Hi all, I have paired samples measured at two different timepoints (before and after treatment). I need to fit an OPLS-DA that takes into account this dependency of samples. Do you know if the ropls package handles paired samples. Thank you

The ropls package does not currently support the analysis of paired data. See for instance the reference below about PLS-DA modeling in case of paired data :

JohanA. Westerhuis, EwoudJ. J. Velzen, HuubC. J. Hoefsloot, et AgeK. Smilde, « Multivariate paired data analysis: multilevel PLSDA versus OPLSDA », Metabolomics, vol. 6, nᵒ 1, p. 119‑128, 2010, doi: 10.1007/s11306-009-0185-z.