soilfoodwebs: An R package for analyzing and simulating nutrient fluxes through food webs

Abstract

Soil food web models can calculate the fluxes of carbon and nitrogen between soil organisms and so estimate the impact of individual organisms on ecosystem processes. These modelling approaches go beyond standard techniques in ecology. So, an open-source tool supporting them along with an analysis of their strengths and weaknesses could help. We present the R package soilfoodwebs, which calculates carbon and nitrogen fluxes through food webs and contributes four new features that are documented in the literature but unavailable in open-source software: (1) diet and physiological rates that balance multiple chemical elements, (2) estimates of parameter and structural uncertainty, (3) estimates of direct and indirect effects of taxa on ecosystem processes, and (4) a conversion from equilibrium food web analyses to simulations that can estimate the response to change. soilfoodwebs balances carbon and nitrogen demand by adjusting each organism's diet and the efficiency with which they use carbon. We outline the theory behind the package and demonstrate its functions using soil food web models available in the literature. Our analysis shows that the calculation of fluxes and the contributions of individual taxa to mineralization or decomposition rates is the strength of the soilfoodwebs package and soil food web models. We also show that more detailed information on population regulation (i.e., density-dependence) is needed for using these models to predict trends over time. Outputs from soil food web models can be compared with ecosystem measurements (e.g., mineralization, decomposition) and guide empirical work towards functionally important and undocumented soil biodiversity.