Statistical Analyses
All analyses were conducted using R [22]. We used mixed linear
effects models (lme4 [23]) to analyse the coral and fish abundance,
using survey year as fixed and location as a random effect.
Butterflyfish community analyses were conducted using a PERMANOVA from
the Vegan package [24], with 999 permutations using sequential sums
of squares. Location was fitted as the first term in the model, so that
that any variation among location is accounted for before testing the
effect of years (full model: abundance ~ location +
year). Pairwise analyses between years were conducted with the
PairwiseAdonis package [25].