Hi everyone, I wanted to allow for different variances across treatment levels so I headed towards nlme:lme in order to use varIdent(). However, I also have crossed random effects (year and plot) which needs a little hack in nlme:lme to specify. Hence the final model is: dat$Grp=1 ### fake grouping in order to create grouped data object gr=groupedData(response~time|Grp,data=dat) ### grouped data object mod4 <- lme(response~ block+treatment*time, random = pdBlocked(list(pdIdent(~ year - 1),pdIdent(~ plot - 1))),weights=varIdent(form=~1|treatment), data=gr,method="ML") The question now is: is it possible to supply such a model to monet::test_terms() ? I cannot find such examples in https://rdrr.io/github/singmann/monet/src/examples/examples.test_terms.R Thank you all once again for you help. Sincerely, Guillaume ADEUX Nb: if I understood correctly from previous messages, this type of model (crossed random effects, specific variance structure) could also be fitted with glmmTMB
test_terms for lme model with crossed random effects and weights
2 messages · Guillaume Adeux, Maarten Jung
I don't know if monet::test_terms() can do this. But maybe the emmeans package can help here. The joint_tests() function computes Type-III test for each effect in a model [1]. Also (what I find quite interesting), "[t]here is an experimental mode = "satterthwaite" option that determines degrees of freedom approximately: It estimates a needed gradient in the covariance matrix experimentally by randomly perturbing the response values. Thus, the degrees of freedom will vary slightly (or possibly even a lot) if the reference grid is re-calculated" [2]. Cheers, Maarten [1] https://cran.r-project.org/web/packages/emmeans/vignettes/interactions.html [2] https://cran.r-project.org/web/packages/emmeans/vignettes/models.html#K On Tue, Oct 23, 2018 at 12:06 PM Guillaume Adeux <
guillaumesimon.a2 at gmail.com> wrote:
Hi everyone, I wanted to allow for different variances across treatment levels so I headed towards nlme:lme in order to use varIdent(). However, I also have crossed random effects (year and plot) which needs a little hack in nlme:lme to specify. Hence the final model is: dat$Grp=1 ### fake grouping in order to create grouped data object gr=groupedData(response~time|Grp,data=dat) ### grouped data object mod4 <- lme(response~ block+treatment*time, random = pdBlocked(list(pdIdent(~ year - 1),pdIdent(~ plot - 1))),weights=varIdent(form=~1|treatment), data=gr,method="ML") The question now is: is it possible to supply such a model to monet::test_terms() ? I cannot find such examples in https://rdrr.io/github/singmann/monet/src/examples/examples.test_terms.R Thank you all once again for you help. Sincerely, Guillaume ADEUX Nb: if I understood correctly from previous messages, this type of model (crossed random effects, specific variance structure) could also be fitted with glmmTMB [[alternative HTML version deleted]]
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