Issue calling $

Hi there, thank you for the great package!

I am having some trouble with obtaining the Q2 values after running perf() for pls regression. Since a few weeks the call for tune.spls$, using your case study data as example, returns NULL. I thought that tune.spls$measures$ would give me the same values, however they seem to be considerably different from what I used to get except for the first PC. Am I missing something here? I am very grateful for any help!

Sorry that I am not including a reproducible example but I am also having some issue with reprex/pandoc. Here is what I get calling tune.spls$measures$ with your case study data for spls:

feature comp mean sd
1 Y 1 2.437408e-01 7.869266e-03
2 Y 2 -9.833899e-02 1.675195e-02
3 Y 3 -3.115617e-01 2.603249e-02
4 Y 4 -2.873965e+00 5.546602e-01
5 Y 5 -1.853856e+00 1.934992e-01
6 Y 6 -2.654221e+03 9.403738e+02
7 Y 7 -1.691935e+06 3.204353e+06
8 Y 8 -5.014191e+09 3.839735e+09
9 Y 9 -2.052687e+12 6.323096e+12
10 Y 10 -2.022491e+16 3.444245e+16

And my sessionInfo

R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] mixOmics_6.17.28 ggplot2_3.3.5 lattice_0.20-44 MASS_7.3-54

loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 RSpectra_0.16-0 pillar_1.6.2 compiler_4.1.1
[5] RColorBrewer_1.1-2 plyr_1.8.6 tools_4.1.1 lifecycle_1.0.0
[9] tibble_3.1.3 gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.11
[13] Matrix_1.3-4 igraph_1.2.6 ggrepel_0.9.1 parallel_4.1.1
[17] gridExtra_2.3 stringr_1.4.0 withr_2.4.2 dplyr_1.0.7
[21] generics_0.1.0 vctrs_0.3.8 grid_4.1.1 tidyselect_1.1.1
[25] glue_1.4.2 ellipse_0.4.2 R6_2.5.1 fansi_0.5.0
[29] rARPACK_0.11-0 BiocParallel_1.26.2 tidyr_1.1.3 purrr_0.3.4
[33] reshape2_1.4.4 corpcor_1.6.9 magrittr_2.0.1 scales_1.1.1
[37] ellipsis_0.3.2 matrixStats_0.60.1 colorspace_2.0-2 utf8_1.2.2
[41] stringi_1.7.3 munsell_0.5.0 crayon_1.4.1

hi @lperez ,

I am pinging @aljabadi here so that he can tell you what may have changed recently in the code.


Hi @lperez ,

This is possibly due to the fact that the tune.spls function has changed substantially now and now allows variable selection on Y as well. It also supports additional measures of tuning. Can you paste here the code you used?