vignettes/window_analysis_vignette.Rmd
window_analysis_vignette.Rmd
Our Experiment: Each eyetrackingR vignette uses the eyetrackingR package to analyze real data from a simple 2-alternative forced choice (2AFC) word recognition task administered to 19- and 24-month-olds. On each trial, infants were shown a picture of an animate object (e.g., a horse) and an inanimate object (e.g., a spoon). After inspecting the images, they disappeared and they heard a label referring to one of them (e.g., “The horse is nearby!”). Finally, the objects re-appeared on the screen and they were prompted to look at the target (e.g., “Look at the horse!”).
In this vignette, we want to take an initial look at our data and perform the most fundamental eye-tracking analysis there is: a window analysis. This allows us to ascertain whether, in a certain window, infants looked more to the ‘animate’ when it was named than when the ‘inanimate’ was named.
Before performing this analysis, we’ll need to prepare and clean our dataset. Here we will to do this quickly and with few notes but, for more information, see the vignette on preparing your data.
## Loading required package: dplyr
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
data("word_recognition")
data <- make_eyetrackingr_data(word_recognition,
participant_column = "ParticipantName",
trial_column = "Trial",
time_column = "TimeFromTrialOnset",
trackloss_column = "TrackLoss",
aoi_columns = c('Animate','Inanimate'),
treat_non_aoi_looks_as_missing = TRUE
)
# subset to response window post word-onset
response_window <- subset_by_window(data,
window_start_time = 15500,
window_end_time = 21000,
rezero = FALSE)
## Avg. window length in new data will be 5500
# remove trials with > 25% of trackloss
response_window_clean <- clean_by_trackloss(data = response_window,
trial_prop_thresh = .25)
## Performing Trackloss Analysis...
## Will exclude trials whose trackloss proportion is greater than : 0.25
## ...removed 33 trials.
Here, we’ll inspect the descriptive statistics for our data, and make
some initial visualizations just to make sure everything is in order. We
basically want a glance at each subject’s looking to the
Animate
for each condition. To do so, we’ll:
describe_data
function to generate a quick data
summary (telling us the means and variance within each Target condition
for each subject, and the number of trials contributed after cleaning
above), and(data_summary <- describe_data(response_window_clean,
describe_column='Animate', group_columns=c('Target','ParticipantName')))
## # A tibble: 54 × 10
## Target ParticipantName Mean SD LowerQ UpperQ Min Max N NumTrials
## <fct> <fct> <dbl> <dbl> <dbl> <dbl> <int> <int> <int> <int>
## 1 Animate ANCAT18 0.359 0.481 0 1 0 1 330 1
## 2 Animate ANCAT22 0.791 0.407 0 1 0 1 990 3
## 3 Animate ANCAT23 0.815 0.388 0 1 0 1 1320 4
## 4 Animate ANCAT26 0.699 0.459 0 1 0 1 660 2
## 5 Animate ANCAT39 0.880 0.325 0 1 0 1 1320 4
## 6 Animate ANCAT45 0.715 0.452 0 1 0 1 660 2
## 7 Animate ANCAT50 0.896 0.306 0 1 0 1 660 2
## 8 Animate ANCAT53 0.727 0.446 0 1 0 1 660 2
## 9 Animate ANCAT55 0.955 0.208 0 1 0 1 990 3
## 10 Animate ANCAT58 0.855 0.352 0 1 0 1 1320 4
## # ℹ 44 more rows
plot(data_summary)
The first way to ask our question is to get a single mean proportion score (of looking to the Animate AOI) for each Target condition (Animate, Inanimate) for each subject and perform a paired t-test.
To do so, we will use the make_time_window_data
function
to aggregate by participant and calculate this mean value. We also
specify a couple additional predictors (Age, MCDI_Total [vocabulary
score]) that we will use in a follow-up analysis.
Note that the dataframe returned by
make_time_window_data
will actually give us a few different
dependent variables to choose from:
Prop
– The mean of raw proportion-lookingLogitAdjusted
– The logit is defined as
log( Prop / (1 - Prop) )
. This transformation attempts to
map bounded 0,1
data to the real number line.
