The Walsh transform is a type of spectral analysis (for finding periodicities) of binary or ordinal data. It assumes even spacing of data points, and expects one column of binary (0/1) or ordinal (integer) data.
The normal methods for spectral analysis are perhaps not optimal for binary data, because they decompose the time series into sinusoids rather than "square waves". The Walsh transform may then be a better choice, using basis functions that flip between -1 and +1. These basis functions have varying "frequencies" (number of transitions divided by two), known as sequencies. In PAST, each pair of even ("cal") and odd ("sal") basis functions is combined into a power value using cal2+sal2, producing a "power spectrum" that is comparable to the Lomb periodogram.
The Walsh transform is slightly exotic compared with the Fourier transform, and the results must be interpreted cautiously. For example, the effects of the duty cycle (percentage of ones versus zeros) are somewhat difficult to understand.
In PAST, the data values are pre-processed by multiplying with two and subtracting one, bringing 0/1 binary values into the -1/+1 range optimal for the Walsh transform. The data are zero-padded to the next power of 2 if necessary, as required by the method.