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'))

Datasets:

Acetogens - Acetogens dataframe
Bacteroides - Bacteroides dataframe
ButyrateProducers1 - ButyrateProducers1 dataframe
ButyrateProducers2 - ButyrateProducers2 dataframe
ButyrateProducers3 - ButyrateProducers3 dataframe
LactateProducers - LactateProducers dataframe
MFG - Microbial Functional Group (MFG) dataframes
Methanogens - Methanogens dataframe
NoButyFibreDeg - NoButyFibreDeg dataframe
NoButyStarchDeg - NoButyStarchDeg dataframe
PropionateProducers - PropionateProducers dataframe
Xaa - Xaa dataframe
Xh2 - Xh2 dataframe
Xsu - Xsu dataframe
microbeSysInfo - MicrobeSysInfo
microbeSysInfoHuman - MicrobeSysInfoHuman dataframe
microbeSysInfoRumen - MicrobeSysInfoRumen dataframe
resourceSysInfo - ResourceSysInfo
resourceSysInfoHuman - ResourceSysInfoHuman dataframe
resourceSysInfoRumen - ResourceSysInfoRumen dataframe
strainParams - StrainParams dataframe
systemInfoMicrobesPhyto - SystemInfoMicrobesPhyto dataframe
systemInfoMicrobesVirus - SystemInfoMicrobesVirus dataframe
systemInfoResourcesPhyto - SystemInfoResourcesPhyto dataframe
systemInfoResourcesVirus - SystemInfoResourcesVirus dataframe

On CRAN:

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

50 exports 0.71 score 51 dependencies 2 mentions 11 scripts 259 downloads

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

Target	Result	Date
Doc / Vignettes	OK	Aug 22 2024
R-4.5-win	NOTE	Aug 22 2024
R-4.5-linux	NOTE	Aug 22 2024
R-4.4-win	NOTE	Aug 22 2024
R-4.4-mac	NOTE	Aug 22 2024
R-4.3-win	NOTE	Aug 22 2024
R-4.3-mac	NOTE	Aug 22 2024

Exports:applyTraitTradeOffs assignStrainTraits checkSolution checkStoichiom combineGrowthLimFuncDefault combinePathsFuncDefault convertFlowsToMoles convertStatesToMoles createDF derivsDefault entryRateFuncDefault extraGrowthLimFuncDefault getAllResources getGroupName getKeyRes getNonBoostFrac getNumPaths getPHcorners getStrainParamsFromFile getStrainPHcorners getValues getVNPlotObject growthLimFuncDefault makeInflowFromSoln makeNetworkMatrices massBalanceFuncDefault meanTraitFunc microPopModel networkDFfromMPinput networkDFfromMPoutput pHcentreOfMass pHFuncDefault pHLimFuncDefault plotMicrobes plotResources plotTraitChange productionFuncDefault quickPlot quickPlot1 quickPlot2 rateFuncsDefault removalRateFuncDefault replaceListItems reshapeFlowMat runMicroPopExample subsetFunc sumConcOverStrains sumFlowOverStrains sumFlowsOverPaths uptakeFuncDefault

Dependencies:base64enc brio bslib cachem callr cli crayon desc deSolve diffobj digest evaluate fansi fastmap fontawesome fs glue highr htmltools htmlwidgets jquerylib jsonlite knitr lifecycle magrittr memoise mime pillar pkgbuild pkgconfig pkgload praise processx ps R6 rappdirs rematch2 rlang rmarkdown rprojroot sass testthat tibble tinytex utf8 vctrs visNetwork waldo withr xfun yaml

microPop Tutorial

Helen Kettle

Rendered frommicroPopTutorial.Rmdusingknitr::rmarkdownon Aug 22 2024.

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

Networks

Helen Kettle

Rendered fromplottingNetworks.Rmdusingknitr::rmarkdownon Aug 22 2024.

