/// <summary>
/// Generates the R script which performs the optimization.
/// </summary>
/// <param name="fileName">File path to which the R code will be saved.</param>
/// <param name="outputPath">Directory/path to which output results will be saved. This is passed as a parameter to croptimizR.</param>
/// <param name="apsimxFileName">Name of the .apsimx file to be run by the optimisation.</param>
private void GenerateRScript(string fileName, string outputPath, string apsimxFileName)
{
// tbi: package installation. Need to test on a clean VM.
StringBuilder contents = new StringBuilder();
contents.AppendLine($"variable_names <- c({string.Join(", ", VariableNames.Select(x => $"'{x.Trim()}'").ToArray())})");
// If we're reading from the PredictedObserved table, need to fix
// Predicted./Observed. suffix for the observed variables.
string[] sanitisedObservedVariables = GetObservedVariableName().Select(x => $"'{x.Trim()}'").ToArray();
string dateVariable = VariableNames.Any(v => v.StartsWith("Predicted.")) ? "Predicted.Clock.Today" : "Clock.Today";
contents.AppendLine($"observed_variable_names <- c({string.Join(", ", sanitisedObservedVariables)}, '{dateVariable}')");
contents.AppendLine($"apsimx_path <- '{typeof(IModel).Assembly.Location.Replace(@"\", @"\\")}'");
contents.AppendLine($"apsimx_file <- '{apsimxFileName.Replace(@"\", @"\\")}'");
contents.AppendLine($"simulation_names <- {GetSimulationNames()}");
contents.AppendLine($"predicted_table_name <- '{PredictedTableName}'");
contents.AppendLine($"observed_table_name <- '{ObservedTableName}'");
contents.AppendLine($"param_info <- {GetParamInfo()}");
contents.AppendLine();
contents.AppendLine(OptimizationMethod.GenerateOptimizationOptions("optim_options"));
contents.AppendLine($"optim_options$path_results <- '{outputPath.Replace(@"\", @"\\")}'");
if (RandomSeed != null)
{
contents.AppendLine($"optim_options$ranseed <- {RandomSeed}");
}
contents.AppendLine();
contents.AppendLine($"crit_function <- {OptimizationMethod.CritFunction}");
contents.AppendLine($"optim_method <- '{OptimizationMethod.ROptimizerName}'");
contents.AppendLine();
contents.Append(ReflectionUtilities.GetResourceAsString("Models.Resources.RScripts.OptimizR.r"));
File.WriteAllText(fileName, contents.ToString());
}
private string[] GetObservedVariableName()
{
if (PredictedTableName == ObservedTableName)
{
return(VariableNames.Select(x => x.Replace("Predicted.", "Observed.")).ToArray());
}
return(VariableNames);
}
/// <summary>
/// Generates the R script which performs the optimization.
/// </summary>
/// <param name="fileName">File path to which the R code will be saved.</param>
/// <param name="outputPath">Directory/path to which output results will be saved. This is passed as a parameter to croptimizR.</param>
/// <param name="apsimxFileName">Name of the .apsimx file to be run by the optimisation.</param>
private void GenerateRScript(string fileName, string outputPath, string apsimxFileName)
{
// tbi: package installation. Need to test on a clean VM.
StringBuilder contents = new StringBuilder();
contents.AppendLine($"variable_names <- c({string.Join(", ", VariableNames.Select(x => $"'{x.Trim()}'").ToArray())})");
// In theory, it would be better to always use relative path to
// the input file, by setting the working directory of the R
// process appropriately. Unfortunately, this will require some
// refactoring of the R wrapper which I don't really want to do
// right now. So for now I'm going to just use relative path if
// using docker.
if (RDocker.UseDocker())
{
apsimxFileName = Path.GetFileName(apsimxFileName);
}
// If we're reading from the PredictedObserved table, need to fix
// Predicted./Observed. suffix for the observed variables.
string escapedOutputPath = outputPath.Replace(@"\", "/");
string[] sanitisedObservedVariables = GetObservedVariableName().Select(x => $"'{x.Trim()}'").ToArray();
string dateVariable = VariableNames.Any(v => v.StartsWith("Predicted.")) ? "Predicted.Clock.Today" : "Clock.Today";
contents.AppendLine($"observed_variable_names <- c({string.Join(", ", sanitisedObservedVariables)}, '{dateVariable}')");
contents.AppendLine($"apsimx_path <- '{PathToModels().Replace(@"\", "/")}'");
contents.AppendLine($"apsimx_file <- '{apsimxFileName.Replace(@"\", "/")}'");
contents.AppendLine($"simulation_names <- {GetSimulationNames()}");
contents.AppendLine($"predicted_table_name <- '{PredictedTableName}'");
contents.AppendLine($"observed_table_name <- '{ObservedTableName}'");
contents.AppendLine($"param_info <- {GetParamInfo()}");
contents.AppendLine();
contents.AppendLine(OptimizationMethod.GenerateOptimizationOptions("optim_options"));
contents.AppendLine($"optim_options$path_results <- '{escapedOutputPath}'");
if (RandomSeed != null)
{
contents.AppendLine($"optim_options$ranseed <- {RandomSeed}");
}
contents.AppendLine();
contents.AppendLine($"crit_function <- {OptimizationMethod.CritFunction}");
contents.AppendLine($"optim_method <- '{OptimizationMethod.ROptimizerName}'");
contents.AppendLine();
contents.AppendLine(ReflectionUtilities.GetResourceAsString("Models.Resources.RScripts.OptimizR.r"));
// Don't use Path.Combine() - as this may be running in a (linux) docker container.
// R will work with forward slashes for path separators on win and linux,
// but backslashes will not work on linux.
string rDataExpectedPath = $"{escapedOutputPath}/optim_results.Rdata";
contents.AppendLine(CreateReadRDataScript(rDataExpectedPath));
File.WriteAllText(fileName, contents.ToString());
}