CompareRuns.R

#!/usr/bin/env Rscript
# This script creates plots to compare different scenarios.
# Command line arguments:
#    folder: the relative folder of where to find output files.
# Will create plots in the "Plots/Comparsons" subfolder of folder

# Requires a set of input runs in a base folder
# Puts out a set of plots in the /Plots/Comparisons subfolder of the base folder
# Edit the Parameters section to customize

# code sent by d.laydon@imperial.ac.uk
# first refactoring pass wunderalbert@github.com




#### Parameters ####

# May later refactor to take inputs from seperate file or command line

# Where will the run data be located?
DefaultInFolder <- "."

# Where will the plots be outputted to?
PlotOutputDirRelativeToBaseFolder <- c("Plots", "Comparisons")

# Date range
Day_0 <- as.Date("2020-01-01")
NumDaysToPlot <- 186

# resolution of output files
PNG_res <- 300

# list the scenarios to compare (or set NULL to take all available)
Scenarios <- NULL

## Which comparison should we run?
## The name will determine title and filename.
#ComparisonName 	 <- "Number ICU beds"
## The severity variable is the variable to compare
#SeverityVariable <- "incCritical"

# consider the following R value:
R <- 2.2

# default console output width
defaultOutputWidth <- 172L


#### Set up ####

options(width = defaultOutputWidth)

if (!require(sp)){
  do_install <- readline("Need to install package `sp`. Continue (Y/n)? ")
  if (!(do_install == "" | tolower(do_install) == "y")) stop("Cannot continue script without dependencies.")
  install.packages("sp")
  library(sp)
}

# parse command line arguments
args = commandArgs(trailingOnly=TRUE)
InFolder <- if (length(args > 0)) args[1] else DefaultInFolder
CompPlotDir <- do.call(file.path, c(list(InFolder), as.list(PlotOutputDirRelativeToBaseFolder)))

# Create comparison plot directory
dir.create(CompPlotDir, showWarnings = FALSE, recursive = TRUE)
stopifnot(dir.exists(CompPlotDir))


#### Hardcoded values about the simulation API ####

# variables put out in the severity file
SeverityVariables <- c("incI", "incMild", "incILI", "incSARI", "incCritical", "incDeath",
		"cumMild", "cumILI", "cumSARI", "cumCritical", "cumDeath")
# severity output from c labelled as incidence of death, but it's actually cumulative deaths. correct here for now but will later fix in c code.
CORRECT_INC_DEATH <- TRUE #
# filenames to look for
Pattern 			    <- ".avNE.severity.xls"

# where do we find the info we want?
Suffix <- ".avNE.severity.xls"

#### Define processing functions ####

CalcPlotWindow <- function(EpiCurves, Threshold = 0, PlotFromTo = NULL) {
  if (!is.null(PlotFromTo) && length(PlotFromTo) != 2) stop("PlotFromTo must be character of length 2")
  # set default
  MinTime <- 1
  MaxTime <- dim(EpiCurves)[1]
  PlotWindow <- MinTime:MaxTime
  if (is.null(PlotFromTo)) {
    if (Threshold > 0) {
      MinTime <- 1
      MaxTime <- dim(EpiCurves)[1]
      for (timestep in 1:dim(EpiCurves)[1]) if (any(EpiCurves[timestep, ] > Threshold)) {	MinTime = timestep; break }
      for (timestep in dim(EpiCurves)[1]:1) if (any(EpiCurves[timestep, ] > Threshold)) {	MaxTime = timestep; break }
      if ((MaxTime - MinTime) <= 0)  ## reset in weird cases where exactly one time step is left. Breaks everything. Think of proper solution later.
      {
        MinTime <- 1
        MaxTime <- dim(EpiCurves)[1];
      }
      PlotWindow <- MinTime:MaxTime
    }
  } else {
    PlotWindow <- as.numeric(as.Date(PlotFromTo[1]) - Day_0):as.numeric(as.Date(PlotFromTo[2]) - Day_0)
  }

  return(PlotWindow)
}

#### Define Plotting Functions ####

CompareEpiCurves <- function(Filenames, SeverityVariable = "incI", ComparisonName = "AllRuns", Names,
                             Threshold = 0, PlotFromTo = NULL, YLAB = SeverityVariable, LWD = 4, LegendPosition = "topright"){
  if (!is.null(PlotFromTo) && length(PlotFromTo) != 2) stop("PlotFromTo must be of length 2")

  Index 	<- 1
  Flag    <- TRUE
  cat(paste0(SeverityVariable, "\n"))
  for (Index in 1:length(Filenames)) {
    FileName	<- Filenames[Index]
    cat(paste0(Index, "/", length(Filenames), ": Scenario ", sub(InFolder, "", FileName), "\n"))
    Results		<- read.delim(FileName, header = TRUE)
    if (Flag) {
      EpiCurves	<- matrix(nrow = dim(Results)[1], ncol = length(Filenames))
      Flag <- FALSE
    }
    EpiCurves[, Index]  <- Results[, SeverityVariable]
  }

