Package: microPop 1.6

microPop: Process-Based Modelling of Microbial Populations

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.

Authors:Helen Kettle [aut, cre]

microPop_1.6.tar.gz
microPop_1.6.zip(r-4.5)microPop_1.6.zip(r-4.4)microPop_1.6.zip(r-4.3)
microPop_1.6.tgz(r-4.4-any)microPop_1.6.tgz(r-4.3-any)
microPop_1.6.tar.gz(r-4.5-noble)microPop_1.6.tar.gz(r-4.4-noble)
microPop_1.6.tgz(r-4.4-emscripten)microPop_1.6.tgz(r-4.3-emscripten)
microPop.pdf |microPop.html✨
microPop/json (API)

# Install 'microPop' in R:
install.packages('microPop', repos = c('https://helenkettle.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.64 score 11 scripts 234 downloads 2 mentions 50 exports 44 dependencies

Last updated 3 years agofrom:ad3fb02ac9. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winNOTENov 20 2024
R-4.5-linuxNOTENov 20 2024
R-4.4-winNOTENov 20 2024
R-4.4-macNOTENov 20 2024
R-4.3-winNOTENov 20 2024
R-4.3-macNOTENov 20 2024

Exports:applyTraitTradeOffsassignStrainTraitscheckSolutioncheckStoichiomcombineGrowthLimFuncDefaultcombinePathsFuncDefaultconvertFlowsToMolesconvertStatesToMolescreateDFderivsDefaultentryRateFuncDefaultextraGrowthLimFuncDefaultgetAllResourcesgetGroupNamegetKeyResgetNonBoostFracgetNumPathsgetPHcornersgetStrainParamsFromFilegetStrainPHcornersgetValuesgetVNPlotObjectgrowthLimFuncDefaultmakeInflowFromSolnmakeNetworkMatricesmassBalanceFuncDefaultmeanTraitFuncmicroPopModelnetworkDFfromMPinputnetworkDFfromMPoutputpHcentreOfMasspHFuncDefaultpHLimFuncDefaultplotMicrobesplotResourcesplotTraitChangeproductionFuncDefaultquickPlotquickPlot1quickPlot2rateFuncsDefaultremovalRateFuncDefaultreplaceListItemsreshapeFlowMatrunMicroPopExamplesubsetFuncsumConcOverStrainssumFlowOverStrainssumFlowsOverPathsuptakeFuncDefault

Dependencies:base64encbriobslibcachemcallrclicrayondescdeSolvediffobjdigestevaluatefastmapfontawesomefsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimepkgbuildpkgloadpraiseprocessxpsR6rappdirsrlangrmarkdownrprojrootsasstestthattinytexvisNetworkwaldowithrxfunyaml

microPop Tutorial

Helen Kettle

Rendered frommicroPopTutorial.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2022-02-03
Started: 2022-02-03

Networks

Helen Kettle

Rendered fromplottingNetworks.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2022-02-03
Started: 2022-02-03

