Transcript Title of Presentation

7/17/2015
Group/Presentation Name
SimpleR: Taking on the “Evil Empire” to
Build Simple R Applications for NonStatistical Users
Nicholas Lewin-Koh
Bert Gunter
Genentech Nonclinical Statistics
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Slide 2
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Outline:
• Background and Context: The working environment
and needs
• Strategy: The Approach
• Example: Tumor Xenograft Study Analysis
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Slide 3
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Context: Pharmaceutical industry, but regulation
is not an issue
• We collaborate on many projects that investigate drug
efficacy, toxicity, biomarkers, dose determination,
manufacturing methods, assay methods, etc.
• Data may be complex, so analyses can be tricky.
• We need to provide consistent, clear, interpretable
analyses to aid scientific assessment
• Complex statistical analyses are unsuitable
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Example: Tumor Xenograft Studies
• Implant special tumor cell lines in mice, then compare tumor
growth under different treatment regimens.
Measure Tumor Volume
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Example: Tumor Xenograft Studies
• Xenograft studies help determine which drugs to work on in which
cancers, dosing in human studies, biomarkers that can identify
subgroups who may or may not benefit, …
• Data are challenging, consists of repeated measures of tumor
volume over time per animal.
• Nonlinear growth/stasis/shrinkage
• dropouts due to toxicity or animal care requirements
• left censoring when tumors shrink below LOD
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Ad hoc analyses and plots using Excel are most
widely used approaches
Poor analyses compromise
scientific decision making and our
ability to find and develop good
drugs.
DRUG 1
DRUG 2
DRUG 2
DRUG 2
DRUG 3
Realities:
• Scientists/engineers usually have neither
the background nor time to learn and use
sophisticated statistical methods
• Wider audience of decision makers cannot
consume fancy statistical results anyway
• Not nearly enough of us (statisticians) to
handle all of this for them (scientists and
engineers)
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Context for Solutions
• Rapid change – in technologies, needs, methods, computer
hardware and software…
• Need safe and robust methods: reasonable answers quickly in
a variety of real circumstances, alert or failure otherwise.
– Searching for statistical “optimality” is waste of time.
• Communicate all results via graphs and tables.
• Users will treat software as “black box” yielding answers.
– User interface, not software documentation is key
• Developers need to meet rapidly evolving user needs
– Rapid prototyping, development, ease of modification, and feature
addition are important factors
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R provides a way to meet these challenges
• Many built-in procedures and packages  rapid
prototyping
• Graphics packages (lattice, ggplot, …) ,provide
framework for informative, flexible graphical displays
– Changes the paradigm !
• Close collaboration with customers during
development:
Try
Modify
Review/
Test
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Strategy
• Initially, Windows desktop application on only very few (1 or 2)
desktops
– Simple menu interface automatically starts up when user clicks on R
icon.
– e.g. Use startup options to read in .RData file with all functions and
execute code that sets up menus, etc.
– We do it with .Rprofile file, but many alternatives are available
• Once customers are satisfied and code has stabilized, port to
Web-based interface to ease maintenance for larger user base
• So far, we haven’t found the extra overhead for converting to
packages worthwhile, but this may change.
– Remember, for users it’s a black box that provides solutions, not a
tool.
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Demo
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Menu Interface
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Output: Model fit
XXXXXXXX
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Output: Views derived from the model.
X
X
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Web Interface
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Summary:
• Excel is ubiquitous data analysis software, so
opportunities for major improvements abound.
• To replace it, we need:
– rapid development of flexible, robust solutions
– “intelligent” graphs and tables to communicate results
– Workable user interfaces that shield users from technical
details
– A way to scale solutions, that does not require a large ongoing
effort to support
• R and its supporting packages meet these needs.
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Slide 16
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Thanks:
Translational Oncology
Bruno Alicke
Steven Gould
Bioinformatics
Dana Caulder
Vivek Ramaswamy
Kathryn Woods
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