/// <summary>
/// Return the base R script for running morris.
/// </summary>
private string GetMorrisRScript()
{
string paramNames = StringUtilities.Build(Parameters.Select(p => p.Name), ",", "\"", "\"");
string lowerBounds = StringUtilities.Build(Parameters.Select(p => p.LowerBound), ",");
string upperBounds = StringUtilities.Build(Parameters.Select(p => p.UpperBound), ",");
string script = string.Format
("library('sensitivity')" + Environment.NewLine +
"params <- c({0})" + Environment.NewLine +
"apsimMorris<-morris(model=NULL" + Environment.NewLine +
" ,params #string vector of parameter names" + Environment.NewLine +
" ,{1} #no of paths within the total parameter space" + Environment.NewLine +
" ,design=list(type=\"oat\",levels={2},grid.jump={3})" + Environment.NewLine +
" ,binf=c({4}) #min for each parameter" + Environment.NewLine +
" ,bsup=c({5}) #max for each parameter" + Environment.NewLine +
" ,scale=T" + Environment.NewLine +
" )" + Environment.NewLine,
paramNames, NumPaths, NumIntervals + 1, Jump, lowerBounds, upperBounds);
return(script);
}
/// <summary>
/// Get a list of parameter values that we are to run. Call R to do this.
/// </summary>
private void RunRPostSimulation(DataTable predictedValues, out DataTable eeDataRaw, out DataTable statsDataRaw)
{
string morrisParametersFileName = GetTempFileName("parameters", ".csv");
string apsimVariableFileName = GetTempFileName("apsimvariable", ".csv");
string rFileName = GetTempFileName("morrisscript", ".r");
string eeFileName = GetTempFileName("ee", ".csv");
string statsFileName = GetTempFileName("stats", ".csv");
// write predicted values file
using (StreamWriter writer = new StreamWriter(apsimVariableFileName))
DataTableUtilities.DataTableToText(predictedValues, 0, ",", true, writer);
// Write parameters
using (StreamWriter writer = new StreamWriter(morrisParametersFileName))
DataTableUtilities.DataTableToText(ParameterValues, 0, ",", true, writer);
string paramNames = StringUtilities.Build(Parameters.Select(p => p.Name), ",", "\"", "\"");
string lowerBounds = StringUtilities.Build(Parameters.Select(p => p.LowerBound), ",");
string upperBounds = StringUtilities.Build(Parameters.Select(p => p.UpperBound), ",");
string script = GetMorrisRScript();
script += string.Format
("apsimMorris$X <- read.csv(\"{0}\")" + Environment.NewLine +
"values = read.csv(\"{1}\", check.names = F)" + Environment.NewLine +
"allEE <- data.frame()" + Environment.NewLine +
"allStats <- data.frame()" + Environment.NewLine +
"for (columnName in colnames(values))" + Environment.NewLine +
"{{" + Environment.NewLine +
" apsimMorris$y <- values[[columnName]]" + Environment.NewLine +
" tell(apsimMorris)" + Environment.NewLine +
" ee <- data.frame(apsimMorris$ee)" + Environment.NewLine +
" ee$variable <- columnName" + Environment.NewLine +
" ee$path <- c(1:{2})" + Environment.NewLine +
" allEE <- rbind(allEE, ee)" + Environment.NewLine +
" mu <- apply(apsimMorris$ee, 2, mean)" + Environment.NewLine +
" mustar <- apply(apsimMorris$ee, 2, function(x) mean(abs(x)))" + Environment.NewLine +
" sigma <- apply(apsimMorris$ee, 2, sd)" + Environment.NewLine +
" stats <- data.frame(mu, mustar, sigma)" + Environment.NewLine +
" stats$param <- params" + Environment.NewLine +
" stats$variable <- columnName" + Environment.NewLine +
" allStats <- rbind(allStats, stats)" + Environment.NewLine +
"}}" + Environment.NewLine +
"write.csv(allEE,\"{3}\", row.names=FALSE)" + Environment.NewLine +
"write.csv(allStats, \"{4}\", row.names=FALSE)" + Environment.NewLine,
morrisParametersFileName.Replace("\\", "/"),
apsimVariableFileName.Replace("\\", "/"),
NumPaths,
eeFileName.Replace("\\", "/"),
statsFileName.Replace("\\", "/"));
File.WriteAllText(rFileName, script);
// Run R
R r = new R();
r.RunToTable(rFileName);
eeDataRaw = ApsimTextFile.ToTable(eeFileName);
statsDataRaw = ApsimTextFile.ToTable(statsFileName);
}
/// <summary>Main run method for performing our calculations and storing data.</summary>
public void Run()
{
if (dataStore?.Writer != null && !dataStore.Writer.TablesModified.Contains("Report"))
{
return;
}
DataTable predictedData = dataStore.Reader.GetData("Report", filter: "SimulationName LIKE '" + Name + "%'", orderBy: "SimulationID");
if (predictedData != null)
{
IndexedDataTable variableValues = new IndexedDataTable(null);
// Determine how many years we have per simulation
DataView view = new DataView(predictedData);
view.RowFilter = "SimulationName='" + Name + "Simulation1'";
var Years = DataTableUtilities.GetColumnAsIntegers(view, "Clock.Today.Year");
// Create a results table.
