R package: PACT

In a recent study, we analysed the probability of congruent cophylogenies given the method, association and ecosystem (Citation: Trivellone & al., 2022) Trivellone, V. & Panassiti, B. (2022). A field synopsis, systematic review and meta-analyses of cophylogenetic studies: What is affecting congruence between phylogenies. Under Review. .

R package: HostSwitch

The R package ‘‘HostSwitch’’ simulates host switches by a consumer.

Background

Symbiosis describes the interaction between to different biological organisms. In a biological system with a parasite (or consumer) and a host (or resource) we may encounter (stochastic) events where the parasite switches to a new host. This so called ‘Host switching’ was first simulated by (Citation: Araujo & al., 2015) Araujo, S., Braga, M., Brooks, D., Agosta, S., Hoberg, E., Hartenthal, F. & Boeger, W. (2015). Understanding Host-Switching by Ecological Fitting. PLOS ONE, 10(10). e0139225. https://doi.org/10.1371/journal.pone.0139225 to explore the host switch of a consumer under different settings. This simulation model was the basis for the Stockholm paradigm, a theoretical framework explaining the evolution of new biological associations.

The R package

Based on the simulation model by (Citation: Araujo & al., 2015) Araujo, S., Braga, M., Brooks, D., Agosta, S., Hoberg, E., Hartenthal, F. & Boeger, W. (2015). Understanding Host-Switching by Ecological Fitting. PLOS ONE, 10(10). e0139225. https://doi.org/10.1371/journal.pone.0139225 , we developed a R-package, called ‘HostSwitch’. This package contains all functionalities to simulate host switching by a consumer, and additionally:

• let you choose between different scenarios
• offers enhanced visualisation options
• provides you the possibility to test between two different hypotheses and much more…

A recent paper by (Citation: Trivellone & al., 2021) Trivellone, V., Araujo, S. & Panassiti, B. (2021). HostSwitch: An R Package to Simulate the Extent of Host-Switching by a Consumer. Under Review. provides an in-depth description of the ‘‘HostSwitch’’ package.

The R-package is available on CRAN: https://cran.r-project.org/web/packages/HostSwitch/index.html

To install the package from CRAN and load the package:

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install.packages("HostSwitch")
library(HostSwitch)

The R-package is also available on GitHub: https://github.com/berndpanassiti/HostSwitch

To install the package from GitHub repository:

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devtools::install_github(repo = "berndpanassiti/HostSwitch",build_vignettes = TRUE)

Bibliography