isotracer: An R package for the analysis of tracer addition experiments

Abstract

O_LITracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. C_LIO_LIWe present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. C_LIO_LIThe isotracer package is capable of handling a variety of tracer study designs, including continuous tracer drips, pulse experiments, and pulse-chase experiments. It can also take into account tracer decay when radioactive isotopes are used. C_LIO_LITo illustrate its use, we present three case studies based on published data and spanning different levels of biological organization: a molecular-level study of protein synthesis and degradation in Arabidopsis thaliana, an organismal-level study of phosphorus incorporation in the eelgrass Zostera marina, and an ecosystem-level study of nitrogen dynamics in Trinidadian montane streams. C_LIO_LIWith these case studies, we illustrate how isotracer can be used to estimate uptake rates, turnover rates, and total flows, as well as their uncertainty. We also show how to perform model selection to compare alternative hypotheses. C_LIO_LIWe conclude by discussing isotracers further applications, limitations, and possible future improvements and expansions. C_LI