analysis(matlab): per-variation subfolders (grouping x window) for the paper LME
Add make_variations.m + variation_analyze.m generating 20 self-contained subfolders under analysis/matlab/variations/, one per grouping x day-window, each with exactly three files: data.csv (curated subset), analyze.m (a simple standalone script fitting behavior ~ stim + day + stim:day + (1|rat) on the success COUNT), and result.txt (its output). Plus variations/SUMMARY.csv. Groupings (stim=1 / stim=0, other groups dropped): unmerge B2 vs A2 right_only B2+Right vs A2 (Box-A dropped) naive_a2 B2 vs A2+Naive (Right, Box-A dropped) naive_boxa B2 vs A2+Naive+Box-A (Right dropped) Windows: 0-10, 0-13, 0-5, 6-10, 6-13. All 20 have equal day coverage. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Experiments DB Dev
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% Variation analysis -- the paper's linear mixed model on the successful-reach
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% COUNT, fit on this folder's curated data subset.
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%
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% model: behavior ~ stim + day + stim:day + (1|rat)
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% behavior = successful reaches (count per session)
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% stim = 1 for the treatment group(s), 0 for the control group(s)
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% day = training day within this window (0 = first analyzed day)
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% rat = subject (random intercept)
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%
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% Self-contained: reads data.csv beside this script and writes result.txt.
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% Run headless from this folder with: matlab -batch "analyze"
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% (This is a copy of analysis/matlab/variation_analyze.m; see make_variations.m.)
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here = fileparts(mfilename('fullpath'));
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if isempty(here); here = pwd; end
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vname = regexprep(here, '.*[/\\]', ''); % folder name = variation id
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D = readtable(fullfile(here, 'data.csv'), 'TextType', 'string');
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tbl = table(D.success, D.day - min(D.day), double(D.stim), categorical(D.subject), ...
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'VariableNames', {'behavior', 'day', 'stim', 'rat'});
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m = fitlme(tbl, 'behavior ~ stim + day + stim:day + (1|rat)');
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C = m.Coefficients; A = anova(m); ci = coefCI(m);
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gi = @(t) find(strcmp(C.Name, t), 1);
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ga = @(t) find(strcmp(A.Term, t), 1);
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row = @(nm, t) sprintf('%-26s t(%d)=%6.2f F(%d)=%8.3f p=%.4g\n', nm, ...
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C.DF(gi(t)), C.tStat(gi(t)), A.DF1(ga(t)), A.FStat(ga(t)), C.pValue(gi(t)));
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maxT = max(D.day(D.stim == 1)); minT = min(D.day(D.stim == 1));
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maxC = max(D.day(D.stim == 0)); minC = min(D.day(D.stim == 0));
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if abs(maxT - maxC) > 2
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cov = '** WARNING: unequal day coverage -- interaction may be confounded. **';
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else
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cov = '(equal day coverage over this window)';
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end
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ii = gi('day:stim'); pI = C.pValue(ii); eI = C.Estimate(ii);
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if pI >= 0.05
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verdict = 'n.s. -- slopes parallel (no differential learning rate)';
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elseif eI > 0
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verdict = 'SIGNIFICANT positive -- treatment improves FASTER (benefit accumulates)';
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else
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verdict = 'SIGNIFICANT negative -- treatment improves SLOWER (groups converge)';
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end
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bar = repmat('=', 1, 78);
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raw = regexprep(evalc('disp(m)'), '</?strong>', '');
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s = sprintf('%s\nVARIATION: %s\n%s\n', bar, vname, bar);
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s = [s sprintf('model: behavior ~ stim + day + stim:day + (1|rat) (behavior = success COUNT)\n')];
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s = [s sprintf('day = training day within window (0 = first analyzed day)\n')];
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s = [s sprintf('treatment (stim=1): %s\n', strjoin(cellstr(unique(D.group(D.stim == 1))), ', '))];
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s = [s sprintf('control (stim=0): %s\n', strjoin(cellstr(unique(D.group(D.stim == 0))), ', '))];
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s = [s sprintf('N = %d rats, %d sessions raw day coverage: treat %d..%d, control %d..%d\n', ...
