Hi, dear all. I've built a glmm (model) with glmmTMB; it had fitted without, neither error message, nor warnings; but, since I've added the following ziformula=~village (village is a 6 levels grouping factor variable), I got the warning message "Model convergence problem; non-positive-definite Hessian matrix" Trying to resolve this, I've used ziformula=~(1|village) instead; then, the model fits without neither error message, nor warnings; but when I'd ran "summary(model)", I got the following error message "Error in reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get such an error message and I don't know any idea about its possible cause; so, any help to solve it will be much appreciated. In advance, thanks. Kind regards,
Error in reS$ziReStruc[[i]]
8 messages · C. AMAL D. GLELE, Mollie Brooks, Ben Bolker +1 more
~village would treat village as a fixed effect in the zero-inflation model; ~1|village would
On Mon, Aug 13, 2018 at 9:11 AM C. AMAL D. GLELE <altessedac2 at gmail.com> wrote:
Hi, dear all.
I've built a glmm (model) with glmmTMB; it had fitted without, neither
error message, nor warnings;
but, since I've added the following ziformula=~village (village is a 6
levels grouping factor variable), I got the warning message
"Model convergence problem; non-positive-definite Hessian matrix"
Trying to resolve this, I've used ziformula=~(1|village) instead;
then, the model fits without neither error message, nor warnings; but when
I'd ran "summary(model)", I got the following error message "Error in
reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get
such an error message and I don't know any idea about its possible cause;
so, any help to solve it will be much appreciated.
In advance, thanks.
Kind regards,
[[alternative HTML version deleted]]
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Sorry, hit 'send' by accident.
~village would treat village as a fixed effect in the zero-inflation
model; ~1|village [or ~(1|village)] would treat it as a random effect.
I can't reproduce a problem with summary(); here's a reproducible
example. Can you construct a reproducible example that fails ?
dd <- data.frame(village=factor(rep(1:6,50)))
set.seed(101)
zp <- c(0.2,0.8,0.3,0.5,0.6,0.7)
dd$z <- rbinom(300,size=1,prob=zp[dd$village])
dd$z[dd$z==1] <- rpois(sum(dd$z),lambda=3)
library(glmmTMB)
g1 <- glmmTMB(z~1,ziformula=~1|village,data=dd,
family=poisson)
g2 <- update(g1,ziformula=~village)
summary(g1)
summary(g2)
On Mon, Aug 13, 2018 at 9:11 AM C. AMAL D. GLELE <altessedac2 at gmail.com> wrote:
Hi, dear all.
I've built a glmm (model) with glmmTMB; it had fitted without, neither
error message, nor warnings;
but, since I've added the following ziformula=~village (village is a 6
levels grouping factor variable), I got the warning message
"Model convergence problem; non-positive-definite Hessian matrix"
Trying to resolve this, I've used ziformula=~(1|village) instead;
then, the model fits without neither error message, nor warnings; but when
I'd ran "summary(model)", I got the following error message "Error in
reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get
such an error message and I don't know any idea about its possible cause;
so, any help to solve it will be much appreciated.
In advance, thanks.
Kind regards,
[[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
I think this bug was fixed in the development version (https://github.com/glmmTMB/glmmTMB/issues/370). It might still be in the CRAN version. Install from Github and it should work. https://github.com/glmmTMB/glmmTMB Cheers, Mollie
On 13Aug 2018, at 15:11, C. AMAL D. GLELE <altessedac2 at gmail.com> wrote: Hi, dear all. I've built a glmm (model) with glmmTMB; it had fitted without, neither error message, nor warnings; but, since I've added the following ziformula=~village (village is a 6 levels grouping factor variable), I got the warning message "Model convergence problem; non-positive-definite Hessian matrix" Trying to resolve this, I've used ziformula=~(1|village) instead; then, the model fits without neither error message, nor warnings; but when I'd ran "summary(model)", I got the following error message "Error in reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get such an error message and I don't know any idea about its possible cause; so, any help to solve it will be much appreciated. In advance, thanks. Kind regards, [[alternative HTML version deleted]]
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Thanks to you all for your replies. I will first try Mollie's suggestion and keep you informed. All the best, Amal 2018-08-13 20:34 GMT+02:00 Mollie Brooks <mollieebrooks at gmail.com>:
I think this bug was fixed in the development version ( https://github.com/glmmTMB/glmmTMB/issues/370). It might still be in the CRAN version. Install from Github and it should work. https://github.com/glmmTMB/glmmTMB Cheers, Mollie On 13Aug 2018, at 15:11, C. AMAL D. GLELE <altessedac2 at gmail.com> wrote: Hi, dear all. I've built a glmm (model) with glmmTMB; it had fitted without, neither error message, nor warnings; but, since I've added the following ziformula=~village (village is a 6 levels grouping factor variable), I got the warning message "Model convergence problem; non-positive-definite Hessian matrix" Trying to resolve this, I've used ziformula=~(1|village) instead; then, the model fits without neither error message, nor warnings; but when I'd ran "summary(model)", I got the following error message "Error in reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get such an error message and I don't know any idea about its possible cause; so, any help to solve it will be much appreciated. In advance, thanks. Kind regards, [[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
5 days later
Hi, dear Mollie.