IndexedDataTable results;
if (Years.Count() > 1)
{
results = new IndexedDataTable(new string[] { "Year" });
}
else
{
results = new IndexedDataTable(null);
}
// Loop through all years and perform analysis on each.
List <string> errorsFromR = new List <string>();
foreach (double year in Years)
{
view.RowFilter = "Clock.Today.Year=" + year;
foreach (DataColumn predictedColumn in predictedData.Columns)
{
if (predictedColumn.DataType == typeof(double))
{
var values = DataTableUtilities.GetColumnAsDoubles(view, predictedColumn.ColumnName);
if (values.Distinct().Count() > 1)
{
variableValues.SetValues(predictedColumn.ColumnName, values);
}
}
}
string paramNames = StringUtilities.Build(Parameters.Select(p => p.Name), ",", "\"", "\"");
string sobolx1FileName = GetTempFileName("sobolx1", ".csv");
string sobolx2FileName = GetTempFileName("sobolx2", ".csv");
string sobolVariableValuesFileName = GetTempFileName("sobolvariableValues", ".csv");
// Write variables file
using (var writer = new StreamWriter(sobolVariableValuesFileName))
DataTableUtilities.DataTableToText(variableValues.ToTable(), 0, ",", true, writer, excelFriendly: false, decimalFormatString: "F6");
// Write X1
using (var writer = new StreamWriter(sobolx1FileName))
DataTableUtilities.DataTableToText(X1, 0, ",", true, writer, excelFriendly: false, decimalFormatString: "F6");
// Write X2
using (var writer = new StreamWriter(sobolx2FileName))
DataTableUtilities.DataTableToText(X2, 0, ",", true, writer, excelFriendly: false, decimalFormatString: "F6");
string script = string.Format(
$".libPaths(c('{R.PackagesDirectory}', .libPaths()))" + Environment.NewLine +
$"library('boot', lib.loc = '{R.PackagesDirectory}')" + Environment.NewLine +
$"library('sensitivity', lib.loc = '{R.PackagesDirectory}')" + Environment.NewLine +
"params <- c({0})" + Environment.NewLine +
"n <- {1}" + Environment.NewLine +
"nparams <- {2}" + Environment.NewLine +
"X1 <- read.csv(\"{3}\")" + Environment.NewLine +
"X2 <- read.csv(\"{4}\")" + Environment.NewLine +
"sa <- sobolSalt(model = NULL, X1, X2, scheme=\"A\", nboot = 100)" + Environment.NewLine +
"variableValues = read.csv(\"{5}\")" + Environment.NewLine +
"for (columnName in colnames(variableValues))" + Environment.NewLine +
"{{" + Environment.NewLine +
" sa$y <- variableValues[[columnName]]" + Environment.NewLine +
" tell(sa)" + Environment.NewLine +
" sa$S$Parameter <- params" + Environment.NewLine +
" sa$T$Parameter <- params" + Environment.NewLine +
" sa$S$ColumnName <- columnName" + Environment.NewLine +
" sa$T$ColumnName <- columnName" + Environment.NewLine +
" sa$S$Indices <- \"FirstOrder\"" + Environment.NewLine +
" sa$T$Indices <- \"Total\"" + Environment.NewLine +
" if (!exists(\"allData\"))" + Environment.NewLine +
" allData <- rbind(sa$S, sa$T)" + Environment.NewLine +
" else" + Environment.NewLine +
" allData <- rbind(allData, sa$S, sa$T)" + Environment.NewLine +
"}}" + Environment.NewLine +
"write.table(allData, sep=\",\", row.names=FALSE)" + Environment.NewLine
,
paramNames, NumPaths, Parameters.Count,
sobolx1FileName.Replace("\\", "/"),
sobolx1FileName.Replace("\\", "/"),
sobolVariableValuesFileName.Replace("\\", "/"));
DataTable resultsForYear = null;
try
{
resultsForYear = RunR(script);
// Put output from R into results table.
if (Years.Count() > 1)
{
results.SetIndex(new object[] { year.ToString() });
}
foreach (DataColumn col in resultsForYear.Columns)
{
if (col.DataType == typeof(string))
{
results.SetValues(col.ColumnName, DataTableUtilities.GetColumnAsStrings(resultsForYear, col.ColumnName));
}
else
{
results.SetValues(col.ColumnName, DataTableUtilities.GetColumnAsDoubles(resultsForYear, col.ColumnName));
}
}
}
catch (Exception err)
{
string msg = err.Message;
if (Years.Count() > 1)
{
msg = "Year " + year + ": " + msg;
}
errorsFromR.Add(msg);
}
}
var resultsRawTable = results.ToTable();
resultsRawTable.TableName = Name + "Statistics";
dataStore.Writer.WriteTable(resultsRawTable);
if (errorsFromR.Count > 0)
{
string msg = StringUtilities.BuildString(errorsFromR.ToArray(), Environment.NewLine);
throw new Exception(msg);
}
}
}
