inti H2cal function errors for metabolite data with heterogeneous concentration values

[TizianaS92]

Hello, I'm running the H2cal function in the context of phenotype treatment for a GWAS analysis as follows:

  cat_h2cal <- H2cal(data = InputDataFrame
                     , trait = "C_001"
                     , gen.name = "ID"
                     , rep.n = 2
                     , fixed.model = "(1|Habitus) + ID"
                     , random.model = "(1|Habitus) + (1|ID)"
                     , emmeans = FALSE
                     , plot_diag = TRUE
                     , outliers.rm = TRUE )

The traits of interest are metabolites, varying greatly in concentration. The function works correctly, generates plots and individuates outliers with some traits, but not with others. In particular, I get this kind of errors for the traits the function can't process:

Errore in lme4::lFormula(formula = C_001 ~ (1 | Habitus) + (1 | ID), :
0 (non-NA) cases
In aggiunta: Messaggi di avvertimento:
1: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model failed to converge with max|grad| = 26.0806 (tol = 0.002, component 1)
2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model is nearly unidentifiable: very large eigenvalue

• Rescale variables?

I've noticed that if I change the random.model formula term 1|ID with ID, plots are generated. But I'd like to always apply the same model to all my metabolites. If I look at the concentrations of the traits H2Cal is unable to process, I've noticed that troublesome ones have very low concentrations and often many values (with one single exception, >80%), are 0. However, some metabolites with a pretty high 0 frequency (50-60%) are processed correctly.

Also, some of my samples have one replicate, others two.

Can you help me here? How can I handle my dataset in this case? Maybe with a different formula for the random model?
I've found some tips online, about re-scaling variables (for a similar function, called lme4), but I was wondering what the exact cause of my problems could be.

I'm attaching a part of my dataset

SampleToAttach_H2Cal.txt

Here, the troublesome metabolites are C_001, C_002, C_003, C_004, C_009 and C_013.

Thank you in advance

[Flavjack]

Dear @TizianaS92, sorry for the late answer. Now I noticed your open issue.
I hope you were able to solve the problem.
If you could share the solution maybe would be useful for other users.
Thanks,