# Blog Archives

## Paper Summary: Natural Disturbance and Logging Effects on Salamanders

Paper Summary:

Hocking, D.J., K.J. Babbitt, and M. Yamasaki. 2013. Comparison of Silvicultural and Natural Disturbance Effects on Terrestrial Salamanders in Northern Hardwood Forests. Biological Conservation 167:194-202. doi: http://dx.doi.org/10.1016/j.biocon.2013.08.006

Unfortunately, this paper is behind a paywall. Please email me if you would like a copy for educational purposes.

We were interested in how red-backed salamanders respond to various logging practices compared with natural disturbance. Specifically, we compared abundance of salamanders in the two years following a major ice-storm with clearcuts, patch cuts, group cuts, single-tree selection harvests, and undisturbed forest patches in the White Mountains of New Hampshire (Northern Appalachian Mountains). The 100-year ice storm caused ~65% percent canopy loss in the effected areas. We know that clearcutting has detrimental effects on populations of woodland salamanders but the impacts of less intense harvesting and natural disturbances is less well understood.

We used transects of coverboards from 80m inside each forest patch extending to 80m outside each patch into the surround, undisturbed forest. Repeated counts of salamanders under these coverboards allowed us to employ a Dail-Madsen open population model to estimate abundance in each treatment, while accounting for imperfect detection. The results were quite clear as demonstrated in this figure:

There were slightly fewer salamanders in the ice-storm damaged sites compared with undisturbed reference sites. The single-tree selection sites were most similar to the ice-storm damage sites. The group cut, patch cut, and clearcut didn’t differ from each other and all had ~88% fewer salamanders compared with reference sites.

In addition to comparing natural and anthropogenic disturbances, we were interested in examining how salamanders respond along the edge of even-aged harvests. Wind, solar exposure, and similar factors are altered in the forest edge adjacent to harvested areas. This can result in salamander abundance being reduced in forest edges around clearcuts. Previous researchers have used nonparametric estimates of edge effects. A limitation of this methods is that effects cannot be projected well across the landscape. These methods are also unable to account for imperfect detection. We developed a method to model edge effects as a logistic function while accounting for imperfect detection. As with the treatment effects, the results are quite clear with very few salamanders in the center of the even-aged harvests, a gradual increase in abundance near the forest edge, increasingly more salamanders in the forest moving away from the edge, and eventually leveling off at carrying capacity. In this case, red-backed salamander abundance reached 95% of carrying capacity 34 m into the surrounding forest. As the model is parametric, predictions can be projected across landscapes. The equation can be used in GIS and land managers can predict the total number of salamanders that would be lost from a landscape given a variety of alternative timber harvest plans.

Hopefully other researchers find this method useful and apply it for a variety of taxa. It could also be incorporated into ArcGIS or QGIS toolboxes/plugins as a tool for land managers. You can read our paper for more details if you’re interested. In addition to methodological details there is more information on environmental factors that affect detection and abundance of salamanders in this landscape.

## 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!

## GLMM Hell

I have been starting to analyze some data I have of repeated counts of salamanders from 5 plots over 4 years. I am trying to develop a predictive model of salamander nighttime surface activity as a function of weather variables. The repeated counting leads to the need for Generalized Linear Mixed Models (GLMM). Count data often results in data that are best described with a Poisson distribution, hence the “generalized” term. Because the counts were repeated on the same plots, plot needs to be considered a random effect. If the plot term was not included in this way it would suggest that all the counts were independent but in reality counts on one plot over time are likely to have some correlation that needs to be accounted for to avoid pseudoreplication. So I am stuck with a GLMM. The problem with GLMM in a frequentist statistical framework is that they are difficult to analyze. Bolker and colleagues give the best overview of the analysis process and it’s challenges in: Generalized Linear Mixed Models: A Practical Guide for Ecology and Evolution. They do have an online supplement to that paper that provides a workthrough example complete with R code using the lme4 package. I HIGHLY recommend everyone read Bolker’s paper if considering using GLMMs. Personally, I like the idea of analyzing GLMMs with Bayesian statistics rather than traditional frequentist stats. Below are a few emails that I’ve recently been exchanging with colleagues regarding GLMM. Let me know what you think.