Unfortunately, for data that is exactly 0 or 1, this is undefined. One
solution is add a very small value to any datapoints that equal 0, and
subtract a small value to any datapoints that equal 1 (we use 1/2 the
smallest nonzero value for this adjustment).Elog
– Another way of calculating a corrected logit
transformation is to add a small value epsilon
to both the
numerator and denominator of the logit equation (we use 0.5).ArcSin
– The arcsine-root transformation of the raw
proportions, defined as asin(sqrt(Prop))
.While the first DV is the most intuitive, you might consider using the others to account for the bounded nature of proportions. The boundedness of proportions is an issue because it can mean that CI’s around your estimates fall above 1 or below 0 (which is not possible) and that there is an inherent link between group means and variance (means closer to 0 and 1 will necessarily have lower variance than means around .5). These are violations of many parametric models, such as OLS regression and t-tests.
(EyetrackingR also lets you specify any arbitrary DV aside from the
above. For example, you could analyze mean pupil-dilation by supplying a
column name to the other_dv_columns
argument. This is true
for make_time_sequence_data
as well.)
We will start out by using the ArcSin DV.
# aggregate by subject across the response window
response_window_agg_by_sub <- make_time_window_data(response_window_clean,
aois='Animate',
predictor_columns=c('Target','Age','MCDI_Total'),
summarize_by = "ParticipantName")
# take a quick peek at data
plot(response_window_agg_by_sub, predictor_columns="Target", dv = "ArcSin")
# show condition means
describe_data(response_window_agg_by_sub, describe_column = "ArcSin", group_columns = "Target")
## # A tibble: 2 × 8
## Target Mean SD LowerQ UpperQ Min Max N
## <fct> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <int>
## 1 Animate 1.08 0.206 0.653 1.43 0.643 1.57 27
## 2 Inanimate 0.692 0.248 0.186 1.08 0 1.14 27
# simple paired t-test between conditions
with(response_window_agg_by_sub, t.test(ArcSin[Target == 'Animate'], ArcSin[Target == 'Inanimate'], paired=TRUE))
##
## Paired t-test
##
## data: ArcSin[Target == "Animate"] and ArcSin[Target == "Inanimate"]
## t = 7.2705, df = 26, p-value = 1.012e-07
## alternative hypothesis: true mean difference is not equal to 0
## 95 percent confidence interval:
## 0.2803975 0.5014410
## sample estimates:
## mean difference
## 0.3909192
That t-test looks pretty good. But we also want to know whether this effect of Target is mediated by age and vocabulary. To do so, we can fit a quick linear model:
# you should almost always sum-code and center your predictors when performing regression analyses
response_window_agg_by_sub$AgeC <- response_window_agg_by_sub$Age - mean(response_window_agg_by_sub$Age)
response_window_agg_by_sub$MCDI_TotalC <- response_window_agg_by_sub$MCDI_Total - mean(response_window_agg_by_sub$MCDI_Total)
model <- lm(ArcSin ~ Target*AgeC*MCDI_TotalC, data=response_window_agg_by_sub)
summary(model)
##
## Call:
## lm(formula = ArcSin ~ Target * AgeC * MCDI_TotalC, data = response_window_agg_by_sub)
##
## Residuals:
## Min 1Q Median 3Q Max
## -0.43847 -0.14408 -0.01695 0.14882 0.48809
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 1.0775721 0.0462383 23.305 < 2e-16 ***
## TargetInanimate -0.4054232 0.0653909 -6.200 1.45e-07 ***
## AgeC 0.0315232 0.0413260 0.763 0.449
## MCDI_TotalC -0.0014167 0.0033328 -0.425 0.673
## TargetInanimate:AgeC -0.0012671 0.0584438 -0.022 0.983
## TargetInanimate:MCDI_TotalC -0.0040145 0.0047133 -0.852 0.399
## AgeC:MCDI_TotalC 0.0009042 0.0025599 0.353 0.726
## TargetInanimate:AgeC:MCDI_TotalC 0.0024107 0.0036202 0.666 0.509
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.2265 on 46 degrees of freedom
## Multiple R-squared: 0.5045, Adjusted R-squared: 0.4291
## F-statistic: 6.691 on 7 and 46 DF, p-value: 1.777e-05
This linear model shows no main effects or interactions of Target with those predictors, but confirms the large effect of Target.
