GAMM for Intra-annual Shift Toward Frugivory
We used a Generalized Additive Mixed Model (GAMM) in this analysis to
investigate the non-linear shift toward frugivory throughout the
calendar year, as outlined by Pedersen et al. (2019). For this purpose,
we employed the ordbetareg package (Kubinec 2022), which acts as a
wrapper for the Bayesian brms package (Bürkner 2017, 2018, 2021). We
decided on this combination of a GAMM with the ordbetareg package
because of the combined suitability for handling the zero-inflated,
ordered, and proportional characteristics of the response variable.
Ordered beta regressions, like the one we applied here, enabled us to
model relationships between the lower bound (0), upper bound (1), and
the continuous proportions in between without overfitting the model to
the data (Kubinec 2022).
To investigate nonlinearity in frugivory over the calendar year, we
specified the calendar day in which samples were collected as the smooth
predictor with the response variable representing the proportion of
fecal volume attributed to fruit. This approach allowed us to visualize
frugivory patterns over time. To account for variability in frugivory
among individuals and sites, we introduced a random effect that
represented the individual providing each sample. Since individuals were
nested entirely within the three sites, the site-level variances were
inherently captured in the individual tortoise random effect terms,
simplifying the model.