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

Citation

Readme and manuals

Help Manual

Help page	Topics
Microbial Population modelling	microPop-package microPop
Acetogens dataframe	Acetogens
Internal function to trade off one trait against another (used when assigning randomly generated strain traits)	applyTraitTradeOffs
Internal function to assign stochastic strain traits	assignStrainTraits
Bacteroides dataframe	Bacteroides
ButyrateProducers1 dataframe	ButyrateProducers1
ButyrateProducers2 dataframe	ButyrateProducers2
ButyrateProducers3 dataframe	ButyrateProducers3
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 values	checkSolution
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 adjusted	checkStoichiom
combines the growth limitation functions and max growth rates to get the growth rate of strain	combineGrowthLimFunc combineGrowthLimFuncDefault
Combine microbial growth on different pathways by one microbe	combinePathsFunc combinePathsFuncDefault
convertFlowsToMoles	convertFlowsToMoles
convertStatesToMoles	convertStatesToMoles
Create a dataframe from a CSV file	createDF
Differential Equations called by ODE solver	derivsDefault
entry Rate Function	entryRateFunc entryRateFuncDefault
Extra Growth Limitation Function	extraGrowthLimFunc extraGrowthLimFuncDefault
Makes vector of unique resource names	getAllResources
Convert strain name to its group name e.g. 'Bacteroides.1' becomes 'Bacteroides' updated (Dec 2019) so that MFG names can contain dots	getGroupName
Finds the name of the key resource for each path for each MFG	getKeyRes
obtains the none boosting fraction of growth for given MFG if there is a boosting resource	getNonBoostFrac
get the number of metabolic pathways for the given group	getNumPaths
get pH corners Function	getPHcorners
get strain parameter values from a csv file	getStrainParamsFromFile
get stochastically generated pH corners for each strain	getStrainPHcorners
get system quantity (e.g. startValue, inflowRate, washOut) for all state variables (convention is that microbes are before resources)	getValues
getVNPlotObject	getVNPlotObject
growth rate limitation function	growthLimFunc growthLimFuncDefault
LactateProducers dataframe	LactateProducers
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 compartment	makeInflowFromSoln
makeNetworkMatrices	makeNetworkMatrices
mass balance Function	massBalanceFunc massBalanceFuncDefault
calculate the mean trait at the end of the model run	meanTraitFunc
Methanogens dataframe	Methanogens
Microbial Functional Group (MFG) dataframes	MFG
microbeSysInfo	microbeSysInfo
microbeSysInfoHuman dataframe	microbeSysInfoHuman
microbeSysInfoRumen dataframe	microbeSysInfoRumen
Runs the microbial population model	microPopModel
networkDFfromMPinput	networkDFfromMPinput
networkDFfromMPoutput	networkDFfromMPoutput
NoButyFibreDeg dataframe	NoButyFibreDeg
NoButyStarchDeg dataframe	NoButyStarchDeg
Find the pH value which is the centre of mass of the pH limitation function (used for the pH trait)	pHcentreOfMass
pH Function	pHFunc pHFuncDefault
pH Limitation Function	pHLimFunc pHLimFuncDefault
Generic plotting of microbes over time	plotMicrobes
Generic plotting of resources over time	plotResources
plot changes in trait over time	plotTraitChange
Production Function	productionFunc productionFuncDefault
PropionateProducers dataframe	PropionateProducers
Generic plotting showing results of microPop	quickPlot
Generic plotting showing results of microPop	quickPlot1
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 Function	removalRateFunc removalRateFuncDefault
used to replace items in list.in in list.default needed for processing microPop input args like plotOptions	replaceListItems
reshapeFlowMat	reshapeFlowMat
resourceSysInfo	resourceSysInfo
resourceSysInfoHuman dataframe	resourceSysInfoHuman
resourceSysInfoRumen dataframe	resourceSysInfoRumen
runMicroPopExample	runMicroPopExample
strainParams dataframe	strainParams
sumConcOverStrains	sumConcOverStrains
sumFlowOverStrains	sumFlowOverStrains
sumFlowsOverPaths	sumFlowsOverPaths
systemInfoMicrobesPhyto dataframe	systemInfoMicrobesPhyto
systemInfoMicrobesVirus dataframe	systemInfoMicrobesVirus
systemInfoResourcesPhyto dataframe	systemInfoResourcesPhyto
systemInfoResourcesVirus dataframe	systemInfoResourcesVirus
Uptake Function	uptakeFunc uptakeFuncDefault
Xaa dataframe	Xaa
Xh2 dataframe	Xh2
Xsu dataframe	Xsu