Package: microPop
Type: Package
Title: Process-Based Modelling of Microbial Populations
Version: 1.6
Date: 2022-02-02
Authors@R: person("Helen", "Kettle", email = "Helen.Kettle@bioss.ac.uk",role = c("aut", "cre"))
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.
License: GPL-3 | file LICENSE
URL:
        https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12873
Depends: deSolve, visNetwork
Imports: testthat, methods
Suggests: rmarkdown, R.rsp, knitr, webshot
VignetteBuilder: knitr
RoxygenNote: 7.1.2
LazyData: true
Collate: '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' 'removalRateFuncDefault.R' 'uptakeFuncDefault.R'
        'rateFuncsDefault.R' 'replaceListItems.R' 'reshapeFlowMat.R'
        'runMicroPopExample.R' 'subsetFunc.R' 'sumConcOverStrains.R'
        'sumFlowOverStrains.R' 'sumFlowsOverPaths.R'
        'waterUptakeRatio.R'
NeedsCompilation: no
Packaged: 2022-02-03 11:19:51 UTC; helen
Author: Helen Kettle [aut, cre]
Maintainer: Helen Kettle <Helen.Kettle@bioss.ac.uk>
Repository: CRAN
Date/Publication: 2022-02-03 11:50:02 UTC
Built: R 4.6.0; ; 2026-04-29 05:06:27 UTC; unix
