pythonnumpy

numpy sum of squares for matrix

I do have a matrix with observations in rows (measurements at differnt pH) with data points as columns (concentration over time). So one row consists of differnt data points for one pH.

I do want to fit an ODE to the data. So i defined a cost function and would like to calculate the sum of squares for all observatoins. Taking the sum of sqares for this matrix should work like:

res = y - yhat                        # calculate residuals
ssq = np.diag(np.dot(res.T,res))      # sum over the diagonal

is that correct ?

Solution

  • If you would take the sum of the last array it would be correct. But it's also unnecessarily complex (because the off-diagonal elements are also calculated with np.dot) Faster is:

    ssq = np.sum(res**2)

    If you want the ssd for each experiment, you can do:

    ssq = np.sum(res**2, axis=1)