Experiments DB Dev
7b5c27df8c
Adds tdcs_paper_lme replicating the paper's exact formula/variable names (paper_* switch cases): mergeA2 reproduces the interaction F(1)=7.09 vs 7.12, p=0.009 vs 0.008, with a coverage-confound warning. Rewrites tdcs_power_sim to fit that same formula (interaction term canonicalized to day:stim). Adds a replication test. Suite 37/37. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
92 lines
4.0 KiB
Matlab
92 lines
4.0 KiB
Matlab
function L = tdcs_paper_lme(mergeKey, cfg)
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%TDCS_PAPER_LME Replicate the paper's linear mixed model, verbatim formula:
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% behavior ~ stim + day + stim:day + (1|rat)
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% fit with fitlme on the Box-B2 (stim = 1, tDCS) vs Box-A2 (stim = 0, control)
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% subset of the MERGEKEY grouping ('unmerged'|'mergeA2'|'mergeB2'), over the
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% full training range. `behavior` = successful reaches, `day` = training day
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% (raw; day 0 = the paper's "Day 1"), `rat` = subject. Reports the three
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% effects (stim x day interaction, day, stim) as t(df) / F(1) / p with the
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% interaction 95% CI, alongside the paper's reference values, and writes
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% results/paper_<MERGEKEY>.txt.
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%
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% (This is the same model as tdcs_lme -- success ~ day*tDCS + (1|subject) --
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% written with the paper's exact term order and variable names.)
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%
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% L fields: .model .nRats .nObs and .stim/.day/.interaction effect structs
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% (.estimate .se .t .df .p from Coefficients; .F .df1 .df2 .Fp from ANOVA;
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% .ci = coefficient 95% CI).
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Sfull = tdcs_scenario_data([mergeKey '_full']);
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A = Sfull(ismember(Sfull.group, {cfg.anchorLow, cfg.anchorHigh}), :);
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tbl = table();
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tbl.behavior = A.success;
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tbl.day = A.day;
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tbl.stim = double(A.group == cfg.anchorHigh); % Box-B2 = 1, Box-A2 = 0
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tbl.rat = A.subject;
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model = fitlme(tbl, 'behavior ~ stim + day + stim:day + (1|rat)');
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C = model.Coefficients; An = anova(model); ci = coefCI(model);
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L.model = model;
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L.nRats = numel(unique(tbl.rat));
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L.nObs = height(tbl);
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L.maxDayCtrl = max(tbl.day(tbl.stim == 0));
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L.maxDayStim = max(tbl.day(tbl.stim == 1));
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L.stim = localTerm(C, An, ci, 'stim');
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L.day = localTerm(C, An, ci, 'day');
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L.interaction = localTerm(C, An, ci, 'day:stim'); % MATLAB canonicalizes stim:day -> day:stim
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localReport(L, mergeKey, cfg);
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end
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function e = localTerm(C, An, ci, name)
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i = strcmp(C.Name, name);
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if ~any(i)
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error('tdcs_paper_lme:missingTerm', 'No "%s" coefficient (have: %s).', ...
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name, strjoin(C.Name, ', '));
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end
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ai = strcmp(An.Term, name);
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e = struct('estimate', C.Estimate(i), 'se', C.SE(i), 't', C.tStat(i), ...
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'df', C.DF(i), 'p', C.pValue(i), 'F', An.FStat(ai), 'df1', An.DF1(ai), ...
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'df2', An.DF2(ai), 'Fp', An.pValue(ai), 'ci', ci(i, :));
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end
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function localReport(L, mergeKey, cfg)
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bar = repmat('=', 1, 78);
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s = sprintf('%s\n', bar);
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s = [s sprintf('PAPER LME REPLICATION -- %s\n', mergeKey)];
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s = [s sprintf('%s\n', bar)];
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s = [s sprintf('model: behavior ~ stim + day + stim:day + (1|rat) [stim: %s=1 vs %s=0]\n', ...
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cfg.anchorHigh, cfg.anchorLow)];
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s = [s sprintf('N = %d rats, %d sessions (day raw; day 0 = paper "Day 1")\n', L.nRats, L.nObs)];
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s = [s sprintf('day coverage: stim(B2) 0..%d, control(A2) 0..%d\n', L.maxDayStim, L.maxDayCtrl)];
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if abs(L.maxDayStim - L.maxDayCtrl) > 2
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s = [s sprintf(['** WARNING: unequal day coverage -- the full-range stim:day interaction\n' ...
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' extrapolates the control group''s line and is CONFOUNDED here (the paper''s\n' ...
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' groups had equal coverage). See the _d0_13 fair-window and phased analyses. **\n'])];
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end
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s = [s sprintf('\n%-26s %-13s %-13s %s\n', 'effect', 't (df)', 'F (df1)', 'p')];
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s = [s sprintf('%s\n', repmat('-', 1, 66))];
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s = [s localRow('stim x day (interaction)', L.interaction)];
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s = [s localRow('day (learning)', L.day)];
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s = [s localRow('stim (main, Day 1)', L.stim)];
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s = [s sprintf('interaction 95%% CI: [%+.2f, %+.2f]\n', L.interaction.ci(1), L.interaction.ci(2))];
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s = [s sprintf(['\nPaper (N=24): interaction t(227)=2.68, F(1)=7.12, p=0.008; ' ...
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'day t(227)=9.64,\n F(1)=267.64, p=1.2e-18; stim t(227)=0.23, F(1)=0.053, p=0.81.\n'])];
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fprintf('%s', s);
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thisDir = fileparts(mfilename('fullpath'));
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resDir = fullfile(thisDir, 'results');
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if ~exist(resDir, 'dir'); mkdir(resDir); end
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fid = fopen(fullfile(resDir, ['paper_' mergeKey '.txt']), 'w');
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if fid < 0; error('tdcs_paper_lme:fopen', 'Cannot open results file.'); end
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cleanup = onCleanup(@() fclose(fid)); %#ok<NASGU>
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fprintf(fid, '%s', s);
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end
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function r = localRow(name, e)
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r = sprintf('%-26s t(%d)=%6.2f F(%d)=%8.3f p=%.4g\n', name, e.df, e.t, e.df1, e.F, e.p);
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end
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