Error in chol.default(varcov) : the leading minor of order 3 is not positive

[rossneville]

Dear Cécile and Viviane,

Following on from a closed issues about externvar #274

I have updated my input model for use in externvar and I am now receiving an error:

Error in chol.default(varcov): the leading minor of order 3 is not positive

My input model is:

m1 <- lcmm(fixed = y ~ ns(Age_rescaled, knots = c(0.33, 0.67)), mixture = ~ns(Age_rescaled, knots = c(0.33, 0.67)), random = ~ns(Age_rescaled, knots = c(0.33, 0.67)), subject = "ID", ng = 3, nwg = T, link = "thresholds", data = df)

df1 <- df %>% group_by(ID) %>% mutate(agemax = max(Age_rescaled)) %>% ungroup %>% mutate(DVlast = ifelse(Age_rescaled==agemax,DV,NA))

This model converged when I checked (m1$conv), and all of the usual lcmm functions work fine with it.

Then, my externvar model is:

ext1 <- externVar(m1,fixed= AttentionLAST ~ 1, mixture=~1, data=df1,method="conditional",M=10,varest = "paramBoot")

This model gives the error.

Perhaps it has something to do with the proportion of convergence on bootstrap iterations, as shown in bold below (70%).

The m1 input model seems to work fine for external outcomes where I have observations at each level of Age_rescaled. However, this model where I only have an observation for AttentionLAST at the final Age_rescaled observation seems to be having problems running.

Is there any advice you could give?

Regards Ross

**Secondary linear mixed model fitted by maximum likelihood method primary model variance accounted for through parametric boostrap

externVar(model = mthresholds3, fixed = ISTlast ~ 1, mixture = ~1, data = paq, method = "conditional", varest = "paramBoot", M = 10)

Statistical Model: Dataset: paq Number of subjects: 412 Number of observations: 412 Number of observations deleted: 1838 Number of latent classes: 3 Number of parameters: 4

Iteration process:

Proportion of convergence on bootstrap iterations (%)= 70 Goodness-of-fit statistics: maximum log-likelihood: -1349.77 AIC: 2712.09 BIC: 2728.17**

[VivianePhilipps]

Hi,

I made a change in the externVar function (commit 2e23623). Could you please check it ?

Viviane

[rossneville]

Hi Viviane ExternVar seems to be working fine - I've used it multiple times today and not encountered the issue. Thanks for fixing it. Regards Ross

On Wed, 13 Nov 2024 at 13:20, VivianePhilipps @.***> wrote:

Hi,

I made a change in the externVar function (commit 2e23623 https://github.com/CecileProust-Lima/lcmm/commit/2e2362329400f6ebd83caac3be0cb9a76f07b3ec). Could you please check it ?

Viviane

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