iDynoR: R Analysis package for iDynoMiCS Simulation Results

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, where a full tutorial on using both the simulation and this R package is provided.

Install the latest version of this package by entering the following in R:
AuthorKieran Alden, Jan-Ulrich Kreft
Date of publication2014-01-14 11:14:43
MaintainerKieran Alden <>

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agent_getMeasureOverTime Man page
agent_returnGridResolution Man page
agent_returnIVoxels Man page
agent_returnJVoxels Man page
agent_returnKVoxels Man page
agent_returnNumSpecies Man page
agent_returnSimIteration Man page
agent_returnSimTime Man page
agent_returnSpeciesColumnTotal Man page
agent_returnSpeciesResultData Man page
env_returnConcentrationAndRateChange Man page
env_returnGlobalProductionRates Man page
env_returnMaxBiofilmThickness Man page
env_returnMeanBiofilmThickness Man page
env_returnSimIteration Man page
env_returnSimTime Man page
env_returnSoluteGridIVoxels Man page
env_returnSoluteGridJVoxels Man page
env_returnSoluteGridKVoxels Man page
env_returnSoluteGridRes Man page
env_returnSpecifiedSoluteData Man page
env_returnStdDevBiofilmThickness Man page
env_soluteProductionRateOverTime Man page
getSpeciesAbundance Man page
getSpeciesSpecificAbundance Man page
plotAgents Man page
plotContour Man page
plotTimeCourseAbund Man page
plotTimeCourseAgents Man page
readSimResultFile Man page
simpsonIndex Man page

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