixedeffects.w(1:end-1); -% -% figure; subplot(221); -% plot(w_simul, 'k', 'linewidth', 3); hold on; -% plot(sim.w_fixedeffects', 'k--', 'linewidth', 3); hold on; -% plot(mean(sim.w), 'k:', 'linewidth', 3); -% plot(sim.w'); diff --git a/barplots_DIC_previousresponse_outcome.m b/old_code/barplots_DIC_previousresponse_outcome.m similarity index 100% rename from barplots_DIC_previousresponse_outcome.m rename to old_code/barplots_DIC_previousresponse_outcome.m diff --git a/compare_correlations_correct_error.m b/old_code/compare_correlations_correct_error.m similarity index 100% rename from compare_correlations_correct_error.m rename to old_code/compare_correlations_correct_error.m diff --git a/compare_svgroups.m b/old_code/compare_svgroups.m similarity index 100% rename from compare_svgroups.m rename to old_code/compare_svgroups.m diff --git a/conditional_bias_functions.m b/old_code/conditional_bias_functions.m similarity index 100% rename from conditional_bias_functions.m rename to old_code/conditional_bias_functions.m diff --git a/individual_correlation_independentfits.m b/old_code/individual_correlation_independentfits.m similarity index 100% rename from individual_correlation_independentfits.m rename to old_code/individual_correlation_independentfits.m diff --git a/kostis_all_correlations.m b/old_code/kostis_all_correlations.m similarity index 100% rename from kostis_all_correlations.m rename to old_code/kostis_all_correlations.m diff --git a/kostis_makeTable.m b/old_code/kostis_makeTable.m similarity index 100% rename from kostis_makeTable.m rename to old_code/kostis_makeTable.m diff --git a/kostis_plainDDM.m b/old_code/kostis_plainDDM.m similarity index 100% rename from kostis_plainDDM.m rename to old_code/kostis_plainDDM.m diff --git a/kostis_plotDDM.m b/old_code/kostis_plotDDM.m similarity index 100% rename from kostis_plotDDM.m rename to old_code/kostis_plotDDM.m diff --git a/kostis_plotDDMCol_BIC.m b/old_code/kostis_plotDDMCol_BIC.m similarity index 100% rename from kostis_plotDDMCol_BIC.m rename to old_code/kostis_plotDDMCol_BIC.m diff --git a/kostis_plotDDMCol_correlation.m b/old_code/kostis_plotDDMCol_correlation.m similarity index 100% rename from kostis_plotDDMCol_correlation.m rename to old_code/kostis_plotDDMCol_correlation.m diff --git a/kostis_plotDDMDCol_correlation.m b/old_code/kostis_plotDDMDCol_correlation.m similarity index 100% rename from kostis_plotDDMDCol_correlation.m rename to old_code/kostis_plotDDMDCol_correlation.m diff --git a/kostis_plotDDM_BIC.m b/old_code/kostis_plotDDM_BIC.m similarity index 100% rename from kostis_plotDDM_BIC.m rename to old_code/kostis_plotDDM_BIC.m diff --git a/kostis_plotDDM_correlation.m b/old_code/kostis_plotDDM_correlation.m similarity index 100% rename from kostis_plotDDM_correlation.m rename to old_code/kostis_plotDDM_correlation.m diff --git a/kostis_plotOUD_BIC.m b/old_code/kostis_plotOUD_BIC.m similarity index 100% rename from kostis_plotOUD_BIC.m rename to old_code/kostis_plotOUD_BIC.m diff --git a/kostis_plotOUD_correlation.m b/old_code/kostis_plotOUD_correlation.m similarity index 100% rename from kostis_plotOUD_correlation.m rename to old_code/kostis_plotOUD_correlation.m diff --git a/kostis_plotOU_BIC.m b/old_code/kostis_plotOU_BIC.m similarity index 100% rename from kostis_plotOU_BIC.m rename to old_code/kostis_plotOU_BIC.m diff --git a/kostis_plotOU_correlation.m b/old_code/kostis_plotOU_correlation.m similarity index 100% rename from kostis_plotOU_correlation.m rename to old_code/kostis_plotOU_correlation.m diff --git a/kostis_plotRamp_BIC.m b/old_code/kostis_plotRamp_BIC.m similarity index 100% rename from kostis_plotRamp_BIC.m rename to old_code/kostis_plotRamp_BIC.m diff --git a/kostis_plotRamp_CBFs.m b/old_code/kostis_plotRamp_CBFs.m similarity index 100% rename from kostis_plotRamp_CBFs.m rename to old_code/kostis_plotRamp_CBFs.m diff --git a/kostis_plotRamp_correlation.m b/old_code/kostis_plotRamp_correlation.m similarity index 100% rename from kostis_plotRamp_correlation.m rename to old_code/kostis_plotRamp_correlation.m diff --git a/kostis_summary.m b/old_code/kostis_summary.m similarity index 100% rename from kostis_summary.m rename to old_code/kostis_summary.m diff --git a/multiplicative_vbias_DIC.m b/old_code/multiplicative_vbias_DIC.m similarity index 100% rename from multiplicative_vbias_DIC.m rename to old_code/multiplicative_vbias_DIC.m diff --git a/multiplicative_vbias_psychfuncs_ppc.m b/old_code/multiplicative_vbias_psychfuncs_ppc.m similarity index 100% rename from multiplicative_vbias_psychfuncs_ppc.m rename to old_code/multiplicative_vbias_psychfuncs_ppc.m diff --git a/plot_TORC.m b/old_code/plot_TORC.m similarity index 100% rename from plot_TORC.m rename to old_code/plot_TORC.m diff --git a/plot_dynamic_bias_signal.m b/old_code/plot_dynamic_bias_signal.m similarity index 100% rename from plot_dynamic_bias_signal.m rename to old_code/plot_dynamic_bias_signal.m diff --git a/regression_models.py b/old_code/regression_models.py similarity index 100% rename from regression_models.py rename to old_code/regression_models.py diff --git a/simulate_correlations.m b/old_code/simulate_correlations.m similarity index 100% rename from simulate_correlations.m rename to old_code/simulate_correlations.m diff --git a/stoposjob_matlab.sh b/stoposjob_matlab.sh deleted file mode 100644 index bb19a1c..0000000 --- a/stoposjob_matlab.sh +++ /dev/null @@ -1,11 +0,0 @@ -#!/bin/bash - -#PBS -o /home/aeurai/jobs -#PBS -e /home/aeurai/jobs -#PBS -lnodes=1 -lwalltime=00:05:00 - -# load necessary modules -module load matlab - -# run the plotting script -matlab -nodesktop -nodisplay -r "disp(pwd); plot_all; end; exit"