# Blog Archives

## GEE QIC update

Here is improved code for calculating QIC from geeglm in geepack in R (original post). Let me know how it works. I haven’t tested it much, but is seems that QIC may select overparameterized models. In the code below, I had to replace <- with = because wordpress didn’t except <- within code or pre tags. It should still work just fine.

Here is a quick example of how to run this function. First, highlight and run the code below in R. That will save the function in your workspace. Then run your gee model using geeglm in geepack (package available from CRAN). Next, run QIC(your_gee_model) and you get the QIC. You can then repeat this with alternative a priori models. Below the function is an example using data available as part of geepack.

**[UPDATE: IMPROVED CODE AND EXTENSIONS ARE NOW AVAILABLE ON https://github.com/djhocking/qicpack INCLUDING AS AN R PACKAGE]**

############################################################ # QIC for GEE models # Daniel J. Hocking ############################################################ QIC = function(model.R) { library(MASS) model.indep = update(model.R, corstr = "independence") # Quasilikelihood mu.R = model.R$fitted.values y = model.R$y type = family(model.R)$family quasi.R = switch(type, poisson = sum((y*log(mu.R)) - mu.R), gaussian = sum(((y - mu.R)^2)/-2), binomial = sum(y*log(mu.R/(1 - mu.R)) + log(1 - mu.R)), Gamma = sum(-y/(mu.R - log(mu.R))), stop("Error: distribution not recognized")) # Trace Term (penalty for model complexity) omegaI = ginv(model.indep$geese$vbeta.naiv) # Omega-hat(I) via Moore-Penrose generalized inverse of a matrix in MASS package #AIinverse = solve(model.indep$geese$vbeta.naiv) # solve via indenity Vr = model.R$geese$vbeta trace.R = sum(diag(omegaI %*% Vr)) px = length(mu.R) # number non-redunant columns in design matrix # QIC QIC = 2*(trace.R - quasi.R) [EDIT: original post was missing '*'] #QICu = (-2)*quasi.R + 2*px # Approximation assuming model structured correctly output = c(QIC, quasi.R, trace.R, px) names(output) = c('QIC', 'Quasi Lik', 'Trace', 'px') return(output) }

Here’s an example you can run in R.

library(geepack) data(dietox) dietox$Cu = as.factor(dietox$Cu) mf = formula(Weight ~ Cu * (Time + I(Time^2) + I(Time^3))) gee1 = geeglm(mf, data = dietox, id = Pig, family = poisson, corstr = "ar1") gee1 summary(gee1) mf2 = formula(Weight ~ Cu * Time + I(Time^2) + I(Time^3)) gee2 = geeglm(mf2, data = dietox, id = Pig, family = poisson, corstr = "ar1") summary(gee2) anova(gee2) anova(gee1, gee2) mf3 = formula(Weight ~ Cu + Time + I(Time^2)) gee3 = geeglm(mf3, data = dietox, id = Pig, family = poisson, corstr = "ar1") gee3.I = update(gee3, corstr = "independence") gee3.Ex = update(gee3, corstr = "exchangeable") sapply(list(gee1, gee2, gee3, gee3.I, gee3.Ex), QIC)

In the output of this model it suggests that model gee1 is the best model. I have some concerns that QIC will almost inevitably choose the most complex model. More testing with simulated data will be necessary.

[,1] [,2] [,3] [,4] [,5] QIC -333199.7 -333188.0 -333187.5 -333181.8 -333153.6 Quasi Lik 166623.0 166622.7 166620.4 166622.2 166615.4 Trace 23.2 28.7 26.6 31.3 38.6 px 861.0 861.0 861.0 861.0 861.0

You will get warnings when running this model because it uses a Poisson distribution for continuous data. I will work on finding a better example in the future before I make this available as an R package.

## Conference Presentations

I recently gave a talk at the Ecological Society of America (ESA) annual meeting in Portland, OR and a poster presentation at the World Congress of Herpetology meeting in Vancouver, BC, Canada. Both presentations were comparing generalized linear mixed models (GLMM) and generalized estimating equations (GEE) for analyzing repeated count data. I advocate for using GEE over the more common GLMM to analyze longitudinal count (or binomial) data when the specific subjects (sites as random effects) are not of special interest. The overall confidence intervals are much smaller in the GEE models and the coefficient estimates are averaged over all subjects (sites). This means the interpretation of coefficients is the log change in Y for each 1 unit change in X on average (averaged across subjects). Below you can see my two presentations for more details.