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numel(unique(D.subject)), height(D), minT, maxT, minC, maxC)];
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s = [s sprintf('%s\n\n%s\nFULL MODEL SUMMARY -- fitlme\n%s\n%s\n', cov, bar, bar, raw)];
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s = [s sprintf('%-26s %-13s %-13s %s\n%s\n', 'effect', 't (df)', 'F (df1)', 'p', repmat('-', 1, 66))];
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s = [s row('stim x day (interaction)', 'day:stim')];
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s = [s row('day (learning)', 'day')];
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s = [s row('stim (main, window start)', 'stim')];
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s = [s sprintf('interaction 95%% CI: [%+.2f, %+.2f]\n', ci(ii, 1), ci(ii, 2))];
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s = [s sprintf('INTERPRETATION: stim x day interaction %s (p=%.4g, slope diff=%+.2f)\n', verdict, pI, eI)];
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s = [s sprintf('Paper (N=24): interaction t(227)=2.68, F(1)=7.12, p=0.008.\n')];
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fprintf('%s', s);
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fid = fopen(fullfile(here, 'result.txt'), 'w');
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fprintf(fid, '%s', s);
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fclose(fid);
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% Machine-readable handoff for the summary table (see make_variations.m).
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VARRESULT = struct('name', vname, 'nRats', numel(unique(D.subject)), ...
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'nObs', height(D), 'interP', pI, 'interEst', eI, ...
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'stimP', C.pValue(gi('stim')), 'dayP', C.pValue(gi('day')), ...
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'covEqual', abs(maxT - maxC) <= 2);
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subject,group,day,success,total,stim
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Banh-mi-1,Electrode-Box-B2,0,13,84,1
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Banh-mi-1,Electrode-Box-B2,1,35,86,1
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Banh-mi-1,Electrode-Box-B2,2,47,110,1
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Banh-mi-1,Electrode-Box-B2,3,65,140,1
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Banh-mi-1,Electrode-Box-B2,4,70,127,1
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Banh-mi-1,Electrode-Box-B2,5,102,142,1
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Banh-mi-2,Electrode-Box-A2,0,25,97,0
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Banh-mi-2,Electrode-Box-A2,1,22,101,0
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Banh-mi-2,Electrode-Box-A2,2,22,119,0
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Banh-mi-2,Electrode-Box-A2,3,29,118,0
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Banh-mi-2,Electrode-Box-A2,4,27,136,0
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Banh-mi-2,Electrode-Box-A2,5,43,146,0
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Egg-tart-1,Electrode-Box-B2,0,7,56,1
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Egg-tart-1,Electrode-Box-B2,1,16,78,1
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Egg-tart-1,Electrode-Box-B2,2,23,103,1
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Egg-tart-1,Electrode-Box-B2,3,63,120,1
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Egg-tart-1,Electrode-Box-B2,4,69,132,1
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Egg-tart-1,Electrode-Box-B2,5,83,136,1
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Egg-tart-2,Electrode-Box-A2,0,9,32,0
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Egg-tart-2,Electrode-Box-A2,1,2,38,0
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Egg-tart-2,Electrode-Box-A2,2,31,93,0
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Egg-tart-2,Electrode-Box-A2,3,44,101,0
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Egg-tart-2,Electrode-Box-A2,4,54,131,0
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Egg-tart-2,Electrode-Box-A2,5,84,139,0
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Khoai-lang-2,Naive,0,0,0,0
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Khoai-lang-2,Naive,1,0,0,0
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Khoai-lang-2,Naive,2,10,47,0
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Khoai-lang-2,Naive,3,11,52,0
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Khoai-lang-2,Naive,4,9,56,0
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Khoai-lang-2,Naive,5,34,95,0
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Khoai-tay-2,Naive,1,21,68,0
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Khoai-tay-2,Naive,2,6,79,0
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Khoai-tay-2,Naive,3,0,83,0
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Khoai-tay-2,Naive,4,28,87,0
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Khoai-tay-2,Naive,5,31,125,0
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OM-2,Naive,0,1,7,0
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OM-2,Naive,1,11,33,0
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OM-2,Naive,2,19,62,0
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OM-2,Naive,3,29,117,0
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OM-2,Naive,4,73,126,0
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OM-2,Naive,5,53,135,0
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Root-beer-1,Electrode-Box-B2,0,11,85,1
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Root-beer-1,Electrode-Box-B2,1,18,76,1
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Root-beer-1,Electrode-Box-B2,2,40,105,1
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Root-beer-1,Electrode-Box-B2,3,55,134,1
