#human colon 2
#Note not all NSP is useable therefore must adjust input values so just put in useable amount
#Look at 3 MFGs: 'Bacteroides','NoButyStarchDeg','Acetogens'
#Dependence of microbial growth on pH is included and pH changes from 5.5 to 6.5 halfway through the simulation time
simulation.times=seq(0,4,1/24)
myRateFuncs=rateFuncsDefault
myRateFuncs$pHFunc=function(time,parms){
if (time<=max(simulation.times)/2){pH=5.5}else{pH=6.5}
return(pH)
}
out=microPopModel(
microbeNames=c('Bacteroides','NoButyStarchDeg','Acetogens'),
times=simulation.times,
resourceSysInfo=resourceSysInfoHuman,
microbeSysInfo=microbeSysInfoHuman,
rateFuncs=myRateFuncs,
plotOptions=list(yLabel='concentration (g/l)',xLabel='time (d)',
plotFig=TRUE,sumOverStrains=FALSE,saveFig=FALSE,
figType='eps',figName='Human2'),
pHLimit=TRUE
)
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