Creating a new Standard Output file from scratch

Creating a simple SO with PopulationEstimate

This section will walk you through the creation of a simple SO file.

First we create the data structure with the maximum likelihood parameter estimates.

MLE <- data.frame(POP_CL=2.23, POP_V=40, IVCL=0.4, IVV=0.3)

Next we add the additional columnType attribute.

attributes(MLE)$columnType <- list(c("structuralParameter"), c("structuralParameter"), c("varParameter", "variance"), c("varParameter", "variance"))

This sets POP_CL and POP_V to be structural parameters and IVCL and IVV to be variability parameters on the variance scale.

The next step is to create the PopulationEstimates object.

library(libsoc)
popest <- so_PopulationEstimates$new()

The MLE data.frame can now be attached.

popest$MLE <- MLE

Now we create the parent objects of the PopulationEstimates.

est <- so_Estimation$new()
est$PopulationEstimates <- popest
block <- so_SOBlock$new()
block$blkId <- "myEstimationRun"
block$Estimation <- est
so <- so_SO$new()
so$add_SOBlock(block)

It is possible to add messages using a convenient method

block$add_message("WARNING", "myTool", "name_of_warning", "This is the description", 2)

Another method adds a rawresults datafile from the tool.

block$add_rawresults_datafile("Description", "file", "id1")

The resulting structure can be inspected

so

## Reference class object of class "so_SO"
## Field "id":
## NULL
## Field "metadataFile":
## NULL
## Field "Description":
## NULL
## Field "PharmMLRef":
## NULL
## Field "SOBlock":
## [[1]]
## Reference class object of class "so_SOBlock"
## Field "blkId":
## [1] "myEstimationRun"
## Field "ToolSettings":
## NULL
## Field "RawResults":
## Reference class object of class "so_RawResults"
## Field "DataFile":
## [[1]]
## data frame with 0 columns and 0 rows
## 
## Field "GraphicsFile":
## NULL
## Field ".cobj":
## <pointer: 0x557d3be2cc30>
## Field "TaskInformation":
## Reference class object of class "so_TaskInformation"
## Field "Message":
## [[1]]
## Reference class object of class "so_Message"
## Field "type":
## [1] "WARNING"
## Field "Toolname":
## [1] "myTool"
## Field "Name":
## [1] "name_of_warning"
## Field "Content":
## [1] "This is the description"
## Field "Severity":
## [1] 2
## Field ".cobj":
## <pointer: 0x557d3cd77b60>
## 
## Field "OutputFilePath":
## NULL
## Field "RunTime":
## NULL
## Field "NumberChains":
## NULL
## Field "NumberIterations":
## NULL
## Field ".cobj":
## <pointer: 0x557d3bf964e0>
## Field "Estimation":
## Reference class object of class "so_Estimation"
## Field "PopulationEstimates":
## Reference class object of class "so_PopulationEstimates"
## Field "MLE":
##   POP_CL POP_V IVCL IVV
## 1   2.23    40  0.4 0.3
## Field "Bayesian":
## NULL
## Field "OtherMethod":
## NULL
## Field ".cobj":
## <pointer: 0x557d3c874d40>
## Field "PrecisionPopulationEstimates":
## NULL
## Field "IndividualEstimates":
## NULL
## Field "PrecisionIndividualEstimates":
## NULL
## Field "Residuals":
## NULL
## Field "Predictions":
## NULL
## Field "OFMeasures":
## NULL
## Field "TargetToolMessages":
## NULL
## Field ".cobj":
## <pointer: 0x557d3b6e5080>
## Field "Simulation":
## NULL
## Field "ModelDiagnostic":
## NULL
## Field "OptimalDesign":
## NULL
## Field ".cobj":
## <pointer: 0x557d3b517fa0>
## 
## Field ".cobj":
## <pointer: 0x557d3d6dd040>

And written using so$so_write(“filename.SO.xml”)