Search Archives

Hi Ebhodaghe, I invite you to look at the effects package : https://cran.r-project.org/web/packages/effects/index.html and the hook-up ggplot package: https://cran.r-project.org/web/packages/ggeffects/index.html Cheers, GA2 Le...

Hi everyone, I am looking for a package which can handle "hurdle.lognormal" distribution family and multiple grouping factors. GLMMadaptive seemed as the way to go but unfortunately, to the best of my knowledge, it does not handle multiple grouping...

Hello everyone, I am trying to test the effect of tillage on weed communities using CCA. I would like to make sure my permuting scheme is correct. My experimental lay-out is the following: 4 blocks 3 plots within each...

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...

Hello everyone, I'm looking for a method/function in order to produce an Anova table based on Likelihood Ratio Tests (LRT) for a glmmTMB model (R software). In my case it is with a beta distribution and log link...

Sorry, my intent was definetely not to shortcut anyone or anything. I thought I would give you all a little feedback on your propositions. The problem with drop1 (when an interaction is in the model) is when you want it...

Have you tried downloading the package "Rcpp"? and trying again? GA2 Le ven. 6 mars 2020 ? 17:27, Ebhodaghe Faith <ebhodaghefaith at gmail.com> a ?crit : > Many thanks, Adeux and Ben. > I successfully installed the *effects* package but I'm...

Hello everyone, I am currently exploring the relationship between weed biomass during the fallow period and cover crop productivity (in interaction with tillage type, nitrogen fertilization, and cover crop species, as imposed by the 3-way factorial experimental design). This...

Hello Becky, Even though I cannot directly answer your question... a Chisq of 0 with such a difference in AIC seems indeed suspicious. To test the effect of your predictor in a GLMM context through LRT tests, you could (should...

Hi John, Thank you very much for your answer. I am very grateful. I had indeed set sum contrasts before running car::Anova(mod,type="III") (i.e. *options(contrasts = c("contr.sum", "contr.poly"))* ). However, I think the high...

As mentionned by Roman, linear regression does not imply that the response is normally distributed, rather that the residuals of the model are normally distributed. The choice of the distribution family should mainly be based on knowledge, that is to...

Hi everyone, Does anybody have any experience with multivariate "mixed" models? And more specifically with the RRPP package or other alternatives to vegan::adonis for complex hierarchical designs? I took knowledge of the RRPP package (associated publication: https://besjournals.onlinelibrary...

Hi everyone, I am trying to investigate how to set up a permutation scheme for community data originating from a split plot experiment with pseudoreplicates at the lowest level. A theoretical design could be the following: 4 blocks 2 tillage...

Thank you all for continuing to provide valuable information. Indeed, I ruled out glmmadaptive because it does not handle crossed random effects (such a pity in my case, as it is the only downside). My dataset is not massive (480...

Hi mixmoders, I have the following model: mod=glmer(Weed_density~block+scale(year)*syst*timing+(1|year)+(1|plot)+(1|plot:year)+(1|ID_quadrat)+(1|OLRE)+offset(log(size_quadrat)),family=poisson(link="log"),dat=WEED) I have...

Hi Julian, You should look into the {emmeans} package and the function emmeans. The vignettes are very nice, the package has a lot of features and from what I can remember, glmmTMB is handled. Maybe time should be treated as...

Hello everyone, I'm currently trying to analyse the relationship between crop diversity and pesticide use at a national scale (4k farms covering 7 climatic regions), while accounting for crop identity effects (proportion of each crop in the cropping system...

Hi, An alternative could be to code your linear and quadratic effect as poly(Var,2) (this ensures orthogonality) and use ggemmeans() or ggeffects() (the difference between the two will depend on whether you have non focal factors or not...

Hi Aoibheann, I think that anova on glmmTMB objects only produce Wald tests, which don't seem to be very reliable. You might want to look at the monet package (or its little brother afex) that can produce LRT tests...

Hi David, For plotting interactions between two continuous variables, maybe a gamm model might be more adapted? However, by defaut, in the visreg package, you can facet one of your continuous variables (which is subsetted relative to its distribution) and...