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DirectoryFunctions.R
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DirectoryFunctions.R
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MAX_ONSET_DAY = 549
##### ===== ..... ##### ===== ..... ##### ===== ..... ##### ===== ..... ##### ===== ..... ##### ===== ..... ##### ===== ..... ##### ===== ..... ##### ===== ..... ##### ===== .....
##### after everything put in a data frame
PrintToDesiredPrecision = function(Vec, ndigits = 2) ### e.g. if Vec = 0.2 and ndigits = 3, will print "0.200"
{
sprintf(paste0("%.", ndigits, "f"), Vec)
}
GetMinDate = function(MR_index)
{
return(min(ModelRuns[MR_index,]$Pruning_Range[[1]]))
}
GetMaxDate = function(MR_index)
{
return(max(ModelRuns[MR_index,]$Pruning_Range[[1]]))
}
ChooseOutputString = function(MR_index, StringPrefix = "", Folder = FALSE, n_digits = 2)
{
MR = ModelRuns[MR_index, ]
if (!(MR$VacCampStrategy %in% c("REACTIVE", "PROACTIVE")))
stop("ChooseOutputString error: MR$VacCampStrategy not reactive")
OutputString = StringPrefix
if (MR$Efficacy_Start == 0) OutputString = paste0(OutputString, "_NoHumans") else
OutputString = paste0(OutputString, "_Eff_", PrintToDesiredPrecision(MR$Efficacy_Start, ndigits = n_digits))
if (MR$Efficacy_CamelControls > 0)
OutputString = paste0(OutputString, "_CamelsControlEff_", PrintToDesiredPrecision(MR$Efficacy_CamelControls, ndigits = n_digits))
if (MR$Efficacy_Start != 0) ## i.e. if vaccinating humans
{
if (MR$VacCampStrategy == "PROACTIVE")
{
OutputString = paste0(OutputString, "_ProAct")
if (!MR$ExpWaning) OutputString = paste0(OutputString, "_Hill_", PrintToDesiredPrecision(MR$HillPower, 0))
OutputString = paste0(OutputString, "_Dur_", PrintToDesiredPrecision(MR$VaccineDuration , ndigits = n_digits))
OutputString = paste0(OutputString, "_Lag_", PrintToDesiredPrecision(MR$TimeSinceVaccination, ndigits = n_digits))
} else if (MR$VacCampStrategy == "REACTIVE")
{
if (MR$WaningInReactive & MR$VaccineDuration != 0)
{
OutputString = paste0(OutputString, "_RW_Dur_", PrintToDesiredPrecision(MR$VaccineDuration, 2))
if (!MR$ExpWaning) OutputString = paste0(OutputString, "_Hill_", PrintToDesiredPrecision(MR$HillPower, 0))
}
if (MR$ReactLevel != "HOSPITAL")
{
if (MR$ReactLevel == "REGIONAL") OutputString = paste0(OutputString, "_reg") else
if (MR$ReactLevel == "NATIONAL") OutputString = paste0(OutputString, "_nat")
}
if (MR$DoTriggers)
OutputString = paste0(OutputString,
"_Tr", PrintToDesiredPrecision(MR$TrigThreshold, 0),
"_", PrintToDesiredPrecision(MR$TrigTimeframe, 0))
}
if (MR$Coverage != 1.0 ) OutputString = paste0(OutputString, "_Cov" , PrintToDesiredPrecision(MR$Coverage, ndigits = n_digits))
if (MR$ImplementationDelay != 0 ) OutputString = paste0(OutputString, "_ImpDelay" , MR$ImplementationDelay)
if (MR$ImmunityDelay != 0 ) OutputString = paste0(OutputString, "_VacDelay" , MR$ImmunityDelay )
if (MR$VaccinateAllHumans ) OutputString = paste0(OutputString, "_Blanket" ) else
if (MR$Vaccinate_HCW ) OutputString = paste0(OutputString, "_vHCW" )
}
MinDay_Pruning = min(MR$Pruning_Range[[1]])
MaxDay_Pruning = max(MR$Pruning_Range[[1]])
if (MinDay_Pruning > 0 | MaxDay_Pruning < (MAX_ONSET_DAY - 1))
{
OutputString = paste0(OutputString, "_s", MinDay_Pruning) # start date
OutputString = paste0(OutputString, "_f", MaxDay_Pruning) # end date
}
if (Folder) while (substr(OutputString, 1, 1) == "_") OutputString = sub("_", "", OutputString) ### i.e. don't want underscore as first character if doing the name of a folder, so remove it.
return(OutputString)
}
DefineModelRuns = function(
RemoveDuplicates = TRUE ,
IncludeCompletedRunsOnly = TRUE ,
VacCampStrategies = "REACTIVE" ,
WaningInReactiveAndNot = 0 ,
ReactLevels = c("HOSPITAL") , #c("HOSPITAL", "REGIONAL", "NATIONAL")
Efficacies_Start = seq(0.20, 1, by = 0.20) ,
VaccineDurations = 20000.0 , # In years. VaccineDuration == 0 => no waning.
