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iDynoR (version 1.0)

R Analysis package for iDynoMiCS Simulation Results

Description

iDynoMiCS is a computer program, developed by an international team of researchers, whose purpose is to model and simulate microbial communities in an individual-based way. It is described in detail in the paper "iDynoMiCS: next-generation individual-based modelling of biofilms" by Lardon et al, published in Environmental Microbiology in 2011. The simulation produces results in XML file format, describing the state of each species in each timestep (agent_State), a summary of the species statistics for a timepoint (agent_Sum), the state of each solute grid in each timestep (env_State) and a summary of the solutes for a timestep (env_Sum). This R package provides a means of reading this XML data into R such that the simulation response can be statistically analysed. iDynoMiCS is available from the website iDynoMiCS.org, where a full tutorial on using both the simulation and this R package is provided.

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Version

Install

install.packages('iDynoR')

Monthly Downloads

16

Version

1.0

License

CeCILL

Maintainer

Last Published

January 14th, 2014

Functions in iDynoR (1.0)

Technique 4: Reading Solute Grid State (env_State) and Summary (env_Sum) Files

Technique 4: Reading Solute Grid State (env_State) and Summary (env_Sum) Files
Technique 3: Example Methods for Processing Agent Information

Technique 3: Example Methods for Processing Agent Information
Technique 5: Example Methods for Processing Solute Information

Technique 5: Example Methods for Processing Solute Information
Technique 1: Read in Simulation Results

Technique 1: Read in Simulation Results
Technique 2: Reading Agent State and Agent Sum Files

Technique 2: Reading Agent State and Agent Sum Files