Nothing
#tests which compare outputs of demofiles
test_that('Test demo.human1.R',{
out=microPopModel(
microbeNames=c('Bacteroides','NoButyStarchDeg','Acetogens'),
times=seq(0,4,1/24),
resourceSysInfo=resourceSysInfoHuman,
microbeSysInfo=microbeSysInfoHuman,
plotOptions=list(yLabel='concentration (g/l)',xLabel='time (d)',
plotFig=FALSE,sumOverStrains=FALSE,saveFig=FALSE,
figType='eps',figName='Human1')
)
finalrow=out$solution[nrow(out$solution),]
expected.values=c(4.00, 3.44, 0.06, 0.03, 0.00, 0.00, 0.00, 3.20, 1.51, 2.40, 0.00, 10.01, 2.17, 10.34, 0.00, 0.00, NA)
expected.names=c('time','Bacteroides','NoButyStarchDeg','Acetogens','Protein','NSP','RS','Acetate','Propionate','Succinate','H2','CO2','other','H2O','Sugars','Formate','pH')
expect_equal(unname(round(finalrow,2)),expected.values)
expect_equal(names(finalrow),expected.names)
})
test_that('Test demo.human2.R',{
simulation.times=seq(0,4,1/24)
myRateFuncs=rateFuncsDefault
myRateFuncs$pHFunc=function(time,parms){
if (time<=max(simulation.times)/2){pH=5.5}else{pH=6.5}
return(pH)
}
out=microPopModel(
microbeNames=c('Bacteroides','NoButyStarchDeg','Acetogens'),
times=simulation.times,
resourceSysInfo=resourceSysInfoHuman,
microbeSysInfo=microbeSysInfoHuman,
rateFuncs=myRateFuncs,
plotOptions=list(yLabel='concentration (g/l)',xLabel='time (d)',
plotFig=FALSE,sumOverStrains=FALSE,saveFig=FALSE,
figType='eps',figName='Human2'),
pHLimit=TRUE
)
finalrow=out$solution[nrow(out$solution),]
expected.values=c( 4.00, 2.22, 1.24, 0.10, 0.00, 0.00 , 0.00, 4.86, 0.99 , 1.56 , 0.00, 10.01, 2.17, 10.01, 0.00, 0.00, 6.50)
expected.names=c('time','Bacteroides','NoButyStarchDeg','Acetogens','Protein','NSP','RS','Acetate','Propionate','Succinate','H2','CO2','other','H2O','Sugars','Formate','pH')
expect_equal(unname(round(finalrow,2)),expected.values)
expect_equal(names(finalrow),expected.names)
})
test_that('Test demo.human4.R',{
simulation.times=seq(0,4,1/24)
myRateFuncs=rateFuncsDefault
myRateFuncs$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,
numStrains=5,
rateFuncs=myRateFuncs,
plotOptions=list(yLabel='concentration (g/l)',xLabel='time (d)',
plotFig=FALSE,sumOverStrains=FALSE,
saveFig=FALSE,figType='eps',figName='Human4'),
pHLimit=TRUE,
strainOptions=list(
randomParams=c('halfSat','yield','maxGrowthRate','pHtrait'),
seed=1,
distribution='uniform',
percentTraitRange=5,
maxPHshift=0.05,
applyTradeOffs=TRUE,
tradeOffParams=c('halfSat','maxGrowthRate'),
paramsSpecified=TRUE,
paramDataName=strainParams)
)
finalrow=out$solution[nrow(out$solution),]
expected.names=c('time',paste0('Bacteroides.',seq(1,5)),paste0('NoButyStarchDeg.',seq(1,5)),paste0('Acetogens.',seq(1,5)),'Protein','NSP','RS','Acetate','Propionate','Succinate','H2','CO2','other','H2O','Sugars','Formate','pH')
expected.values=c(4.00, 0.11 , 0.09, 0.09 , 0.08, 1.95, 0.13 , 0.62, 0.06, 0.30 , 0.07, 0.03, 0.02 , 0.02, 0.02 , 0.02, 0.00, 0.00 , 0.00 , 4.80, 1.00 , 1.58, 0.00, 10.00, 2.15 ,10.02 , 0.00, 0.00, 6.50)
expect_equal(unname(round(finalrow,2)),expected.values)
expect_equal(names(finalrow),expected.names)
})
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