rGAI: An R package for fitting the generalised abundance index to
seasonal count data
Abstract
1. The Generalised Abundance Index (GAI) provides a useful tool for
estimating relative population sizes and trends of seasonal
invertebrates from species’ count data, and offers potential for
inferring which external factors may influence phenology and demography
through parametric descriptions of seasonal variation. 2. We provide an
R package that extends previous software with the ability to include
covariates when fitting parametric GAI models, where seasonal variation
is described by either a mixture of Normal distributions or a stopover
model which provides estimates of lifespan. The package also generalises
the model to allow any number of broods/generations in the target
population within a defined season. The option to perform bootstrapping,
either parametrically or non-parametrically, is also provided. 3. The
new package allows models to be far more flexible when describing
seasonal variation, which may be dependent on site-specific
environmental factors or consist of many broods/generations which may
overlap, as demonstrated by two case studies. 4. Our open-source
software, available at
\href{https://github.com/calliste-fagard-jenkin/GAI}{https://github.com/calliste-fagard-jenkin/rGAI},
makes this extension widely and freely available, allowing the
complexity of GAI models used by ecologists and applied statisticians to
increase accordingly.