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analyze.folders() takes sampling as an argument but this variable is not passed to analyze.logfile() so the function proceeds using the default 128 sampling rate. sampling=sampling should be added to analyze.logfile(d, session) for non-default sampling rates.

Basically, the script made the assumption that not all EEG data will have a “Blink” column (i.e., non-Emotiv EEG data), so for any data missing a blink column, it creates its own blink column filled with 0s. This works perfectly for the spectral.analysis. But the coherence.analysis function takes in series1 and series2 (not “series”), so the forming of the blink column wasn't working properly. The way it was:

if (is.null(blink)) {
blink <- rep(0, length(series))
}

if (is.null(quality1)) {
quality1 <- rep(5, length(series)) # Values of 5 are for "Information not available"
}

if (is.null(quality2)) {
quality2 <- rep(5, length(series)) # Values of 5 are for "Information not available"
}

Was fixed by simply changing it to:

if (is.null(blink)) {
blink <- rep(0, length(series1))
}

if (is.null(quality1)) {
quality1 <- rep(5, length(series1)) # Values of 5 are for "Information not available"
}

if (is.null(quality2)) {
quality2 <- rep(5, length(series2)) # Values of 5 are for "Information not available"
}