[This article was first published on Minding the Brain, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)

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We all know that it is important to plot your data and explore the data visually to make sure you understand it. The same is true for your model fits. First, you want to make sure that the model is fitting the data relatively well, without any substantial systematic deviations. This is often evaluated by plotting residual errors, but I like to start with plotting the actual model fit.

Second, and this is particularly important when using orthogonal polynomials, you want to make sure that the statistically significant effects in the model truly correspond to the “interesting” (i.e., meaningful) effects in your data. For example, if your model had a significant effects on higher-order terms like the cubic and quartic, you might want to conclude that this corresponds to a difference between early and late competition. Plotting the model fits with and without that term can help confirm that interpretation.

The first step to plotting model fits is getting those model-predicted values. If you use lmer, these values are stored in the eta slot of the model object. It can be extracted using m@eta, where m is the model object. Let's look at an example based on eye-tracking data from Kalenine, Mirman, Middleton, & Buxbaum (2012).

summary(data.ex)

##       Time           fixS           cond     obj          subj    
##  Min.   : 500   Min.   :0.0000   Late :765   T:510   21     :102  
##  1st Qu.: 700   1st Qu.:0.0625   Early:765   C:510   24     :102  
##  Median : 900   Median :0.1333               U:510   25     :102  
##  Mean   : 900   Mean   :0.2278                       27     :102  
##  3rd Qu.:1100   3rd Qu.:0.3113                       28     :102  
##  Max.   :1300   Max.   :1.0000                       40     :102  
##                                                      (Other):918  
##     timeBin        ot1              ot2               ot3        
##  Min.   : 1   Min.   :-0.396   Min.   :-0.2726   Min.   :-0.450  
##  1st Qu.: 5   1st Qu.:-0.198   1st Qu.:-0.2272   1st Qu.:-0.209  
##  Median : 9   Median : 0.000   Median :-0.0909   Median : 0.000  
##  Mean   : 9   Mean   : 0.000   Mean   : 0.0000   Mean   : 0.000  
##  3rd Qu.:13   3rd Qu.: 0.198   3rd Qu.: 0.1363   3rd Qu.: 0.209  
##  Max.   :17   Max.   : 0.396   Max.   : 0.4543   Max.   : 0.450  
##                                                                  
##       ot4         
##  Min.   :-0.3009  
##  1st Qu.:-0.1852  
##  Median :-0.0231  
##  Mean   : 0.0000  
##  3rd Qu.: 0.2392  
##  Max.   : 0.4012  
##                   

ggplot(data.ex, aes(Time, fixS, color = obj)) + facet_wrap(~cond) + 
    stat_summary(fun.y = mean, geom = "line", size = 2)

I've renamed the conditions "Late" and "Early" based on the timing of their competition effect: looking at fixation proportions for the related Competitor (green lines) relative to the Unrelated distractor, it looks like the “Late” condition had a later competition effect than the “Early” condition. We start by fitting the full model and plotting the model fit. For convenience, we'll make a new data frame that has the modeled observed data and the model fit:

library(lme4)
m.ex <- lmer(fixS ~ (ot1 + ot2 + ot3 + ot4) * obj * cond + (1 + ot1 + ot2 + ot3 + ot4 | subj) + (1 + ot1 + ot2 | subj:obj:cond), data = subset(data.ex, obj != "T"), REML = F)
data.ex.fits <- data.frame(subset(data.ex, obj != "T"), GCA_Full = m.ex@eta)
ggplot(data.ex.fits, aes(Time, fixS, color = obj)) + facet_wrap(~cond) + stat_summary(fun.data = mean_se, geom = "pointrange", size = 1) + stat_summary(aes(y = GCA_Full), fun.y = mean, geom = "line", size = 2) + labs(x = "Time Since Word Onset (ms)", y = "Fixation Proportion")

The fit looks pretty good and the model seems to capture the early-vs.-late competition difference, so now we can use the normal approximation to get p-values for the object-by-condition interaction:

coefs.ex <- as.data.frame(summary(m.ex)@coefs)
coefs.ex$p <- format.pval(2 * (1 - pnorm(abs(coefs.ex[, "t value"]))))
coefs.ex[grep("*objU:cond*", rownames(coefs.ex), value = T), ]

##                     Estimate Std. Error t value       p
## objU:condEarly     -0.004164    0.01701 -0.2448 0.80664
## ot1:objU:condEarly  0.065878    0.07586  0.8685 0.38514
## ot2:objU:condEarly -0.047568    0.04184 -1.1370 0.25554
## ot3:objU:condEarly -0.156184    0.02327 -6.7119 1.9e-11
## ot4:objU:condEarly  0.075709    0.02327  3.2535 0.00114

There are significant object-by-condition interaction effects on the cubic and quartic terms, so that's where competition in the two conditions differed, but does that correspond to the early-vs.-late difference? To answer this question we can fit a model that does not have those cubic and quartic terms and visually compare it to the full model. We'll plot the data with pointrange, the full model with thick lines, and the smaller model with thinner lines.

m.exSub <- lmer(fixS ~ (ot1 + ot2 + ot3 + ot4) * obj + (ot1 + ot2 + ot3 + ot4) * cond + (ot1 + ot2) * obj * cond + (1 + ot1 + ot2 + ot3 + ot4 | subj) + (1 + ot1 + ot2 | subj:obj:cond), data = subset(data.ex, obj != "T"), REML = F)
data.ex.fits$GCA_Sub <- m.exSub@eta
ggplot(data.ex.fits, aes(Time, fixS, color = obj)) + facet_wrap(~cond) + stat_summary(fun.data = mean_se, geom = "pointrange", size = 1) + stat_summary(aes(y = GCA_Full), fun.y = mean, geom = "line", size = 2) + stat_summary(aes(y = GCA_Sub), fun.y = mean, geom = "line", size = 1) + labs(x = "Time Since Word Onset (ms)", y = "Fixation Proportion")

Well, it sort of looks like the thinner lines have less early-late difference, but it is hard to see. It will be easier if we look directly at the competition effect size (that is, the difference between the competitor and unrelated fixation curves):

ES <- ddply(data.ex.fits, .(subj, Time, cond), summarize, Competition = fixS[obj == "C"] - fixS[obj == "U"], GCA_Full = GCA_Full[obj == "C"] - GCA_Full[obj == "U"], GCA_Sub = GCA_Sub[obj == "C"] - GCA_Sub[obj == "U"])
ES <- rename(ES, c(cond = "Condition"))
ggplot(ES, aes(Time, Competition, color = Condition)) + stat_summary(fun.y = mean, geom = "point", size = 4) + stat_summary(aes(y = GCA_Full), fun.y = mean, geom = "line", size = 2) + labs(x = "Time Since Word Onset (ms)", y = "Competition") + stat_summary(aes(y = GCA_Sub), fun.y = mean, geom = "line", size = 1)

Now we can clearly see that the full model (thick lines) captures the early-vs.-late difference, but when we remove the cubic and quartic terms (thinner lines), that difference almost completely disappears. So that shows that those higher-order terms really were capturing the timing of the competition effect.

P.S.: For those that care about behind-the-scenes/under-the-hood things, this post was created (mostly) using knitr in RStudio.

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