HostSwitch: An R Package to Simulate the Extent of Host-Switching by a Consumer

Abstract

In biology a general definition for host switch is when an organism (consumer) uses a new host (which represents a resource). The host switch process by a consumer may happen through its pre-existing capability to use a sub-optimal resource. The HostSwitch R package provides functions to simulate the dynamics of host switching (extent and frequency) in the population of a consumer that interacts with current and potential hosts over the generations. The HostSwitch package is based on a Individual-Based mock-up model published in FORTRAN by Araujo et al. (2015). The package largely improve the previous mock-up model, by implementing numerous new functionalities such as comparison and evaluation of simulations with several customizable parameters to accommodate several types of biological consumer-host associations, an interactive visualization of the model, an in-depth description of the parameters in a biological context. Finally, we provided three real world scenarios taken from the literature selected from ecology, agriculture and parasitology. This package is intended to reach researchers in the broad field of biology interested in simulating the process of host switch of different types of symbiotic biological associations.(1) by increasing the accessibility of the model to researchers that are not familiar with FORTRAN;(2) by including customizable parameters, some previously unreleased (e.g., jump_back), that allow us to extend the mock-up model from strict pathology (i.e., simulating host switches by pathogen) to

Phylogenetic Triage and Risk Assessment: How to Predict Emerging Phytoplasma Diseases

“…We suggest that stakeholders in collaboration with agronomic research institutes in Bavaria launch specific monitoring programs to validate in the field the potential prevalence of infection in the population of the selected insects at the interfaces with fields of susceptible crops where the risk of outbreaks is higher. The DAMA protocol embodies a modeling platform (such as the Individual-Based Model [104,105]) that explores fitness profiles of pathogens and the probability of an individual in a population to disperse and successfully colonize a novel host. A targeted monitoring plan may generate data for the modeling platform to narrow our focus to particular pathogens and vectors in specific habitat interfaces and plant hosts.…”