## Plotting 95% Confidence Bands in R

I am comparing estimates from subject-specific GLMMs and population-average GEE models as part of a publication I am working on. As part of this, I want to visualize predictions of each type of model including 95% confidence bands.

First I had to make a new data set for prediction. I could have compared fitted values with confidence intervals but I am specifically interested in comparing predictions for particular variables while holding others constant. For example, soil temperature is especially important for salamanders, so I am interested in the predicted effects of soil temperature from the different models. I used the expand.grid and model.matrix functions in R to generate a new data set where soil temperature varied from 0 to 30 C. The other variables were held constant at their mean levels during the study. Because of the nature of the contrast argument in the model.matrix function, I had to include more than one level of the factor “season”. I then removed all season except spring. In effect I am asking, what is the effect of soil temperature on salamander activity during the spring when the other conditions are constant (e.g. windspeed = 1.0 m/s, rain in past 24 hours = This code is based on code from Ben Bolker via http://glmm.wikidot.com

# Compare Effects of SoilT with 95% CIs formula(glmm1) newdat.soil <- expand.grid( SoilT = seq(0, 30, 1), RainAmt24 = mean(RainAmt24), RH = mean(RH), windspeed = mean(windspeed), season = c("spring", "summer", "fall"), droughtdays = mean(droughtdays), count = 0 ) newdat.soil$SoilT2 <- newdat.soil$SoilT^2 # Spring newdat.soil.spring <- newdat.soil[newdat.soil$season == 'spring', ] mm = model.matrix(terms(glmm1), newdat.soil)

Next I calculated the 95% confidence intervals for both the GLMM and GEE models. For the GLMM the plo and phi are the low and high confidence intervals for the fixed effects assuming zero effect of the random sites. tlo and thi account for the uncertainty in the random effects.

newdat.soil$count = mm %*% fixef(glmm1) pvar1 <- diag(mm %*% tcrossprod(vcov(glmm1),mm)) tvar1 <- pvar1+VarCorr(glmm1)$plot[1] newdat.soil <- data.frame( newdat.soil , plo = newdat.soil$count-2*sqrt(pvar1) , phi = newdat.soil$count+2*sqrt(pvar1) , tlo = newdat.soil$count-2*sqrt(tvar1) , thi = newdat.soil$count+2*sqrt(tvar1) ) mm.geeEX = model.matrix(terms(geeEX), newdat.soil) newdat.soil$count.gee = mm.geeEX %*% coef(geeEX) tvar1.gee <- diag(mm.geeEX %*% tcrossprod(geeEX$geese$vbeta, mm.geeEX)) newdat.soil <- data.frame( newdat.soil , tlo.gee = newdat.soil$count-2*sqrt(tvar1.gee) , thi.gee = newdat.soil$count+2*sqrt(tvar1.gee) )

The standard error of the fixed effects are larger in the GEE model than in the GLMM, but when the variation associated with the random effects are accounted for, the uncertainty (95% CI) around the estimates is greater in the GLMM. This is especially evident when the estimated values are large since the random effects are exponential on the original scale. This can be seen in the below plots

Although this plot does the job, it isn’t an efficient use of space, nor is it easy to compare exactly where the different lines fall. It would be nice to plot everything on one set of axes. The only trouble is that all the lines could be difficult to see just using solid and dashed/dotted lines. To help with this, I combine the plots but added color and shading using the polygon function. The code and plot are below

plot(newdat.soil.spring$SoilT, exp(newdat.soil.spring$count.gee), xlab = "Soil temperature (C)", ylab = 'Predicted salamander observations', type = 'l', ylim = c(0, 25)) polygon(c(newdat.soil.spring$SoilT , rev(newdat.soil.spring$SoilT)) , c(exp(newdat.soil.spring$thi.gee) , rev(exp(newdat.soil.spring$tlo.gee))) , col = 'grey' , border = NA) lines(newdat.soil.spring$SoilT, exp(newdat.soil.spring$thi.gee), type = 'l', lty = 2) lines(newdat.soil.spring$SoilT, exp(newdat.soil.spring$tlo.gee), type = 'l', lty = 2) lines(newdat.soil.spring$SoilT, exp(newdat.soil.spring$count.gee), type = 'l', lty = 1, col = 2) lines(newdat.soil.spring$SoilT, exp(newdat.soil.spring$count), col = 1) lines(newdat.soil.spring$SoilT, exp(newdat.soil.spring$thi), type = 'l', lty = 2) lines(newdat.soil.spring$SoilT, exp(newdat.soil.spring$tlo), type = 'l', lty = 2)