  Cols 		    	<- bpy.colors(length(Filenames))
  Dates 			<- Day_0 + 0:(dim(Results)[1]-1)
  PlotWindow		<- CalcPlotWindow(EpiCurves, Threshold = Threshold, PlotFromTo = PlotFromTo)
  EpiCurves 		<- EpiCurves[PlotWindow,]
  Dates 		  	<- Dates[PlotWindow	]

  maxY <- max(EpiCurves)
  plot(Dates, EpiCurves[,1],
       xaxt = "n", xlab = "",
       main = ComparisonName,
       col = Cols[1], type = "l", lwd = LWD,
       ylab = YLAB,
       ylim = c(0, maxY))
  for (Index in 2:length(Filenames))
    lines(Dates, EpiCurves[,Index], col = Cols[Index]	, lwd = LWD)
  axis.Date(1, at = seq(min(Dates), max(Dates), by = "months"), format = "%b", las = 2)

  legend (LegendPosition, legend = Names, col = Cols, lty = 1, pch = NA, lwd = LWD, cex = 1)
}


#### Prettify Names for scenarios ####

GetVerboseScenarioName_Single 	= function(AbbreiviatedScenarioName) {
  VerboseScenario <- ""

  if (length(grep("NoInt"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "NoIntervention_"	)
  if (length(grep("MG"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "MassGatherings_"	)
  if (length(grep("PC"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "PlaceClosure_"		)
  if (length(grep("CI"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "CaseIsolation_"	)
  if (length(grep("HQ"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "HomeQuarantine_"	)
  if (length(grep("SDOL"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "SocialDistOlder_"	) else
    if (length(grep("SDO"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "SocialDistOlder_"	) else
      if (length(grep("SD"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "SocialDist_"		)
      if (length(grep("SC"	, AbbreiviatedScenarioName)) > 0) VerboseScenario = paste0(VerboseScenario, "SchoolClosure_"	)

      ### Chop off final "_"

      while (substr(VerboseScenario, nchar(VerboseScenario), nchar(VerboseScenario)) == "_")
        VerboseScenario = substr(VerboseScenario, 1, nchar(VerboseScenario) - 1)
      return(VerboseScenario)
}

GetVerboseScenarioName_Many 	= function(AbbreiviatedScenarioNames) {
  unlist(lapply(AbbreiviatedScenarioNames, GetVerboseScenarioName_Single))
}


#### ==== Get list of scenarios / filenames to compare ####

## this should give every model run in folder (but will be too much info on one plot).
FilesToCheck 	    	<- list.files(path = InFolder, pattern = Pattern)
PossibleScenarios 		<- sub(Pattern, "", FilesToCheck)

if (0 == length(Scenarios)) {
  # take all possible files
  Scenarios <- PossibleScenarios
  message("Using all scenarios that were found: ", length(PossibleScenarios))
} else {
  message("Found scenarios: ", length(intersect(PossibleScenarios, Scenarios)), " of ", length(Scenarios))
}

Filenames <- file.path(InFolder, paste0(Scenarios, Suffix))
if (!all(file.exists(Filenames))){
  stop("Aborted plot generation, because the following files were not found: ", Filenames[!file.exists(Filenames)])
}

GetVerboseVariableString 	= function(InfVariableString)
{
	InfVariableStringLong = sub("inc", "", InfVariableString)
	InfVariableStringLong = sub("cum", "", InfVariableStringLong)
	return(InfVariableStringLong)
}
GetIncPrevOrCumIncString 	= function(InfVariableString)
{
	if (length(grep("inc", InfVariableString)) > 0)
		IncPrevOrCumIncString = "Incidence" 				else
	if (length(grep("cum", InfVariableString)) > 0)
		IncPrevOrCumIncString = "Cumulative Incidence" 		else
		IncPrevOrCumIncString = "Prevalence"
	return(IncPrevOrCumIncString)
}

for (SeverityVariable in SeverityVariables)
{
	InfVariableStringLong 	<- GetVerboseVariableString	(SeverityVariable)
	IncPrevOrCumIncString 	<- GetIncPrevOrCumIncString	(SeverityVariable)
	ComparisonName 			<- paste(InfVariableStringLong, IncPrevOrCumIncString, "by model run")
	OutFileName <- file.path(CompPlotDir, paste0(InfVariableStringLong, "_", IncPrevOrCumIncString, ".png"))
	png(file = OutFileName, res = PNG_res, units = "in", width = 7, height = 7)
	CompareEpiCurves(Filenames, SeverityVariable, ComparisonName,
			Names = Scenarios, Threshold = 1, YLAB = SeverityVariable, LWD = 6)
	invisible(dev.off())
}