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Software

Small Area Estimation

  • SAE for prevalence software summaries at SAE4Health. The next two products are reachable from here.
  • The R package surveyPrev carries out small area estimation using DHS data and a variety of statistically rigorous methods. See also SAE4Health.
  • The associated shinyApp provides a user-friendly interface to the package. See also SAE4Health.
  • Methods for smoothing of direct estimates in time and space, and mapping the subsequent estimates, are contained in the SUMMER package at CRAN: SUMMER.
  • GitHub version of SUMMER (contains the latest version): GitHub SUMMER.
  • Shiny App for SUMMER: SUMMER Shiny App.
  • ShinyApp for TMB/INLA comparison: Shiny App for TMB/INLA Simulations. TMB/INLA paper: here.
  • TMB Code: here. TMB/INLA paper: here.
  • Files to accompany Wakefield, Fuglstad, Riebler, Godwin, Wilson and Clark, "Estimating Under 5 Mortality in Space and Time in a Developing World Context." Paper: here. Supplementary Materials: here.
  • Reference: Chen, Wakefield and Lumley, "The use of sample weights in Bayesian spatial hierarchical models for small area estimation" is here.
  • Code to implement the simulation in Wakefield, Simpson and Godwin is here.

Spatial Epidemiology

  • Details of the R package SpatialEpi to perform various methods in Spatial Epidemiology: SpatialEpi.
  • WinBUGS code for models fitted in Bauer and Wakefield, "Stratified space-time infectious disease modeling: with application to hand, foot and mouth disease in China": here.

Genetic Epidemiology

  • Excel spreadsheet for calculating approximate Bayes factors for genetic epidemiology studies: here. R code: here and here (the latter for combining two studies also). Example: here. The paper "A Bayesian Measure of the Probability of False Discovery in Genetic Epidemiology Studies" is on the publications page.
  • Details of the R package to evaluate methods described in the Biometrics paper: HWEBAYES. WinBUGS code for examining Hardy-Weinberg Equilibrium: here. R script to run the four-allele example from the Biometrics paper: here. Short user manual: here.

Two-Phase Sampling

  • Bayes Analysis of Two-Phase Data: Random Sampling Code is here and example is here. Bayes Analysis of Two-Phase Data: Case-Control Sampling Code is here and example is here. Accompanying paper appears in Biometrics. Code was written by Michelle Ross.
  • The R Code to carry out two-phase sampling in an ecological setting as described in "Overcoming ecological bias using the two-phase study design" by Wakefield and Haneuse, American Journal of Epidemiology (see the publications page) is here, and requires the R functions tps.q — the latter is an R version of the Splus code written by Norm Breslow and Nilanjan Chatterjee. The code works with the North Carolina data infantsAgg.dat.

Longitudinal Data

  • Bayesian population PK/PD modeling developed for BUGS by Jon Wakefield, Dave Lunn, Nicky Best and Dave Spiegelhalter: PKBUGS.
  • BUGS code for the Zhou and Wakefield (2006, Biometrics) paper on curve clustering: here.