sourceR: Fits a Non-Parametric Bayesian Source Attribution Model

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Implements a non-parametric source attribution model to attribute cases of disease to sources in Bayesian framework with source and type effects. Type effects are clustered using a Dirichlet Process. Multiple times and locations are supported.

Author
Poppy Miller [aut, cre], Chris Jewell [aut], Jonathan Marshall [aut], Nigel French [aut]
Date of publication
2016-06-21 19:57:31
Maintainer
Poppy Miller <p.miller@lancaster.ac.uk>
License
GPL-3
Version
0.2.0

View on CRAN

Man pages

campy
Campylobacter source attribution data set from the Manawatu,...
flatten
Flattens the McMC posterior from saBayes output into a data...
heatmap_types
Type effect dendrogram
saBayes
Fits a non-parametric Bayesian model to source attribution...
sim_SA
Simulated data
sim_SA_true
True values of the parameters used to generate the simulated...
sourceR-package
Fits a non-parametric source attribution model
subset_posterior
Subsets the posterior of the McMC posterior from saBayes...
summary
Summary function for saBayes output.

Files in this package

sourceR
sourceR/inst
sourceR/inst/doc
sourceR/inst/doc/source_attribution_vignette_pdfs.R
sourceR/inst/doc/source_attribution_vignette_pdfs.Rnw
sourceR/inst/doc/source_attribution_vignette_pdfs.pdf
sourceR/tests
sourceR/tests/testthat.R
sourceR/tests/testthat
sourceR/tests/testthat/test_run_sim_and_MCMC.R
sourceR/tests/testthat/test_DPM.R
sourceR/src
sourceR/src/Makevars
sourceR/src/calc_ll_pois.cpp
sourceR/src/rcpp_armadillo_calc_li.cpp
sourceR/src/rcpp_armadillo_calc_lj.cpp
sourceR/src/calc_ll_nbinom.cpp
sourceR/src/Makevars.win
sourceR/src/RcppExports.cpp
sourceR/NAMESPACE
sourceR/data
sourceR/data/sim_SA_true.rda
sourceR/data/campy.rda
sourceR/data/sim_SA.rda
sourceR/R
sourceR/R/check_input.R
sourceR/R/heatmap_types.R
sourceR/R/subset_posterior.R
sourceR/R/calc_niter.R
sourceR/R/flatten.R
sourceR/R/RcppExports.R
sourceR/R/wrapper.R
sourceR/R/summary.R
sourceR/R/MCMC_loop.R
sourceR/vignettes
sourceR/vignettes/trace_params_real-1.pdf
sourceR/vignettes/lambda_i_residuals-1.pdf
sourceR/vignettes/type_effect_heatmap-1.pdf
sourceR/vignettes/lambda_i_residuals_real-1.pdf
sourceR/vignettes/source_attribution_vignette_pdfs.Rnw
sourceR/vignettes/Data_case_study
sourceR/vignettes/Data_case_study/PNAS_Figure2b.pdf
sourceR/vignettes/Data_case_study/PNAS_Figure2.csv
sourceR/vignettes/Data_case_study/SourceAttribution.r
sourceR/vignettes/Data_case_study/real_data.csv
sourceR/vignettes/Data_case_study/PNAS_Figure2b.r
sourceR/vignettes/Data_case_study/PNAS_Matrix.xls
sourceR/vignettes/Data_case_study/1-s2.0-S1567134809001981-main.pdf
sourceR/vignettes/trace_acf_sim_data_plots-1.pdf
sourceR/vignettes/source_attribution_jss.bib
sourceR/vignettes/lambda_j_real-1.pdf
sourceR/vignettes/type_effect_heatmap_real-1.pdf
sourceR/vignettes/type_effect_boxplots_real1-1.pdf
sourceR/vignettes/sim_pois_lambdaj_plots-1.pdf
sourceR/vignettes/DAG-1.pdf
sourceR/vignettes/child_docs
sourceR/vignettes/child_docs/Review.tex
sourceR/vignettes/child_docs/Discussion.tex
sourceR/vignettes/child_docs/Case_studies-concordance.tex
sourceR/vignettes/child_docs/McMC_alg.tex
sourceR/vignettes/child_docs/Case_studies.tex
sourceR/vignettes/child_docs/source_attribution_vignette-tikzDictionary
sourceR/vignettes/child_docs/Case_studies-tikzDictionary
sourceR/vignettes/child_docs/Case_studies.log
sourceR/vignettes/child_docs/Inference.tex
sourceR/vignettes/child_docs/Introduction.tex
sourceR/vignettes/child_docs/Motivating_ex.tex
sourceR/vignettes/child_docs/Methods.tex
sourceR/vignettes/child_docs/Conclusions.tex
sourceR/vignettes/child_docs/Case_studies.Rnw
sourceR/README.md
sourceR/MD5
sourceR/build
sourceR/build/vignette.rds
sourceR/DESCRIPTION
sourceR/man
sourceR/man/saBayes.Rd
sourceR/man/subset_posterior.Rd
sourceR/man/campy.Rd
sourceR/man/heatmap_types.Rd
sourceR/man/flatten.Rd
sourceR/man/sourceR-package.Rd
sourceR/man/summary.Rd
sourceR/man/sim_SA.Rd
sourceR/man/sim_SA_true.Rd