A more rigorous approach is not to aggregate by participants
but, instead, to aggregate by trials within participants and fit a
linear mixed-effects model using lme4’s lmer
function. This
predicts infants’ looking to the Animate
AOI based on the
Target
condition of each trial while accounting for random
intercepts and slope across Trial
(i.e., items) and
ParticipantName
(i.e., subjects).
Here, for demonstration’s sake, we’ll predict the Elog
transformed DV.
Note that the make_time_window_data
call no longer
summarizes by Participant. When the summarize_by
argument
is not passed, this function will default to summarizing by trials
within participants.
response_window_agg <- make_time_window_data(response_window_clean,
aois='Animate',
predictor_columns=c('Target','Age','MCDI_Total'))
# sum-code and center predictors
response_window_agg$TargetC <- ifelse(response_window_agg$Target == 'Animate', .5, -.5)
response_window_agg$TargetC <- as.numeric(scale(response_window_agg$TargetC, center=TRUE, scale=FALSE))
# mixed-effects linear model on subject*trial data
model_time_window <- lmer(Elog ~ TargetC + (1 + TargetC | Trial) + (1 | ParticipantName),
data = response_window_agg, REML = FALSE)
## boundary (singular) fit: see help('isSingular')
# cleanly show important parts of model (see `summary()` for more)
(est <- broom.mixed::tidy(model_time_window, effects="fixed"))
## # A tibble: 2 × 5
## effect term estimate std.error statistic
## <chr> <chr> <dbl> <dbl> <dbl>
## 1 fixed (Intercept) 1.15 0.206 5.57
## 2 fixed TargetC 2.48 0.323 7.66
# use model comparison to attain p-values
drop1(model_time_window,~.,test="Chi")
## Single term deletions
##
## Model:
## Elog ~ TargetC + (1 + TargetC | Trial) + (1 | ParticipantName)
## npar AIC LRT Pr(Chi)
## <none> 505.40
## TargetC 1 512.35 8.9491 0.002776 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Those results look very much in line with the results of the simple t-test, though they are slightly more conservative.
The estimates from lmer
can be interpreted as
follows:
Because we sum-coded our TargetC
predictor before
fitting the model, we can calculate the looking to the Animate in the
Animate target condition by taking the intercept estimate, +/- the slope
estimate divided by two.
condition_estimate <- with(est,
c(estimate[term=="(Intercept)"] + estimate[term=="TargetC"] / 2,
estimate[term=="(Intercept)"] - estimate[term=="TargetC"] / 2))
And we can convert that back into a proportion value by reversing the transformation into log-odds:
## [1] 0.9155565 0.4767013
You might notice that these are higher than we might have expected,
based on the raw proportions (the actual proportion-looking for the
animate condition was closer to .80). This could suggest our choice of
transformation (empirical logit) was problematic. It’s important to
choose a transformation that satisfies the assumptions of the model we
are using. We can plot the fitted vs. residuals of our model using the
plot
method for lmer
:
plot(model_time_window)
The empirical-logit transformation appears to have created some problematic outliers, so we might want to consider another transformation, such as the adjusted logit.
model_time_window_logit <- lmer(LogitAdjusted ~ TargetC + (1 + TargetC | Trial) + (1 | ParticipantName),
data = response_window_agg, REML = FALSE)
## boundary (singular) fit: see help('isSingular')
plot(model_time_window_logit)
drop1(model_time_window_logit,~.,test="Chi")
## Single term deletions
##
## Model:
## LogitAdjusted ~ TargetC + (1 + TargetC | Trial) + (1 | ParticipantName)
## npar AIC LRT Pr(Chi)
## <none> 382.11
## TargetC 1 389.80 9.6917 0.001851 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
est_logit <- broom.mixed::tidy(model_time_window_logit, effects="fixed")
condition_estimate_logit <- with(est_logit,
c(estimate[term=="(Intercept)"] + estimate[term=="TargetC"] / 2,
estimate[term=="(Intercept)"] - estimate[term=="TargetC"] / 2))
exp(condition_estimate_logit)/(1+exp(condition_estimate_logit))
## [1] 0.8620136 0.4741567
See Wharton & Hui (2011) for more discussion of these issues.
