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This is taken and copied from github/behinger/permtest: I couldn’t find a simple permutation test for matlab, thus I decided to implement it on my own. I got inspired by the “statmod”-R package and followed Phipson & Smyth 2010’s recommendations. How to Use: [code lang=matlab] permtest(randi([1,5],100),randi([3,8],100)) permtest(randi([1,5],100),randi([3,8],100),10000) permtest(randi([1,5],100),randi([3,8],100),[],\"conservative\") % usually the fastest implementation [/code] Permutations / Randomization I chose to do permutations with repeats. This complicates p-values, but in the end I found it to be faster (and scales better). P-Values There are three methods implemented to get the p-value: b = permutations with greater value than test-statistic m_t = number…

A small fact got me into trouble (spoiler: the intercept in effects coding represents the mean of conditions, not the data-mean). Update 2016-08-11 I found a nice paper that remedies the last point: weighted effects coding Update 2018-11-30 If you enjoyed reading this post, check out my sucessor post on Effect/Sum Coding Update 2019-07-22 I highly recommend this recent paper: How to capitalize on a priori contrasts in linear (mixed) models: A tutorial (2019) which will explain all things of this blogpost in more space, more examples, more code and with better words! The goal We try to model two…

I sometimes give improvised lectures to a small circle of students. These are some of the explanations I use. The goal Find time-points in a time series that differ between two conditions over subjects without performing single independent tests for each time-point. Step by Step Guide In this tutorial, we apply the cluster-permutation test to a single time-series. This could be a single channel, an average over channels, or one “source/component” from an ICA decomposition. We can make use of the neighbour-relation of time: $t$ has the neighbors $t-1$ and $t+1$. We don’t expect the time points to be independent,…

Here in the institute we have a Sun Grid Engine available. It is a tool to post computing-jobs on other workspaces (we have I think up to 60 available). There are certain commands and things that I do regularly which I tend to forget after half a year, or which might be useful for orthes. Show all jobs that are running on the grid qstat -u \* or alternativly for a single user qstat -u behinger exclude a single computer/host from running a job qsub -l mem=5G,h=!computername.domain script.sh to exclude multiple hosts: h=!h4&!h5 or h=!(h4|h5) Source of course mem=5G is…

This is a function I wrote back in 2014. I think it illustrates an advanced functionality in matlab that I hadn’t found written about before. The problem: Calculate the winsorized mean of a multidimensional matrix over an arbitrary dimension. Winsorized Mean The benefits of the winsorized mean can be seen here: We replace the top 10% and bottom 10% by the remaining most extreme value before calculating the mean (left panel). The right panel shows how the mean is influenced by a single outlier, but the winsorized mean is not (ignore the “yuen”-box”) Current Implementation I adapted an implementation from…

Some years ago, I wrote an interactive tutorial for ICA using D3.js and some java-script but never published it. Now I let it fly. I got inspired by this page from Arnould Delorme. Click the Image or the link here I also gave a presentation about ICA using the tool which you can find here If you find mistakes or problems please drop me an email.