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microPop  

Process-Based Modelling of Microbial Populations
View on CRAN: Click here


Download and install microPop package within the R console
Install from CRAN:
install.packages("microPop")

Install from Github:
library("remotes")
install_github("cran/microPop")

Install by package version:
library("remotes")
install_version("microPop", "1.6")



Attach the package and use:
library("microPop")
Maintained by
Helen Kettle
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-03-29
Latest Update: 2022-02-03
Description:
Modelling interacting microbial populations - example applications include human gut microbiota, rumen microbiota and phytoplankton. Solves a system of ordinary differential equations to simulate microbial growth and resource uptake over time. This version contains network visualisation functions.
How to cite:
Helen Kettle (2017). microPop: Process-Based Modelling of Microbial Populations. R package version 1.6, https://cran.r-project.org/web/packages/microPop
Previous versions and publish date:
1.0 (2017-03-29 15:06), 1.1 (2017-04-07 19:01), 1.2 (2017-04-21 20:21), 1.3 (2017-08-04 11:45), 1.4.1 (2019-04-26 16:50), 1.4 (2018-05-22 16:32), 1.5 (2019-09-11 11:50)
Other packages that cited microPop R package
View microPop citation profile
Other R packages that microPop depends, imports, suggests or enhances
Functions, R codes and Examples using the microPop R package
Some associated functions: Acetogens . Bacteroides . ButyrateProducers1 . ButyrateProducers2 . ButyrateProducers3 . LactateProducers . MFG . Methanogens . NoButyFibreDeg . NoButyStarchDeg . PropionateProducers . Xaa . Xh2 . Xsu . applyTraitTradeOffs . assignNAsToMFGs . assignStrainTraits . checkResInfo . checkSolution . checkStoichiom . combineGrowthLimFuncDefault . combinePathsFuncDefault . convertFlowsToMoles . convertStatesToMoles . createDF . derivsDefault . entryRateFuncDefault . extraGrowthLimFuncDefault . getAllResources . getGroupName . getKeyRes . getNonBoostFrac . getNumPaths . getPHcorners . getStrainPHcorners . getStrainParamsFromFile . getVNPlotObject . getValues . growthLimFuncDefault . makeInflowFromSoln . makeNetworkMatrices . makeParamMatrixG . makeParamMatrixS . massBalanceFuncDefault . meanTraitFunc . microPop-package . microPopModel . microbeSysInfo . microbeSysInfoHuman . microbeSysInfoRumen . networkDFfromMPinput . networkDFfromMPoutput . pHFuncDefault . pHLimFuncDefault . pHcentreOfMass . plotMicrobes . plotResources . plotTraitChange . productionFuncDefault . quickPlot . quickPlot1 . quickPlot2 . rateFuncsDefault . removalRateFuncDefault . replaceListItems . reshapeFlowMat . resourceSysInfo . resourceSysInfoHuman . resourceSysInfoRumen . runMicroPopExample . strainParams . subsetFunc . sumConcOverStrains . sumFlowOverStrains . sumFlowsOverPaths . systemInfoMicrobesPhyto . systemInfoMicrobesVirus . systemInfoResourcesPhyto . systemInfoResourcesVirus . uptakeFuncDefault . waterUptakeRatio . 
Some associated R codes: applyTraitTradeOffs.R . assignNAsToMFGs.R . assignStrainTraits.R . checkResInfo.R . checkSolution.R . checkStoichiom.R . combineGrowthLimFuncDefault.R . combinePathsFuncDefault.R . convertFlowsToMoles.R . convertStatesToMoles.R . createDF.R . data.R . derivsDefault.R . entryRateFuncDefault.R . extraGrowthLimFuncDefault.R . getAllResources.R . getGroupName.R . getKeyRes.R . getMolarStoichiom.R . getMolarYields.R . getNonBoostFrac.R . getNumPaths.R . getPHcorners.R . getStrainPHcorners.R . getStrainParamsFromFile.R . getVNPlotObject.R . getValues.R . growthLimFuncDefault.R . makeInflowFromSoln.R . makeNetworkMatrices.R . makeParamMatrixG.R . makeParamMatrixS.R . massBalanceFuncDefault.R . meanTraitFunc.R . microPop-package.R . microPopModel.R . networkDFfromMPinput.R . networkDFfromMPoutput.R . pHFuncDefault.R . pHLimFuncDefault.R . pHcentreOfMass.R . plotMicrobes.R . plotResources.R . plotTraitChange.R . productionFuncDefault.R . quickPlot.R . quickPlot1.R . quickPlot2.R . rateFuncsDefault.R . removalRateFuncDefault.R . replaceListItems.R . reshapeFlowMat.R . runMicroPopExample.R . subsetFunc.R . sumConcOverStrains.R . sumFlowOverStrains.R . sumFlowsOverPaths.R . uptakeFuncDefault.R . waterUptakeRatio.R .  Full microPop package functions and examples
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