**Question About Selection of Correlated Predictor Variables and Model Selection:**** **How much correlation among independent variables is too much in a GLMM? If I have correlation in the variables does it affect the interpretation or model selection?

**Answer from a Statistician Friend**:** **0.8 and above is high and often one variable can be replaced by the other, and

both are not necessary in the model.

Below 0.7 typically both variables are needed for a good model fit.

I usually use stepAIC (from the MASS package in R) for model selection.

The difficulty comes in interpreting the regression coefficients: with correlation in the predictor variables, the variable that appears first

on the model statement usually gets the larger absolute value, whereas

the other variable has a smaller (in absolute value) coefficient.

Remember the interpretation of regression coefficients: the change

in the response per unit increase GIVEN ALL THE OTHER VARIABLEs IN THE

MODEL.

If you want coefficients that represent “additive” contributions to the

variation in the response (regardless of the order in which predictors

appear in the model statement), and if you have considerable multicollinearity

you might want to consider doing a principal component regression with all

or perhaps with only a subgroup of similar predictor variables.

As with most issues in statistics, there is not a clear-cut hard-fact simple

answer. Live would be simpler if there was….

**Question of GLMM Bayesian Approach:**

Hey Dan – I’m using GLMM b/c I have a repeated-measures design, count data response (negative binomial distribution), etc. I’m finding admb in R is doing the job – and I read the article you mentioned a few months back, when I started considering GLMMs…

I have never worked with Bayesian stats and wouldn’t even know where to begin. Do you have any recommendations for overview reading, and can I analyze a repeated-measures design (i.e., is there a way to cope with random factors)?

**My Response**:

My data sounds very similar to yours. I usually use lmer in the lme4 package. Right now I am just essentially copying the code in Bolker et al 2009 from the online supplements in the TREE paper previously mentioned. I have never see the admb package and will have to check it out. I’ve tried glmmPQL and glmmML but there are more examples in lmer and it’s Splus predecessor. I am annoyed that in Zuur et al. “Mixed Effects Models and Extensions in Ecology with R” they don’t spend much time on model assumptions or model comparison. I feel like they show users how to do the analysis but not how to evaluate it. Pinheiro and Bates do a better job in “Mixed-Effects Models in S and S-Plus” but they focus on linear mixed models and non-linear mixed models and less on GLMM. Plus the code is similar to but differs enough from R that it can be challenging to use at times. The “SAS for Mixed Models” book is good but SAS isn’t free and the code isn’t as transparent to me. Plus it doesn’t have good graphics so I prefer R.

Anyway, Bayesian stats have their own can of worms but I find it more intuitively appealing and I like the transparency in the code using WinBUGS (no Mac version) called from R. There are two very good, practical books to get started. McCarthy presents a good overview and introduction to bayesian stats in “Bayesian Methods for Ecology” but the examples don’t get very advanced. Personally I recommend getting that from the library and reading the first few chapters. I would then buy Marc Kery’s excellent book, “Introduction to WinBUGS for Ecologists.” It is very well written and has a wider range of examples that typically relate to many animal ecology studies. Clark and Gelfand have a decent modeling book with Bayesian analysis in R examples but it’s more ecosystem/environmentally oriented than animal ecology.

Bayesian analysis treats all factors sort of like random variables from population distributions. Therefore there is not need for explicit random vs. fixed delineation. You get estimates and credibility intervals for all variables. You can essentially write the same GLMM model and then analyze it in a Bayesian framework. The big difference in the philosophy behind frequentist vs Bayesian statistics. Bayesians use prior information (even noninformative priors contain information on the underlying distributions). Some scientists are opposed to this but for various reasons that I won’t go into now, I like it. Some people do want a sensitivity analysis to go along with Bayesian analysis to determine the influence of the priors. I might go as far as to say that in the case of GLMM type data Bayesian statistics are more sound (robust?) than frequentist methods but they differ significantly from a philosophical standpoint.

Anyway, I hope that helps.

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