QMRA-package: Parametric Models for Quantitative Microbial Risk Assessment

In brechtdv/QMRA: Parametric Models for Quantitative Microbial Risk Assessment

Description

The QMRA package provides a suite of functions for performing exposure assessment, dose-response assessment and risk characterisation in the context of microbial risk assessment. Different parametric models are available and can be fitted in both a maximum likelihood and Bayesian framework.

Details

Package:	QMRA
Version:	0.0.14
Date:	2016-03-12
Authors:	Brecht Devleesschauwer, Christel Faes, Arie Havelaar, Niko Speybroeck
Maintainer:	[e-mail]
URL:	https://github.com/brechtdv/QMRA
BugReports:	https://github.com/brechtdv/QMRA/issues
Depends:	R (>= 3.2.0)
Imports:	methods, rjags, lme4, stats4, MASS, SuppDists, HyperbolicDist
SystemRequirements:	JAGS (>= 4.1.0) (see http://mcmc-jags.sourceforge.net)
License:	GPL (>= 2)
LazyLoad:	yes

Available functions in the QMRA package:

Exposure Assessment:

ea_count	ML parametric modelling of exposure concentration from count data.
ea_conc	ML parametric modelling of exposure concentration from (possibly left-censored) concentration data.
ea_presence	ML parametric modelling of exposure concentration from presence/absence data.
bea_count	Bayesian parametric modelling of exposure concentration from count data.
bea_conc	Bayesian parametric modelling of exposure concentration from (possibly left-censored) concentration data.
bea_presence	Bayesian parametric modelling of exposure concentration from presence/absence data.
avg_ea	Model averaging for objects of class "ea".
sim	Simulate from fitted concentration distributions. Method for objects of class "ea" and "bea".
summarize	Summarize fitted concentration distributions. Method for objects of class "ea" and "bea".

Dose-Response Modelling:

drm	Maximum likelihood parametric modelling of dose-response data.
bdrm	Bayesian parametric modelling of dose-response data.
avg_drm	Model averaging for objects of class "drm".
predict	Predict from fitted dose-response curve. Method for objects of class "drm".
sim	Simulate from fitted dose-response curve. Method for objects of class "drm" and "bdrm".
summarize	Summarize fitted dose-response curve. Method for objects of class "drm" and "bdrm".

Datasets:

crypto	Cryptosporidium oocyst counts.
giardia	Giardia oocyst concentrations.
coliform	Coliform presence/absence data.
campy	Campylobacter dose-response data.

Note

The Bayesian functions in the prevalence package call on JAGS (Just Another Gibbs Sampler), through the rjags package. Therefore, JAGS has to be installed on the user's system.

JAGS can be downloaded from http://sourceforge.net/projects/mcmc-jags/

brechtdv/QMRA documentation built on May 13, 2019, 5:06 a.m.