Calling R from .NET:
a case-study using Rapid NCA, the noncompartmental analysis workflow tool
Chris Campbell
Agenda
• Using .NET
• Identify Opportunity
• Design Solution
• Develop Solution
• Connections with R.NET
• Complete & Deploy Tool
Using .NET
What is .NET?
• Object-oriented environment to develop applications
• Safe execution environment
• Choice of programming languages
• Framework consisting of:
• runtime
• class library
• Developed with Visual Studio
Using .NET
Visual Studio
• A graphical programming tool (IDE)
• Also, Visual Studio Express is a free version
Using .NET
Choice of languages
Tried and tested languages
• C# is the main one
• F# is a functional language (not a steep learning curve if you
know OCaml)
• Knowledge of XAML (a Microsoft declarative XML language) is
required for state of the art graphics
• C++/CLI useful for legacy and bespoke parallel processing
(including GPGPU)
Other possibilities..
• Vb.Net is very like C# (no advantage over it)
• Third parties have added languages to the CLI platform
Using .NET
An “ajar source” platform
Not exactly open source, but…
• Most CLI third party languages are open
• C# and VB.Net are not – but many open source projects based
on them
• Microsoft have made F# open source
• There are free (Express) versions of Visual Studio for the
languages
• Compiler is free and other editors / IDEs are available (but not
usually preferred by developers)
Using .NET
Performance and
Computation
Performance is very good
• On graphics (millions of data points will plot with ease and
zoom smoothly)
• Computation is fast enough in C#, calling R adds little overhead
• Standard Maths library is limited; third parties and MS maths for
“drawing” are better
• Data parallel computation is possible on the desktop (GPGPU)
• F# provides further “big data” capabilities
A Project Case Study
Identify Opportunity
• Where can repetitive tasks be automated?
• How can regular outputs be generated?
• How can we make methods and techniques more
accessible to colleagues?
Identify Opportunity
• Customer needed to send monthly reports to dozens of
trial centres
• Small team, so time limited
• Normally simple noncompartmental analysis,
standard report
Design Solution
• What is the simplest way for the task to be performed?
• Which steps can be eliminated?
• What are barriers to understanding for users?
Design Solution
Streamline Workflow
What is Needed?
•
Import data to analysis software
•
Map variables
•
Select units
•
Select non-compartmental
•
Select model
•
Select interpolation
•
Select rules for BLQ
•
Select terminal phase calculation method
•
Perform analysis
•
Choose partial area
•
Export results
•
Export plots
•
Write report
•
Format report
Design Solution
Analysis Engine using R
Let’s get .Net technical..
Connections with R.NET
• What will be provided to R?
• What will be returned from R?
• What happens if something goes wrong?
Connections with R.NET
Using the R Service
• R.NET allows R calls to be submitted to an R service
• R.NET is not the only option
• R.NET connects to R down to Expression level
• So objects can effectively be passed back into .NET
• Recommend a robust .Net framework to do this
Connections with R.NET
_pluginsManager = new RPluginManager(PluginLocation, RLocation);
_pluginsManager.SetActivePlugin();
_session = _pluginsManager.GetSession();
bool sessionOk = _pluginsManager.TryMakeSession(out _session);
R is efficiently accessed,
via R.Net (as pictured in
Visual Studio) via a
Plugin (as above)
Connections with R.NET
“Engineer’s” framework
Connections with R.NET
Robustness
• Function may be passed data outside it’s anticipated
structure
> checkOrderedVector(c(0, 1, 3, 2, 4),
+
description = "Time")
Error in checkOrderedVector(c(0, 1, 3, 2, 4),
description = "Time") :
Error: Time is not ordered. Actual value is 0 1 3 2 4
>
Connections with R.NET
Robustness
• The tool expects a certain return object
• An error in an R call should be trapped by the
communicating function
> check01 <- try(checkOrderedVector(Time,
+
description = "Time"), silent = TRUE)
>
• Return object passed as normal
• An error checking element of the return object can report
information about the error
Connections with R.NET
Using the framework
_pluginsManager = new RPluginManager(PluginLocation, RLocation);
_pluginsManager.SetActivePlugin();
_session = _pluginsManager.GetSession();
bool sessionOk = _pluginsManager.TryMakeSession(out _session);
_session.SetNumericSymbol("TimePtVector", CheckTimePointData(toAnalyse));
_session.SetNumericSymbol("ConcVector", CheckConcentrationPointData(toAnalyse));
var evalString = string.Format("ncaAnalysis(TimePtVector, ConcVector, …
MathEngineDataRowDto<double> ncaGetBack =
_session.PerformNumericEvaluation(evalString, "ROutput_Error");
_lastErrors = ncaGetBack.ErrorStrings;
_session.FlushConsole();
_pluginsManager.RelinquishSession();
A Rapid Solution
Complete & Deploy Tool
• Can users understand how to use tool?
• How confident are we in tool output?
Deploy Tool
Data Import
Map Variables
Review Analysis
Review Grouping
Generate Report
Select Report Type
Add Group Comments
View Report
Conclusions
• Great graphical interfaces can be built using .NET
• Intuitive interactive features are available
• R.NET allows R analysis to be accessed as a service
• Good coding practice will ensure application is robust
• Work on a well engineered framework will be rewarded
with desktop solutions created at high speed