Dear all, This question is generally about glmmTMB, rather than lme4 - apologies if this puts it out of the jurisdiction of r-sig-mixed-models. I've been using glmmTMB to implement beta GLMMs. The data I'm using was collected from a series of plots that were measured continually, every three months, for ~2 years. I would like to use ACF plots to look at possible temporal auto-correlation in the residuals, and in the event that I need to include a correlation structure (e.g. AR1), I would like to see how well any such structure accounts for the auto-correlation. I read here: https://stats.stackexchange.com/questions/80823/do-autocorrelated-residual-patterns-remain-even-in-models-with-appropriate-corre ...and here: http://bbolker.github.io/mixedmodels-misc/ecostats_chap.html ...that it is necessary to use the normalized residuals for ACF plotting, rather than the raw residuals, as the raw residuals contain no information on any correlation terms. The information in the residuals.glm help file also implies that pearson/standardized residuals may be no good for this?: "type: an optional character string specifying the type of residuals to be used. If ?"response"?, the "raw" residuals (observed - fitted) are used; else, if ?"pearson"?, the standardized residuals (raw residuals divided by the corresponding standard errors) are used; else, if ?"normalized"?, the normalized residuals (standardized residuals pre-multiplied by the inverse square-root factor of the estimated error correlation matrix) are used. Partial matching of arguments is used, so only the first character needs to be provided. Defaults to ?"response"?." Assuming it is indeed the normalized residuals that I need, does anyone know how I could derive them from a glmmTMB object? The residuals.glmmTMB function currently only accepts "response" and "pearson" as 'type' arguments. If it is necessary to calculate them 'by hand', then what R code should I use to convert the standardized residuals, as per the definition above? (i.e. "standardized residuals pre-multiplied by the inverse square-root factor of the estimated error correlation matrix"). Apologies if I have misunderstood any concepts here, I am new to analysing time series data. Many thanks in advance, Helen
glmmTMB: how to get normalized residuals for use in ACF plotting
1 message · Helen Waters