Readme and manuals

Help Manual

Help pageTopics
Microbial Population modellingmicroPop-package microPop
Acetogens dataframeAcetogens
Internal function to trade off one trait against another (used when assigning randomly generated strain traits)applyTraitTradeOffs
Internal function to assign stochastic strain traitsassignStrainTraits
Bacteroides dataframeBacteroides
ButyrateProducers1 dataframeButyrateProducers1
ButyrateProducers2 dataframeButyrateProducers2
ButyrateProducers3 dataframeButyrateProducers3
Checks whether the all the resources needed are included in the system information file (e.g. start value, washout rate etc)checkResInfo
Checks whether the solution generated by the ODE solver contains negative valuescheckSolution
Checks whether the stoichiometries in each MFG conserve mass within a specified tolerance If they do not then if reBalanceStoichiom=TRUE the stoichiometry will be adjustedcheckStoichiom
combines the growth limitation functions and max growth rates to get the growth rate of straincombineGrowthLimFunc combineGrowthLimFuncDefault
Combine microbial growth on different pathways by one microbecombinePathsFunc combinePathsFuncDefault
convertFlowsToMolesconvertFlowsToMoles
convertStatesToMolesconvertStatesToMoles
Create a dataframe from a CSV filecreateDF
Differential Equations called by ODE solverderivsDefault
entry Rate FunctionentryRateFunc entryRateFuncDefault
Extra Growth Limitation FunctionextraGrowthLimFunc extraGrowthLimFuncDefault
Makes vector of unique resource namesgetAllResources
Convert strain name to its group name e.g. 'Bacteroides.1' becomes 'Bacteroides' updated (Dec 2019) so that MFG names can contain dotsgetGroupName
Finds the name of the key resource for each path for each MFGgetKeyRes
obtains the none boosting fraction of growth for given MFG if there is a boosting resourcegetNonBoostFrac
get the number of metabolic pathways for the given groupgetNumPaths
get pH corners FunctiongetPHcorners
get strain parameter values from a csv filegetStrainParamsFromFile
get stochastically generated pH corners for each straingetStrainPHcorners
get system quantity (e.g. startValue, inflowRate, washOut) for all state variables (convention is that microbes are before resources)getValues
getVNPlotObjectgetVNPlotObject
growth rate limitation functiongrowthLimFunc growthLimFuncDefault
LactateProducers dataframeLactateProducers
Used for running microPop with multiple compartments Takes the solution (state of system) from the previous compartment (out$solution) and then finds the washout rate of each state variable using removalRateFunc to find the inflow rate to the next downstream compartmentmakeInflowFromSoln
makeNetworkMatricesmakeNetworkMatrices
mass balance FunctionmassBalanceFunc massBalanceFuncDefault
calculate the mean trait at the end of the model runmeanTraitFunc
Methanogens dataframeMethanogens
Microbial Functional Group (MFG) dataframesMFG
microbeSysInfomicrobeSysInfo
microbeSysInfoHuman dataframemicrobeSysInfoHuman
microbeSysInfoRumen dataframemicrobeSysInfoRumen
Runs the microbial population modelmicroPopModel
networkDFfromMPinputnetworkDFfromMPinput
networkDFfromMPoutputnetworkDFfromMPoutput
NoButyFibreDeg dataframeNoButyFibreDeg
NoButyStarchDeg dataframeNoButyStarchDeg
Find the pH value which is the centre of mass of the pH limitation function (used for the pH trait)pHcentreOfMass
pH FunctionpHFunc pHFuncDefault
pH Limitation FunctionpHLimFunc pHLimFuncDefault
Generic plotting of microbes over timeplotMicrobes
Generic plotting of resources over timeplotResources
plot changes in trait over timeplotTraitChange
Production FunctionproductionFunc productionFuncDefault
PropionateProducers dataframePropionateProducers
Generic plotting showing results of microPopquickPlot
Generic plotting showing results of microPopquickPlot1
Generic plotting showing results of microPop Now shows resources and microbes on one plot.quickPlot2
List of functions that are used by the ODE solver these functions can be changed by the user but all must be listed.rateFuncs rateFuncsDefault
Removal Rate FunctionremovalRateFunc removalRateFuncDefault
used to replace items in list.in in list.default needed for processing microPop input args like plotOptionsreplaceListItems
reshapeFlowMatreshapeFlowMat
resourceSysInforesourceSysInfo
resourceSysInfoHuman dataframeresourceSysInfoHuman
resourceSysInfoRumen dataframeresourceSysInfoRumen
runMicroPopExamplerunMicroPopExample
strainParams dataframestrainParams
sumConcOverStrainssumConcOverStrains
sumFlowOverStrainssumFlowOverStrains
sumFlowsOverPathssumFlowsOverPaths
systemInfoMicrobesPhyto dataframesystemInfoMicrobesPhyto
systemInfoMicrobesVirus dataframesystemInfoMicrobesVirus
systemInfoResourcesPhyto dataframesystemInfoResourcesPhyto
systemInfoResourcesVirus dataframesystemInfoResourcesVirus
Uptake FunctionuptakeFunc uptakeFuncDefault
Xaa dataframeXaa
Xh2 dataframeXh2
Xsu dataframeXsu