This package provides a modeling approach that uses biomonitoring data and chemical metabolism information to estimate chemical exposure intake rates while carefully characterizing the uncertainties. Bayesian methods are provided to infer ranges of exposure for parent chemicals consistent with biomarkers identified in urine samples from the U.S population by the National Health and Nutrition Examination Survey (NHANES). Metabolites are linked to potential parent chemicals using the NHANES reports and text mining of PubMed abstracts. The inferred parent chemical exposures have been incorporated into the US EPA's CompTox Chemicals Dashboard for chemicals with available data. The exposure predictions can be found for an individual chemical by clicking Exposure -> Monitoring Data (for example: comptox.epa.gov/dashboard/chemical/monitoring-data/DTXSID7020182).
Biomonitoring data provides insight into the chemicals commonly present in humans, but it is important to know which environmental chemicals contribute to the observed metabolites for estimating exposure and risk. These inferred exposures, when coupled with predicted toxic doses and high throughput TK, allow the identification of public health priority chemicals via risk-based bioactivity:exposure ratios (BER).
- Users will need the freely available R statistical computing language: https://www.r-project.org/
- Users will likely want a development environment like RStudio: https://www.rstudio.com/products/rstudio/download/
- Installing JAGS and rjags JAGS ("Just Another Gibbs Sampler") is a separate program from R, and is needed for MCMC JAGS can be installed from: https://mcmc-jags.sourceforge.io/ NOTE: IF you are using Windows you must use JAGS v4.3.1 if your version of R is >= 4.2.0, but you must use JAGS v4.3.0 if your version of R is < 4.2.0.
If you install JAGS in a place other than it's defaault, set the JAGS_HOME variable within R:
Sys.setenv(JAGS_HOME="C:/Users/jwambaug/AppData/Local/JAGS/JAGS-4.3.0/")
Then install the package "rjags":
install.packages("rjags")
- Getting Started with R Package bayesmarker from the R command line
library(devtools)
install_github("USEPA/CompTox-HumanExposure-bayesmarker/bayesmarker")
- RStudio provides a menu ‘Install Packages’ under ‘Tools’ tab
- Load the bayesmarker data and functions
library(bayesmarker)
- Check what version you are using
packageVersion(bayesmarker)
Lead package developer Zach Stanfield [@stanfield.zachary@epa.gov]
Woodrow Setzer [@woodrow.setzer@epa.gov]
Victoria Hull [@hull.victoria@epa.gov]
Risa Sayre [@sayre.risa@epa.gov]
Kristin Isaacs [@isaacs.kristin@epa.gov]
John Wambaugh [@wambaugh.john@epa.gov]
License: GPL-3 https://www.gnu.org/licenses/gpl-3.0.en.html