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Root-beer-1,Electrode-Box-B2,4,75,136,1
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Root-beer-1,Electrode-Box-B2,5,64,133,1
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Root-beer-2,Electrode-Box-A2,0,22,74,0
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Root-beer-2,Electrode-Box-A2,1,31,87,0
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Root-beer-2,Electrode-Box-A2,2,49,134,0
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Root-beer-2,Electrode-Box-A2,3,31,89,0
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Root-beer-2,Electrode-Box-A2,4,60,140,0
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Root-beer-2,Electrode-Box-A2,5,84,147,0
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Vu-vuong,Naive,0,18,61,0
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Vu-vuong,Naive,1,35,91,0
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Vu-vuong,Naive,2,61,127,0
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Vu-vuong,Naive,3,34,146,0
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Vu-vuong,Naive,4,61,141,0
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Vu-vuong,Naive,5,37,151,0
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==============================================================================
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VARIATION: naive_a2_d0_5
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==============================================================================
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model: behavior ~ stim + day + stim:day + (1|rat) (behavior = success COUNT)
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day = training day within window (0 = first analyzed day)
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treatment (stim=1): Electrode-Box-B2
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control (stim=0): Electrode-Box-A2, Naive
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N = 10 rats, 59 sessions raw day coverage: treat 0..5, control 0..5
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(equal day coverage over this window)
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==============================================================================
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FULL MODEL SUMMARY -- fitlme
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==============================================================================
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Linear mixed-effects model fit by ML
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Model information:
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Number of observations 59
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Fixed effects coefficients 4
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Random effects coefficients 10
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Covariance parameters 2
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Formula:
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behavior ~ 1 + day*stim + (1 | rat)
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Model fit statistics:
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AIC BIC LogLikelihood Deviance
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489.28 501.74 -238.64 477.28
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Fixed effects coefficients (95% CIs):
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Name Estimate SE tStat DF pValue
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{'(Intercept)'} 9.0584 5.0267 1.8021 55 0.077018
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{'day' } 8.2568 1.1279 7.3206 55 1.1254e-09
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{'stim' } 0.44958 9.048 0.049688 55 0.96055
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{'day:stim' } 6.9622 2.0162 3.4532 55 0.0010733
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Lower Upper
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-1.0153 19.132
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5.9965 10.517
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-17.683 18.582
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2.9217 11.003
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Random effects covariance parameters (95% CIs):
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Group: rat (10 Levels)
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Name1 Name2 Type Estimate
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{'(Intercept)'} {'(Intercept)'} {'std'} 9.6432
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Lower Upper
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5.5002 16.907
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Group: Error
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Name Estimate Lower Upper
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{'Res Std'} 12.109 9.9317 14.763
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effect t (df) F (df1) p
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------------------------------------------------------------------
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stim x day (interaction) t(55)= 3.45 F(1)= 11.924 p=0.001073
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day (learning) t(55)= 7.32 F(1)= 53.591 p=1.125e-09
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stim (main, window start) t(55)= 0.05 F(1)= 0.002 p=0.9606
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interaction 95% CI: [+2.92, +11.00]
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INTERPRETATION: stim x day interaction SIGNIFICANT positive -- treatment improves FASTER (benefit accumulates) (p=0.001073, slope diff=+6.96)
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Paper (N=24): interaction t(227)=2.68, F(1)=7.12, p=0.008.
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