Merge pull request DataScienceSpecialization#6 from rdpeng/master

Case Study for air pollution in RR

Author: jtleek

05_ReproducibleResearch/CaseStudy_AP/dominici.png

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+---
+title       : Reproducible Research Case Study
+subtitle    : Identifying Harmful Constituents in Particulate Matter Air Pollution
+author      : Roger D. Peng, Associate Professor of Biostatistics
+job         : Johns Hopkins Bloomberg School of Public Health
+logo        : bloomberg_shield.png
+framework   : io2012        # {io2012, html5slides, shower, dzslides, ...}
+highlighter : highlight.js  # {highlight.js, prettify, highlight}
+hitheme     : tomorrow      # 
+url:
+  lib: ../../libraries
+  assets: ../../assets
+widgets     : [mathjax]            # {mathjax, quiz, bootstrap}
+mode        : selfcontained # {standalone, draft}
+---
+
+
+## What Causes PM to be Toxic?
+
+- PM is composed of many different chemical elements
+
+- Some components of PM may be more harmful than others 
+
+- Some sources of PM may be more dangerous than others
+
+- Identifying harmful chemical constituents may lead us to strategies
+  for controlling sources of PM
+
+
+---
+
+## NMMAPS
+
+- The National Morbidity, Mortality, and Air Pollution Study (NMMAPS)
+  was a national study of the short-term health effects of ambient air
+  pollution
+
+- Focused primarily on particulate matter ($PM_{10}$) and ozone ($O_3$)
+
+- Health outcomes included mortality from all causes and
+  hospitalizations for cardiovascular and respiratory diseases
+
+- Key publications
+  - http://www.ncbi.nlm.nih.gov/pubmed/11098531
+  - http://www.ncbi.nlm.nih.gov/pubmed/11354823
+
+- Funded by the [Health Effects
+  Institute](http://www.healtheffects.org) 
+
+  - Roger Peng currently serves on the Health Effects Institute Health
+  Review Committee
+
+---
+
+## NMMAPS and Reproducibility
+
+- Data made available at the Internet-based Health and Air Pollution
+  Surveillance System (<http://www.ihapss.jhsph.edu>)
+
+- Research results and software also available at iHAPSS
+
+- Many studies (over 67 published) have been conducted based on the
+  public data <http://www.ncbi.nlm.nih.gov/pubmed/22475833>
+
+- Has served as an important test bed for methodological development
+
+---
+
+## What Causes Particulate Matter to be Toxic?
+
+<img src="lippmann.png" width=1000 />
+
+
+<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1665439/>
+
+- Lippmann *et al.* found strong evidence that Ni modified the
+  short-term effect of $PM_{10}$ across 60 US communities
+
+- No other PM chemical constituent seemed to have the same modifying
+  effect
+
+- To simple to be true?
+
+---
+
+
+## A Reanalysis of the Lippmann *et al.* Study
+
+<img src="dominici.png" width=1000 />
+
+<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2137127/>
+
+- Reexamine the data from NMMAPS and link with PM chemical constituent
+  data
+
+- Are the findings sensitive to levels of Nickel in New York City?
+
+---
+
+## Does Nickel Make PM Toxic?
+
+<img src="nickel-beta.png", height=400>
+
+- Long-term average nickel concentrations appear correlated with PM risk
+
+- There appear to be some outliers on the right-hand side (New York City)
+
+---
+
+## Does Nickel Make PM Toxic?
+
+<img src="nickel-beta-lm.png", height=450>
+
+- Regression line statistically significant ($p < 0.01$)
+
+---
+
+## Does Nickel Make PM Toxic?
+
+<img src="nickel-beta-lm-no-ny.png", height=450> 
+
+- Adjusted regression line (blue) no longer statistically significant
+($p < 0.31$)
+
+---
+
+## Does Nickel Make PM Toxic?
+
+<img src="ni-leaveout.png" height=500>
+
+---
+
+## What Have We Learned?
+
+- New York does have very high levels of nickel and vanadium, much
+  higher than any other US community
+
+- There is evidence of a positive relationship between Ni
+  concentrations and $PM_{10}$ risk
+
+- The strength of this relationship is highly sensitive to the
+  observations from New York City
+
+- Most of the information in the data is derived from just 3 observations
+
+---
+
+## Lessons Learned
+
+- Reproducibility of NMMAPS allowed for a secondary analysis (and
+  linking with PM chemical constituent data) investigating a novel
+  hypothesis (Lippmann *et al.*)
+
+- Reproducibility also allowed for a critique of that new analysis
+  and some additional new analysis (Dominici *et al.*)
+
+- Original hypothesis not necessarily invalidated, but evidence not as
+  strong as originally suggested (more work should be done)
+
+- Reproducibility allows for the scientific discussion to occur in a
+  timely and informed manner
+
+- This is how science works
+