Project 2 Resources and Packages

Mapping Smoothed Odds Ratios from Individual-Level Data

The MapGAM package (December 2012) is now up on CRAN and can be installed in the usual manner.  It contains functions for mapping risk surfaces using individual-level data such as case-control study data, using generalized additive models (GAMs) to smooth over two-dimensional location while adjusting for any confounding variables. Includes convenient functions for mapping and permutation tests for the null hypothesis that spatial location is not associated with risk (adjusting for confounders).

Authors: Veronica Vieira, Scott Bartell, and Robin Bliss.

To download, go to:
http://cran.r-project.org/web/packages/MapGAM/

Generalized Concentration Addition to Visualize and Test Combination Data

This R code uses the Generalized Concentration Addition (GCA) method (Howard and Webster 2009) to visualize and test combination data. These programs are for use with the R environment. This work is available for use under the General Public License.

plot

Howard, G. J., Schlezinger, J. J., Hahn, M. E., & Webster T. F. (2010). Generalized concentration addition predicts joint effects of aryl hydrocarbon receptor agonists with partial agonists and competitive antagonists.Environmental Health Perspectives, 118(5), 666-672.

Howard, G. J., & Webster, T. F. (2009). Generalized concentration addition: a method for examining mixtures containing partial agonistsJournal of Theoretical Biology, 259(3), 469-477. PMCID: PMC2737481.

Generalized Additive Model for Spatial Epidemiology

Hoffman K, Aschengrau A, Webster T, Bartell S, Vieira VM (2015) Association between residence at birth and mental health disorders: a spatial analysis of retrospective cohort data. BMC Public Health. Jul 20; 15:688.

The following code and synthetic data for testing the Generalized Additive Model method is available. This work is available for use under the General Public License.

  • syndata_Scode.txt: text file of S-Plus code for reproducing our analysis using synthetic data
  • syndata.xls (204 kb):excel file of synthetic data
  • syndata-figs.doc (71 kb): word file of crude and adjusted maps of the synthetic data (output from S-Plus mapped using ArcView)

The following article discusses methods and analyzes both a synthetic and real data set:

Webster, T., Vieira, V., Weinberg, J., & Aschengrau, A. (2006). Method for mapping population-based case-control studies using generalized additive modelsInternational Journal of Health Geographics, 5:26. PMCID: PMC1526437.

The following article discussed methods and analyzes a real data set:

Vieira V, Webster T, Weinberg J, Aschengrau A, and Ozonoff D (2005) Spatial Analysis of lung, colorectal, and breast cancer on Cape Cod: An application of generalized additive models to case-control data.  Environmental Health: A Global Access Science Source, 4:11.

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