TimesSinceVaccination = 0 , # In years.
ExpWaningAndNot = 1 ,
HillPowers = 4 ,
Pruning_Ranges = list( c(0, MAX_ONSET_DAY - 1)),
# camels
Efficacies_CamelControls = 0.0 ,
## Triggers
DoTriggersAndNot = 0 ,
TrigThresholds = 1 ,
TrigTimeframes = 1 ,
Coverages = 1 ,
ImplementationDelays = 0 ,
ImmunityDelays = 0 ,
VaccinateAllHumans_OrNot = 0 ,
Vaccinate_HCW_OrNot = 1 )
{
### Make all possible versions of ModelRuns - note that expand.grid will not account for duplicates or for model runs that have not actually been run.
ModelRuns = expand.grid (
VacCampStrategy = VacCampStrategies ,
ReactLevel = ReactLevels ,
WaningInReactive = WaningInReactiveAndNot,
Efficacy_Start = Efficacies_Start ,
VaccineDuration = VaccineDurations ,
TimeSinceVaccination = TimesSinceVaccination ,
ExpWaning = ExpWaningAndNot ,
HillPower = HillPowers ,
Pruning_Range = Pruning_Ranges ,
# camels
Efficacy_CamelControls = Efficacies_CamelControls,
## Triggers
DoTriggers = DoTriggersAndNot ,
TrigThreshold = TrigThresholds ,
TrigTimeframe = TrigTimeframes ,
Coverage = Coverages ,
ImplementationDelay = ImplementationDelays ,
ImmunityDelay = ImmunityDelays ,
VaccinateAllHumans = VaccinateAllHumans_OrNot,
Vaccinate_HCW = Vaccinate_HCW_OrNot
)
cat("expanded grid, ")
# remove scenarios where neither humans nor camels included
ModelRuns = ModelRuns[!(ModelRuns$Efficacy_Start == 0 & ModelRuns$Efficacy_CamelControls == 0), ]
# remove undefined combinations (ReactLevel irrelevant for PROACTIVE)
ModelRuns = ModelRuns[!(ModelRuns$VacCampStrategy == "PROACTIVE" & ModelRuns$ReactLevel != "HOSPITAL"), ]
# remove undefined combinations (WaningInReactive irrelevant for PROACTIVE)
ModelRuns = ModelRuns[!(ModelRuns$VacCampStrategy == "PROACTIVE" & ModelRuns$WaningInReactive != 0), ]
# remove undefined combinations (ImplementationDelay irrelevant for PROACTIVE)
ModelRuns = ModelRuns[!(ModelRuns$VacCampStrategy == "PROACTIVE" & ModelRuns$ImplementationDelay != 0), ]
# remove undefined combinations (ImmunityDelay == 14 for REACTIVE)
ModelRuns = ModelRuns[!(ModelRuns$VacCampStrategy == "REACTIVE" & ModelRuns$ImmunityDelay == 0), ]
cat("undefined scenarios removed, ")
if (dim(ModelRuns)[1] == 0) stop("ModelRuns empty")
ModelRuns <<- ModelRuns
#### Create OutputStrings for all possible model runs...
cat("Creating output strings, ")
OutputFolderNames = mapply(ChooseOutputString , MR_index = 1:dim(ModelRuns)[1], MoreArgs = list(Folder = TRUE))
cat("choosing min days, ")
MinDay_Pruning = mapply(GetMinDate , MR_index = 1:dim(ModelRuns)[1])
cat("choosing max days, ")
MaxDay_Pruning = mapply(GetMaxDate , MR_index = 1:dim(ModelRuns)[1])
cat("loop finished, ")
#### .... bind them to data.frame
ModelRuns = cbind(ModelRuns, MinDay_Pruning, MaxDay_Pruning, OutputFolderNames)
#### Remove duplicates
if (RemoveDuplicates) ModelRuns = ModelRuns[!duplicated(ModelRuns$OutputFolderNames), ]
#### Remove incomplete runs, if you want (e.g. useful to not compare runs you haven't done)
# Check if either full chains or summary chains available
RunsCompleted = file.exists(file.path(CppOutputDirectory, paste0("CF_Chains_" , ModelRuns$OutputFolderNames, ".txt"))) |
file.exists(file.path(CppOutputDirectory, paste0("CF_ChainsSumm_" , ModelRuns$OutputFolderNames, ".txt")))
if (IncludeCompletedRunsOnly) ModelRuns = ModelRuns[RunsCompleted, ] ### _underscore after ParameterChainOutput depends on Folder argument in ChooseOutputString function called above.
cat("done.")
return(ModelRuns)
}