Flight initiation distance analysis
We first examined the effects of social and environmental factors on
FIDs. Specifically, we ran a univariate mixed model with the following
predictors: year, life-stage (juvenile or adult), sex, individual
trappability, trial number, number of conspecific present, vegetation
cover, starting distance, home site human activity score, and distance
to shelter. We included home site identity, walker identity, and
squirrel identity nested within home site identity as random intercepts.
Home site identity was included as a random intercept because multiple
squirrels were tested from the same home site and thus would more likely
be similar to each other. Walker identity was included to control for
potential experimental variation arising from differences among walkers.
Finally, we recognized that in scenarios where individuals were tested
in the presence of other conspecifics simultaneously, the FID of these
individuals were not independent. Thus, we re-ran our model after
filtering the data to only include the FID of the first individual to
flee within these group testing situations but found that the same
predictor effects remained as in our full dataset model (Table S1).
Individual FID repeatability (RFID) was calculated by
extracting the variance components from our full FID model and using the
following formula:
\begin{equation}
R_{\text{FID}}=\ \frac{V_{\text{ind}}}{(V_{\text{ind}}+V_{\text{home}}+V_{\text{obs}}+\ V_{\text{res}})}\nonumber \\
\end{equation}Where Vind is the among-individual variance,
Vhome is the among-home site variance,
Vobs is the among-observer variance, and
Vres is the residual variance.