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lifecycle Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

The microxanox R Package

Microxanox is an R package to simulate a three functional group system (cyanobacteria, phototrophic sulfur bacteria, and sulfate-reducing bacteria) with four chemical substrates (phosphorus, oxygen, reduced sulfur, and oxidized sulfur) using a set of ordinary differential equations. Simulations can be run individually or over a parameter range, to find stable states. The model features multiple species per functional group, where the number is only limited by computational constraints. The R package is constructed in such a way, that the results contain the input parameter used, so that a saved results can be loaded again and the simulation be repeated.

Installation

The easiest way (and the recommented way) to install microxanox is by using the R-Universe:

install.packages("microxanox", repos = c("https://uzh-peg.r-universe.dev", "https://cloud.r-project.org"))

The bleeding edge version can be installed from github:

You can also install the bleeding edge (sometimes non-stable) version fromthe github repository by using

remotes::install_github( "UZH-PEG/microxanox", ref = "dev", build_vignettes = TRUE, upgrade = FALSE)

For more details see the User Guide and Reproducing some Results of Bush et al 2017