Mean computation from accumulated row values while ignoring NaN in MATLAB

Question

I'm looking for suggestions on how to solve the following problem elegantly. Although performance isn't an issue in my specific case, I'd appreciate comments regarding good practices. Thanks in advance! The short version: I'm trying to average matrix rows according to some logic, while ignoring NaN values. The code I currently have does not handle NaN values the way I want. The long version: My data is built in the following manner: - A single (first) column of "bins". The amount of rows for every bin is not constant. The bins don't have to be integers. Rows are pre-sorted. - A variable number of data columns, possibly including NaNs. Here's an example: ``` DATA = [... 180 NaN NaN 1.733 180 NaN NaN 1.703 200 0.720 2.117 1.738 200 0.706 2.073 1.722 200 0.693 2.025 1.723 200 NaN NaN 1.729 210 NaN NaN 1.820 210 NaN NaN 1.813 210 NaN NaN 1.805 240 NaN NaN 1.951 240 NaN NaN 1.946 240 NaN NaN 1.946 270 NaN NaN 2.061 270 NaN NaN 2.052 300 0.754 2.356 2.103 300 0.758 2.342 2.057 300 NaN NaN 2…

Accepted Answer

One possible approach: find changes in first column (exploiting the fact that it's pre-sorted) and apply `nanmean` to each block of rows:

```
ind = find(diff([-inf; (DATA(:,1)); inf])~=0); %// value changed: start of block
r = arrayfun(@(n) nanmean(DATA(ind(n):ind(n+1)-1,:)), 1:numel(ind)-1, 'uni', 0);
RES = vertcat(r{:});
```

You can replace `arrayfun` by an explicit loop. That may be faster, and avoids the overhead introduced by cells:

```
ind = find(diff([-inf; (DATA(:,1)); inf])~=0); %// value changed: start of block
RES = zeros(numel(ind)-1, size(DATA,2)); %// preallocate
for n = 1:numel(ind)-1 %// loop over blocks
    RES(n,:) = nanmean(DATA(ind(n):ind(n+1)-1,:));
end
```

Your approach can be used as well. You only need to call `accumarray` with a handle to the `nanmean` function. This doesn't require the first column to be pre-sorted.

```
nDataCols = size(DATA,2)-1;
[u, ~, n] = unique(DATA(:,1));
RES = zeros(length(u), nDataCols); %// Preallocation
for ind1 = 1:nDataCols
    RES(:,ind1) = accumarray(n, DATA(:,ind1+1), [], @nanmean);
end
RES = [u, RES];
```

Mean computation from accumulated row values while ignoring NaN in MATLAB

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