We can also throw in some additional predictors to the model, as we
did above, so long as we specified these columns when we called
make_time_window_data
. Here we will look at the effect of
Age and MCDI_Total (after centering, of course):
response_window_agg$AgeC <- response_window_agg$Age - mean(response_window_agg$Age)
response_window_agg$MCDI_TotalC <- response_window_agg$MCDI_Total - mean(response_window_agg$MCDI_Total)
model_time_window_add_predictors <- lmer(Elog ~ TargetC*AgeC*MCDI_TotalC + (1 + TargetC | Trial) + (1 | ParticipantName),
data = response_window_agg, REML = FALSE)
## boundary (singular) fit: see help('isSingular')
# cleanly show important parts of model (see `summary()` for more)
broom.mixed::tidy(model_time_window_add_predictors, effects="fixed")
## # A tibble: 8 × 5
## effect term estimate std.error statistic
## <chr> <chr> <dbl> <dbl> <dbl>
## 1 fixed (Intercept) 1.14 0.201 5.66
## 2 fixed TargetC 2.74 0.353 7.77
## 3 fixed AgeC 0.229 0.173 1.32
## 4 fixed MCDI_TotalC -0.0336 0.0145 -2.33
## 5 fixed TargetC:AgeC 0.0802 0.303 0.265
## 6 fixed TargetC:MCDI_TotalC -0.00126 0.0252 -0.0498
## 7 fixed AgeC:MCDI_TotalC 0.00263 0.0106 0.249
## 8 fixed TargetC:AgeC:MCDI_TotalC -0.0296 0.0183 -1.62
# use model comparison to attain p-values
drop1(model_time_window_add_predictors,~.,test="Chi")
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## boundary (singular) fit: see help('isSingular')
## Single term deletions
##
## Model:
## Elog ~ TargetC * AgeC * MCDI_TotalC + (1 + TargetC | Trial) +
## (1 | ParticipantName)
## npar AIC LRT Pr(Chi)
## <none> 509.26
## TargetC 1 516.59 9.3312 0.002253 **
## AgeC 1 508.95 1.6957 0.192848
## MCDI_TotalC 1 512.14 4.8815 0.027146 *
## TargetC:AgeC 1 507.33 0.0695 0.792084
## TargetC:MCDI_TotalC 1 507.26 0.0025 0.960331
## AgeC:MCDI_TotalC 1 507.32 0.0620 0.803385
## TargetC:AgeC:MCDI_TotalC 1 509.85 2.5966 0.107095
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Here we do see an effect of MCDI_Total (the participants’ productive vocabulary): participants with larger vocabularies looked less to the Animate overall (regardless of Target).
For more of a basic introduction to linear mixed-effects models, covering topics like p-values, confidence intervals, estimates, interpreting random effects, and logistic regression, see this tutorial.
For more information on the empirical-logit transformation, see Barr (2008).
For more information on the dangers of analyzing raw proportion means, see Dixon (2008) and Jaeger (2008).
It is important to consider what we are losing in a window analysis. By collapsing across time within trials or subjects, we are completely removing the greatest asset of eye-tracking data: time. This can mask important properties of our data. Therefore, while window analyses are attractive in terms of parsimony and computational demands – and are often a necessary first step – other analyses may allow you to better understand and report your data.
Barr, D. J. (2008). Analyzing “visual world” eyetracking data using multilevel logistic regression. Journal of Memory and Language, 59, 457–474. https://doi.org/10.1016/j.jml.2007.09.002
Dixon, P. (2008). Models of accuracy in repeated-measures designs. Journal of Memory and Language, 59(4), 447–456. https://doi.org/10.1016/j.jml.2007.11.004
Jaeger, T. F. (2008). Categorical data analysis: Away from ANOVAs (transformation or not) and towards logit mixed models. Journal of Memory and Language, 59(434-446). https://doi.org/10.1016/j.jml.2007.11.007
Warton, D. I., & Hui, F. K. (2011). The arcsine is asinine: the analysis of proportions in ecology. Ecology, 92(1), 3-10.