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<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Dear Fieldtrippers,</div>
<div style="text-align: left; text-indent: 0px; line-height: 1.2; margin-top: 1.2rem; margin-bottom: 0.5rem; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof" id="computing-the-effect-size-for-the-average-over-the-cluster">
We've been trying to calculate the effect size for the average over the significant cluster (we only have one from our cluster-based permutation analysis) that we've identified. We've looked at the section "<span style="font-weight: 500;">Computing the effect
size for the average over the cluster" </span> (<a id="LPlnk823785" href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Fexample%2Fstats%2Feffectsize%2F%23%3A~%3Atext%3DThe%2520effect%2520size%2520is%25201.47%2Cfrom%2520350%2520to%2520550%2520milliseconds.&data=05%7C02%7Cfieldtrip%40science.ru.nl%7Cfd34aecc6e8241cab22e08ddfc7c191b%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638944332124275698%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=VfkJiEJtblcx%2FXvxT3ua1CWUMXQfksi6cKut%2F%2FBmCRQ%3D&reserved=0" originalSrc="https://www.fieldtriptoolbox.org/example/stats/effectsize/#:~:text=The%20effect%20size%20is%201.47,from%20350%20to%20550%20milliseconds.">https://www.fieldtriptoolbox.org/example/stats/effectsize/#:~:text=The%20effect%20size%20is%201.47,from%20350%20to%20550%20milliseconds.</a>)
and have attempted to implement it in the section of the code "ATTEMPT 2" shown below and got a cohens d of 4.6582, which was a lot higher than expected, so we don't think it's correct.</div>
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To solve this, we tried an alternative method to calculate cohens d using ft_freqstatistics, as shown in the section of code "ATTEMPT 1." The outputted cohens d values (shown in the commented sections) seem much more reasonable, but we're not sure that the
code makes sense.</div>
<div style="text-align: left; text-indent: 0px; line-height: 1.2; margin-top: 1.2rem; margin-bottom: 0.5rem; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
Can anyone provide input on calculating effect size over cluster and if either of these attempts at coding it seem accurate?</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
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Here is our code:</div>
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%% CALCULATE COHENS D</div>
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% get cluster</div>
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cluster = squeeze(stat.posclusterslabelmat)==1;</div>
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<br>
</div>
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% get the indices for the cluster</div>
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cluster_inds = find(cluster);</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
cluster_inds_size = size(cluster_inds, 1);</div>
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<br>
</div>
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% GROUP A</div>
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% get number of participants</div>
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num_parts_groupA = size(groupA_data.powspctrm,1);</div>
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<br>
</div>
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% create empty matrix</div>
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groupA_powspctrm_cluster_only = zeros(num_parts_groupA, cluster_inds_size);</div>
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<br>
</div>
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% iterate through each participant</div>
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for ind=1:num_parts_groupA</div>
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% extract their powspctrm matrix</div>
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part_mat = squeeze(groupA_data.powspctrm(ind, :, :, :));</div>
<div style="margin-left: 0px; font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
% extract the values in the cluster</div>
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part_vals_cluster = part_mat(cluster_inds);</div>
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% add participant to list of values for all participants</div>
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groupA_powspctrm_cluster_only(ind, :) = part_vals_cluster;</div>
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End </div>
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<br>
</div>
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% GROUP B</div>
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% get number of participants</div>
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num_parts_groupB = size(groupB_data.powspctrm,1);</div>
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<br>
</div>
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% create empty matrix</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
groupB_powspctrm_cluster_only = zeros(num_parts_groupB, cluster_inds_size);</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
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% iterate through each participant</div>
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for ind=1:num_parts_groupB</div>
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% extract their powspctrm matrix</div>
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part_mat = squeeze(groupB_data.powspctrm(ind, :, :, :));</div>
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<br>
</div>
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% extract the values in the cluster</div>
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part_vals_cluster = part_mat(cluster_inds);</div>
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<br>
</div>
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% add participant to list of values for all participants</div>
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groupB_powspctrm_cluster_only(ind, :) = part_vals_cluster;</div>
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End </div>
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<br>
</div>
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% add back to group_data</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
groupA_data.powspctrm_cluster_only = groupA_powspctrm_cluster_only;</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
groupB_data.powspctrm_cluster_only = groupB_powspctrm_cluster_only;</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
groupA_data.powspctrm_cluster_onlydimord = 'subj_comp';</div>
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groupB_data.powspctrm_cluster_onlydimord = 'subj_comp';</div>
<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);" class="elementToProof">
<br>
</div>
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% ATTEMPT 1: Calculate effect size (Cohen's d) for the cluster</div>
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cfg = [];</div>
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cfg.method = 'analytic';</div>
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cfg.statistic = 'cohensd';</div>
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cfg.parameter = 'powspctrm_cluster_only';</div>
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N_groupA = size(groupA_data.powspctrm_cluster_only, 1);</div>
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N_groupB = size(groupB_data.powspctrm_cluster_only, 1);</div>
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Nsubj = N_groupA + N_groupB;</div>
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design = zeros(1, Nsubj);</div>
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design(1,1:N_groupA) = 1;</div>
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design(1,N_groupA+1:Nsubj) = 2;</div>
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cfg.design = design;</div>
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cfg.ivar = 1;</div>
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<br>
</div>
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cohensD_output = ft_freqstatistics(cfg, groupA_data, groupB_data);</div>
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cohensD_avg = mean(cohensD_output.cohensd); % 0.3958</div>
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cohensD_max = max(cohensD_output.cohensd); % 0.5312</div>
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<br>
</div>
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%% ATTEMPT 2: https://www.fieldtriptoolbox.org/example/stats/effectsize/</div>
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<br>
</div>
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groupA_means = mean(groupA_data.powspctrm_cluster_only, 1);</div>
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groupB_means = mean(groupB_data.powspctrm_cluster_only, 1);</div>
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<br>
</div>
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x1= groupA_means;</div>
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x2 = groupB_means;</div>
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cohensd = mean(x1-x2) ./ std(x1-x2); % we get value 4.6582</div>
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<div style="font-family: Aptos, Aptos_EmbeddedFont, Aptos_MSFontService, Calibri, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Thanks!</div>
<p style="margin-top: 1em; margin-bottom: 1em;"><span style="color: black;">Annie</span></p>
<p style="margin-top: 1em; margin-bottom: 1em;"> </p>
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