When installing from Github "
devtools::install_github("glmmTMB/glmmTMB/glmmTMB")";
I've encountered several errors that I corrected; but I do not have a
solution for the last
one (pasted below) yet:
"Installation failed: Cannot change working directory"
In advance thanks.
All the best.
Amal
2018-08-13 20:34 GMT+02:00 Mollie Brooks <mollieebrooks at gmail.com>:
I think this bug was fixed in the development version ( https://github.com/glmmTMB/glmmTMB/issues/370). It might still be in the CRAN version. Install from Github and it should work. https://github.com/glmmTMB/glmmTMB Cheers, Mollie On 13Aug 2018, at 15:11, C. AMAL D. GLELE <altessedac2 at gmail.com> wrote: Hi, dear all. I've built a glmm (model) with glmmTMB; it had fitted without, neither error message, nor warnings; but, since I've added the following ziformula=~village (village is a 6 levels grouping factor variable), I got the warning message "Model convergence problem; non-positive-definite Hessian matrix" Trying to resolve this, I've used ziformula=~(1|village) instead; then, the model fits without neither error message, nor warnings; but when I'd ran "summary(model)", I got the following error message "Error in reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get such an error message and I don't know any idea about its possible cause; so, any help to solve it will be much appreciated. In advance, thanks. Kind regards, [[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
This seems like a permissions problem. As https://github.com/satijalab/seurat/issues/94 says, try running as administrator? (i.e., run R as administrator, then run install_github(...) within that session
On 2018-08-19 10:45 AM, C. AMAL D. GLELE wrote:
Hi, dear Mollie.
When installing from Github "
devtools::install_github("glmmTMB/glmmTMB/glmmTMB")";
I've encountered several errors that I corrected; but I do not have a
solution for the last
one (pasted below) yet:
"Installation failed: Cannot change working directory"
In advance thanks.
All the best.
Amal
2018-08-13 20:34 GMT+02:00 Mollie Brooks <mollieebrooks at gmail.com>:
I think this bug was fixed in the development version ( https://github.com/glmmTMB/glmmTMB/issues/370). It might still be in the CRAN version. Install from Github and it should work. https://github.com/glmmTMB/glmmTMB Cheers, Mollie On 13Aug 2018, at 15:11, C. AMAL D. GLELE <altessedac2 at gmail.com> wrote: Hi, dear all. I've built a glmm (model) with glmmTMB; it had fitted without, neither error message, nor warnings; but, since I've added the following ziformula=~village (village is a 6 levels grouping factor variable), I got the warning message "Model convergence problem; non-positive-definite Hessian matrix" Trying to resolve this, I've used ziformula=~(1|village) instead; then, the model fits without neither error message, nor warnings; but when I'd ran "summary(model)", I got the following error message "Error in reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get such an error message and I don't know any idea about its possible cause; so, any help to solve it will be much appreciated. In advance, thanks. Kind regards, [[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
[[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
In case you have a single grouping factor for the random effects, you can also try package GLMMadaptive that uses adaptive Gaussian quadrature: https://drizopoulos.github.io/GLMMadaptive/ More info for zero-inflated models at: https://drizopoulos.github.io/GLMMadaptive/articles/ZeroInflated_and_TwoPart_Models.html Best, Dimitris From: C. AMAL D. GLELE <altessedac2 at gmail.com<mailto:altessedac2 at gmail.com>> Date: Sunday, 19 Aug 2018, 4:46 PM To: Mollie Brooks <mollieebrooks at gmail.com<mailto:mollieebrooks at gmail.com>> Cc: R SIG Mixed Models <r-sig-mixed-models at r-project.org<mailto:r-sig-mixed-models at r-project.org>> Subject: Re: [R-sig-ME] Error in reS$ziReStruc[[i]] Hi, dear Mollie. When installing from Github " devtools::install_github("glmmTMB/glmmTMB/glmmTMB")"; I've encountered several errors that I corrected; but I do not have a solution for the last one (pasted below) yet: "Installation failed: Cannot change working directory" In advance thanks. All the best. Amal 2018-08-13 20:34 GMT+02:00 Mollie Brooks <mollieebrooks at gmail.com>:
I think this bug was fixed in the development version ( https://github.com/glmmTMB/glmmTMB/issues/370). It might still be in the CRAN version. Install from Github and it should work. https://github.com/glmmTMB/glmmTMB Cheers, Mollie On 13Aug 2018, at 15:11, C. AMAL D. GLELE <altessedac2 at gmail.com> wrote: Hi, dear all. I've built a glmm (model) with glmmTMB; it had fitted without, neither error message, nor warnings; but, since I've added the following ziformula=~village (village is a 6 levels grouping factor variable), I got the warning message "Model convergence problem; non-positive-definite Hessian matrix" Trying to resolve this, I've used ziformula=~(1|village) instead; then, the model fits without neither error message, nor warnings; but when I'd ran "summary(model)", I got the following error message "Error in reS$ziReStruc[[i]] : subscript out of bounds": it's my first time to get such an error message and I don't know any idea about its possible cause; so, any help to solve it will be much appreciated. In advance, thanks. Kind regards, [[alternative HTML version deleted]]
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
_______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models