Hi @kasias,
R² (coefficient of determination) and R (correlation coefficient) are two different things, evaluating different aspects with different equations.
Using the same Therm.jmp dataset as in the example or here : Example of Comparing Matched Pairs, I can find the same correlation coefficient than in the Matched Pairs analysis platform between the two responses with the Multivariate platform, estimating correlations in a row-wise manner :
So the correlation coefficient used in the Matched Pairs analysis is the Pearson Product-Moment Correlation.
Hope this answer will clear any doubts,
Victor GUILLER
"It is not unusual for a well-designed experiment to analyze itself" (Box, Hunter and Hunter)