Now you can directly compare the results of the GLMM and GEE models. The predicted values (population-averaged) for the GEE is represented by the red line, while the average (random effects = 0, just fixed effects) from the GLMM are represented by the solid black line. The dashed lines represent the 95% confidence intervals for the GLMM and the shaded area is the 95% confidence envelope for the GEE model. As you can see, the GEE has much higher confidence in it’s prediction of soil temperature effects on salamander surface activity than the GLMM model. This would not be apparent without visualizing the predictions with confidence intervals because the standard errors of the fixed effects were lower in the GLMM than in the GEE. This is because the SEs in the GEE include the site-level (random effect) variation while the GLMM SEs of the covariates do not include this variation and are interpreted as the effect of a change of 1 X on Y * at a given site*.

## Model Validation: Interpreting Residual Plots

When conducting any statistical analysis it is important to evaluate how well the model fits the data and that the data meet the assumptions of the model. There are numerous ways to do this and a variety of statistical tests to evaluate deviations from model assumptions. However, there is little general acceptance of any of the statistical tests. Generally statisticians (which I am not but I do my best impression) examine various diagnostic plots after running their regression models. There are a number of good sources of information on how to do this. My recommendation is Fox and Weisberg’s An R Companion to Applied Regression (Chp 6). You can refer to Fox’s book, Applied Regression Analysis and Generalized Linear Models for the theory and details behind these plots but the corresponding R book is more of the “how to” guide. A very brief but good introduction to checking linear model assumptions can be found here.

The point of this post isn’t to go over the details or theory but rather discuss one of the challenges that I and others have had with interpreting these diagnostic plots. Without going into the differences between standardized, studentized, Pearson’s and other residuals, I will say that most of the model validation centers around the residuals (essentially the distance of the data points from the fitted regression line). Here is an example from Zuur and Colleagues’ excellent book, Mixed Effects Models and Extensions in Ecology with R:

So these residuals appear exhibit homogeneity, normality, and independence. Those are pretty clear, although I’m not sure if the variation in residuals associated with the predictor (independent) variable Month is a problem. This might be a problem with heterogeneity. Most books just show a few examples like this and then residuals with clear patterning, most often increasing residual values with increasing fitted values (i.e. large values in the response/dependent variable results in greater variation, which is often correct with a log transformation). A good example of this can be see in (d) below in fitted vs. residuals plots (like top left plot in figure above).

These are the type of idealized examples usually shown. I think it’s important to show these perfect examples of problems but I wish I could get expert opinions on more subtle, realistic examples. These figures are often challenging to interpret because the density of points also changes along the x-axis. I don’t have a good example of this but will add one in when I get one. Instead I will show some diagnostic plots that I’ve generated as part of a recent attempt to fit a Generalized Linear Mixed Model (GLMM) to problematic count data.

The assumption of normality (upper left) is probably sufficient. However, the plot of the fitted vs. residuals (upper right) seems to have more variation at mid-level values compared with the low or high fitted values. Is this patten enough to be problematic and suggest a poor model fit? Is it driven by greater numbers of points at mid-level fitted values? I’m not sure. The diagonal dense line of points is generated by the large number of zeros in the dataset. My model does seem to have some problem fitting the zeros. I have two random effects in my GLMM. The residuals across plots (5 independent sites/subjects on which the data was repeatedly measured – salamanders were counted on the same 5 plots repeatedly over 4 years) don’t show any pattern. However, there is heterogeneity in residuals among years (bottom right). This isn’t surprising given that I collected much more data over a greater range of conditions in some years. This is a problem for the model and this variation will need to be modeled better.

