warning and errors: matrix is not symmetric, arguments imply differing number of rows: 11, 9

[connor-morozumi]

I am getting the following warnings and errors.

CARlasso(Didymellaceae + Cladosporium ramotenellum+Didymella sp.+ Didymosphaeriaceae + Didymellaceae.1 + Gibberella intricans+Colletotrichum spaethianum+Alternaria alternata+Coniothyrium sp. + all_others~CO2 , data = forlasso,link = "logit", adaptive = TRUE, n_iter = 5000, n_burn_in = 1000, thin_by = 10)

warning: chol(): given matrix is not symmetric

and then with plot

Error in data.frame(id = c(paste0("resp", 1:n_resp), paste0("pred", 1:n_pred)), : arguments imply differing number of rows: 11, 9

[mariano-molina]

I get the same warning and error when I try to plot. Did you manage to find a solution? @connor-morozumi Please help, thanks @YunyiShen @crsl4

[connor-morozumi]

@mariano-molina I never did get a response nor did I figure this out myself. I think the warning and the plotting error are not inherently related. In playing around with it more I think I get the warning when i try to include too many taxa. How many are you trying to do?

The plot error can happen though even when the warning doesn't occur.

@crsl4 @YunyiShen

[crsl4]

Thanks for reaching out! We are severely understaffed to tackle bugs, but we will definitely get back to you as soon as possible. Thanks for your patience!

[connor-morozumi]

@mariano-molina I did a bit of troubleshooting of this on my own today and actually got mine to run. Here are a few things I tried.

1. at first I only had 1 predictor as my study only has one treatment contrast. Adding a fake predictor with 3 levels seems to have fixed this
2. I also moved some columns around but doubt that matters (mirroring the example df str(mgp154))
3. I also seemed to not be correctly including a col of all_others. So I used rowSums and then deleted the columns that were collapsed. I don't know if that is correct. This on it's own did not fix the issue.

So perhaps see after running CARlasso() if your predictors come back NULL with print(soy_res3$nodes)

If indeed it needs more than 1 predictor I am unsure this package will be very useful for me. But I may be doing something wrong. Cheers!

[crsl4]

Ah interesting! Thanks for tracking down some potential sources of error. In our experiments, we always had more than one predictor, so maybe you are onto something. We'll check the code! Thanks!