Calling R from .NET: a case-study using Rapid NCA, the

non-compartmental analysis

workflow toolChris Campbell

Agenda

• Using .NET

• Identify Opportunity

• Design Solution

• Develop Solution

• Connections with R.NET

• Complete & Deploy Tool

Using .NETWhat 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 .NETVisual Studio

• A graphical programming tool (IDE)

• Also, Visual Studio Express is a free version

Using .NETChoice 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 .NETAn “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 .NETPerformance 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 non-compartmental 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 SolutionStreamline WorkflowWhat 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 SolutionAnalysis 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.NETUsing 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.NETRobustness

• 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.NETRobustness

• The tool expects a certain return object

• An error in an R call should be trapped by the communicating function

• Return object passed as normal

• An error checking element of the return object can report information about the error

> check01 <- try(checkOrderedVector(Time, + description = "Time"), silent = TRUE)>

Connections with R.NETUsing 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