So I refit the model and came up with these plots (different plots for further discussion rather than direct comparison):

Here you can see considerable variation from normality for the overall model (upper left) but okay normality within plots (lower right). The upper right plot is an okay example of what I was talking about with changes in density making interpretation difficult. There are far more points at lower values and a sparsity of points are very high fitted values. The eye is often pulled in the direction of the few points on the right creating difficult in interpretation. To help with this I like to add a loess smoother or smoothing spline (solid line) and a horizontal line at zero (broken line). The smoothing line should be approximately straight and horizontal around zero. Basically it should overlay the horizontal zero line. Here’s the code to do it in R for a fitted linear mixed model (lme1):**plot(fitted(lme1), residuals(lme1), xlab = “Fitted Values”, ylab = “Residuals”) abline(h=0, lty=2) lines(smooth.spline(fitted(lme1), residuals(lme1)))**

This also helps determine if the points are symmetrical around zero.** **I often also find it useful to plot the absolute value of the residuals with the fitted values. This helps visualize if there is a trend in direction (bias). It can also help to better see changes in spread of the residuals indicating heterogeneity. The bias can be detected with a sloping loess or smooth spline. In the lower left plot, you can see little evidence of bias but some evidence of heterogeneity (change in spread of points). Again, I an not sure if this is bad enough to invalidate the model but in combination with the deviation from normality I would reject the fit of this model.

In a mixed model it can be important to look at variation across the values of the random effects. In my case here is an example of fitted vs. residuals for each of the plots (random sites/subjects). I used the following code, which takes advantage of the lattice package in R.**# Check for residual pattern within groups and difference between groups xyplot(residuals(glmm1) ~ fitted(glmm1) | Count$plot, main = “glmm1 – full model by plot”, panel=function(x, y){ panel.xyplot(x, y) panel.loess(x, y, span = 0.75) panel.lmline(x, y, lty = 2) # Least squares broken line } )**

And here is another way to visualize a mixed model:

You can see that the variation in the two random effects (Plot and Year) is much better in this model but there are problems with normality and potentially heterogeneity. Since violations of normality are off less concern than the other assumptions, I wonder if this model is completely invalid or if I could make some inference from it. I don’t know and would welcome expert opinion.

Regardless, this model was fit using a poisson GLMM and the deviance divided by the residual degrees of freedom (df) was 5.13, which is much greater than 1, indicating overdispersion. Therefore, I tried to fit the regression using a negative binomial distribution:

**# Using glmmPQL via MASS package**

** **

**library(MASS)**

** **

** **

**#recommended to run model first as non-mixed to get a starting value for the theta estimate:**

** **

** **

**#negbin**

** **

** **

**glmNB1 <- glm.nb(count ~ cday +cday2 + cSoilT + cSoilT2 + cRainAmt24 + cRainAmt242 + RHpct + soak24 + windspeed, data = Count, na.action = na.omit)**

** **

**summary(glmNB1)**

** **

**#anova(glmNB1)**

** **

**#plot(glmNB1)**

** **

** **

**# Now run full GLMM with initial theta starting point from glm**

** **

**glmmPQLnb1 <- glmmPQL(count ~ cday +cday2 + cSoilT + cSoilT2 + cRainAmt24 + cRainAmt242 + RHpct + soak24 + windspeed, random = list(~1 | plot, ~1 | year), data = Count, family = negative.binomial(theta = 1.480, link = log), na.action = na.exclude)**

Unfortunately, I got the following validation plots:

Clearly, this model doesn’t work for the data. It is quite surprising given the fit of the poisson and that the negative binomial is a more general distribution than the poisson and handles overdispersed count data well usually. I’m not sure what the problem is in this case.

Next I tried to run the model as if all observations were random:

<!– /* Font Definitions */ @font-face {font-family:Cambria; panose-1:2 4 5 3 5 4 6 3 2 4; mso-font-charset:0; mso-generic-font-family:auto; mso-font-pitch:variable; mso-font-signature:3 0 0 0 1 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0in; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-ascii-font-family:Cambria; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:Cambria; mso-fareast-theme-font:minor-latin; mso-hansi-font-family:Cambria; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} @page Section1 {size:8.5in 11.0in; margin:1.0in 1.25in 1.0in 1.25in; mso-header-margin:.5in; mso-footer-margin:.5in; mso-paper-source:0;} div.Section1 {page:Section1;} — **glmmObs1 <- lmer(count ~ cday +cday2 + cSoilT + cSoilT2 + cRainAmt24 + cRainAmt242 + RHpct + soak24 + windspeed + (1 | plot) + (1 | year) + (1 | obs), data = Count, family = poisson)** Again I end up with more problematic validation/diagnostic plots:

So that’s about it for now. Hopefully this post helps some people with model validation and interpretation of fitted vs. residual plots. I would love to hear opinions regarding interpretation of residuals and when some pattern is too much and when it is acceptable. Let me know if you have examples of other more subtle residual plots.

Happy coding and may all your analyses run smoothly and provide clear interpretations!