iDynoR: R Analysis package for iDynoMiCS Simulation Results

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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.

Author
Kieran Alden, Jan-Ulrich Kreft
Date of publication
2014-01-14 11:14:43
Maintainer
Kieran Alden <kieran.alden@gmail.com>
License
CeCILL
Version
1.0

View on CRAN

Man pages

Technique1-read_simulation_results
Technique 1: Read in Simulation Results
Technique2-reading_agent_files
Technique 2: Reading Agent State and Agent Sum Files
Technique3-example_agent_processing
Technique 3: Example Methods for Processing Agent Information
Technique4-reading_env_files
Technique 4: Reading Solute Grid State (env_State) and...
Technique5-example_env_processing
Technique 5: Example Methods for Processing Solute...

Files in this package

iDynoR
iDynoR/inst
iDynoR/inst/extdata
iDynoR/inst/extdata/multi_species_multi_substrate_nitrification_2D.zip
iDynoR/inst/extdata/Tutorial.pdf
iDynoR/NAMESPACE
iDynoR/R
iDynoR/R/env_soluteProductionRateOverTime.R
iDynoR/R/env_returnSimIteration.R
iDynoR/R/getSpeciesSpecificAbundance.R
iDynoR/R/env_returnSpecifiedSoluteData.R
iDynoR/R/agent_returnSimIteration.R
iDynoR/R/agent_returnSpeciesResultData.R
iDynoR/R/agent_getMeasureOverTime.R
iDynoR/R/agent_returnNumSpecies.R
iDynoR/R/plotTimeCourseAgents.R
iDynoR/R/getSpeciesAbundance.R
iDynoR/R/env_returnSimTime.R
iDynoR/R/simpsonIndex.R
iDynoR/R/agent_returnSpeciesColumnTotal.R
iDynoR/R/plotContour.R
iDynoR/R/env_returnMaxBiofilmThickness.R
iDynoR/R/agent_returnGridResolution.R
iDynoR/R/env_returnSoluteGridIVoxels.R
iDynoR/R/env_returnGlobalProductionRates.R
iDynoR/R/env_returnSoluteGridJVoxels.R
iDynoR/R/plotTimeCourseAbund.R
iDynoR/R/agent_returnKVoxels.R
iDynoR/R/env_returnSoluteGridKVoxels.R
iDynoR/R/env_returnMeanBiofilmThickness.R
iDynoR/R/env_returnSoluteGridRes.R
iDynoR/R/readSimResultFile.R
iDynoR/R/env_returnConcentrationAndRateChange.R
iDynoR/R/plotAgents.R
iDynoR/R/env_returnStdDevBiofilmThickness.R
iDynoR/R/agent_returnSimTime.R
iDynoR/R/agent_returnIVoxels.R
iDynoR/R/agent_returnJVoxels.R
iDynoR/MD5
iDynoR/DESCRIPTION
iDynoR/man
iDynoR/man/Technique4-reading_env_files.Rd
iDynoR/man/Technique1-read_simulation_results.Rd
iDynoR/man/Technique5-example_env_processing.Rd
iDynoR/man/Technique2-reading_agent_files.Rd
iDynoR/man/Technique3-example_agent_processing.Rd