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Marco De Lucia
RedModRphree
Commits
9eb709c1
Commit
9eb709c1
authored
May 06, 2018
by
Marco De Lucia
Browse files
Added Multiple infrastructure
parent
86e5b708
Changes
4
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NAMESPACE
View file @
9eb709c1
# Generated by roxygen2: do not edit by hand
export(AME)
export(Act2pH)
export(AddProp)
export(AdvectionPQC)
export(AllowSomeNegativeColumns)
export(AnalyticalLogK)
export(BalanceEquations)
export(BatchPreProc)
export(BatchPreProc_)
export(BestModelCluster)
export(CHT)
export(CheckBalance)
export(CheckColsNumValues)
export(Cols2Fact)
export(CompareTimesteps)
export(Deltas)
export(Distribute)
export(DistributeKin)
export(DistributeKinMatrix)
export(DistributeMatrix)
export(DownSampler)
export(ElementalBalanceMin)
export(ExtractPphases)
export(ExtractSamples)
export(ExtractSpecies)
export(ExtractTotals)
export(FastClust)
export(Filtering)
export(FindAllMinNames)
export(FindAllSpeciesNames)
export(FindAllTotNames)
export(FindLogK)
export(FindPhase)
export(FitSurrogates)
export(FitWithDice)
export(FormulaFromBal)
export(GetModelNames)
export(GetRanges)
export(InitPreProc)
export(Loadata)
export(MAD)
export(MASE)
export(Matplot)
export(MatplotSingle)
export(ModelSelector)
export(MultiRound)
export(NPSC)
export(NumericallyCompareTables)
export(OverrideValueRange)
export(ParseFormula)
export(PlotModsInSample)
export(RPhreeFile)
export(RPhreeWriteInp)
export(RReadOut)
export(RReadOutKin)
export(RSS)
export(RangeTableCreator)
export(ReactTranspBalanceEq)
export(ReactTranspBalanceKin)
export(RecomposeState)
export(ReduceState)
export(Refit)
export(Relcal)
export(RepSol)
export(Reshaping)
export(RunModelList)
export(RunPQC)
export(RunSurrogates)
export(SAD)
export(SDrift)
export(SelectActiveColumns)
export(SelectColsByPredix)
export(SelectMinActiveColumns)
export(SelectPreProc)
export(ShowTopProfiler)
export(SparseChangeCluster)
export(StoichiometricMatrix)
export(SubstractCommonTableCols)
export(SuppressSim)
export(Surrogate)
export(TByElem)
export(Tminus)
export(TrailSpaces)
export(Train)
export(TranspAsPert)
export(WriteModel)
export(WriteModelResiduals)
export(all_mda_mars_impvars)
export(allcoluniquevals)
export(cf)
export(cfa)
export(coltypes)
export(coluniquevals)
export(coluniratio)
export(colwise_RSS)
export(colwise_rescale)
export(createTuneGrids)
export(custom_scaler)
export(dt2v)
export(exc)
export(exc_type)
export(f2i)
export(hb)
export(mae)
export(mda_mars_importance)
export(mrm)
export(msg)
export(na.to.zero)
export(namewithin)
export(nan.to.zero)
export(outminus)
export(pH2Act)
export(paralap)
export(rescaling)
export(roundbycol)
export(rsi)
export(safe_get_cores)
export(seekcoltypeidx)
export(seekcoltypename)
export(sharedvalues)
export(sliding_join)
export(smartround)
export(splitMultiFix)
export(splitMultiKin)
export(start_up)
export(stopmsg)
export(striplast)
export(striplastx)
export(take_top_pct_cols)
export(to.zero)
export(uvc)
export(uvcm)
export(uvt)
export(write_evals)
import(caret)
import(data.table)
import(graphics)
...
...
R/Surr_Train.R
0 → 100644
View file @
9eb709c1
This diff is collapsed.
Click to expand it.
demo/00Index
View file @
9eb709c1
...
...
@@ -3,4 +3,4 @@ demo-kinetics 1D reactive transport with kinetic chemistry
demo-eq-generate-data Generate the training data set from 3 equilibrium simulations
demo-eq-surr-RF Generate the training data set, train randomForest surrogates and perform Reactive Transport simulations using them
demo-kin-surr Generate the training data set, train randomForest surrogates and perform Reactive Transport simulations using them
demo-TrainMultiple Uses the UNSTABLE infrastructure for comparing different trained surrogates
demo/demo-TrainMultiple.R
0 → 100644
View file @
9eb709c1
des_path
<-
system.file
(
"extdata"
,
"demo_equilibrium_design.csv"
,
package
=
"RedModRphree"
)
res_path
<-
system.file
(
"extdata"
,
"demo_equilibrium_result.csv"
,
package
=
"RedModRphree"
)
des
<-
data.table
::
fread
(
des_path
)
res
<-
data.table
::
fread
(
res_path
)
## We create a directory where to dump the created data structures
path_dumps
<-
"TrainedModels/"
## if it does not exist we create it
if
(
!
dir.exists
(
path_dumps
))
dir.create
(
path_dumps
,
showWarnings
=
FALSE
)
Train
(
c
(
"PolyMARS"
,
"glmStepAIC"
,
"MARS"
),
preprocessing_ind
=
c
(
17
),
input_data
=
des
,
output_data
=
res
,
seed
=
2305
,
train_para
=
TRUE
,
run_para
=
TRUE
,
preproc_para
=
FALSE
,
selection_criteria
=
"MAD"
,
write_full_residuals
=
FALSE
,
tuner
=
FALSE
,
use_cores
=
8
,
training_samples
=
0.95
,
write_filepath_prefix
=
path_dumps
)
a
<-
SelectedSurrogate
(
des
)
par
(
mfrow
=
c
(
4
,
2
))
for
(
i
in
colnames
(
des
))
{
plot
(
res
[,
..i
][[
1
]],
a
[,
i
],
"p"
,
pch
=
3
,
main
=
i
,
xlab
=
"Full physics"
,
ylab
=
"Surrogate"
)
abline
(
0
,
1
,
lty
=
"dashed"
,
col
=
"grey"
)
}
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