FERG

Description Details

The FERG package provides functions for calculating and reporting DALYs in the framework of WHO's Foodborne Disease Burden Epidemiology Reference Group work towards the global burden of foodborne disease. The DALY calculation framework of the FERG package is based on the DALY package.

Package:	FERG
Type:	Package
Version:	0.1.0
Date:	2015-07-16
Authors:	Brecht Devleesschauwer, Scott McDonald
Maintainer:	Brecht Devleesschauwer <brechtdv@gmail.com>
Depends:	R (>= 3.0.0), methods
Imports:	XLConnect, knitr, xtable, lme4, rjags, ggplot2, prevalence, rworldmap, RColorBrewer
License:	GPL (>= 2)
LazyLoad:	yes

Available functions in the FERG package:

Imputation Activity
`extractIncidence`	Get incidence data from Excel database file using `XLConnect`.
`check_db`	Check raw imputation database.
`impute`	Impute missing values based on a Random Effects model.
`merge`	Merge observed with imputed values.
`save_merged_db`	Save merged values to workbook.
`plot_missing`	Plot missing values using `rworldmap`.
`summarize_imputation`	Summarize imputation results.
`get_total_cases`	Obtain cases by WHO subregion & total.
`imputation_report`	Generate report of imputation results.

DALY Calculation Activity
`readDatabase`	Read entire Excel workbook using `XLConnect`.
`check_XL`	Check if sheets are correctly ordered.
`read_XL`	Read Excel and transform to 'DB' list.
`getDALY_per_country`	Calculate DALYs for each country.
`getDALY_per_region`	Aggregate DALYs per region.
`getDALY_per_subregion`	Aggregate DALYs per subregion.
`check_convergence`	Check MC convergence.
`DALY_map`	Produce global burden of disease map.
`FERG_report`	Produce FERG PDF report.
`get_contrib`	Derive node contributions (ie, YLD or YLL)
`get_local_LE`	Obtain the life expectancy table of a given country
`mean_age`	Calculate mean age from age distribution.

Source Attribution Activity
`generate_samples`	Generate normalized samples.
`normalize_by_food`	Normalize samples by proportion foodborne.
`summary_stats`	Summarize samples.
`sa_barplot`	Generate source attribution barplot.
`sa_plot`	Generate source attribution line plot.
`sa_report`	Generate source attribution report.
`apply_prop_fb`	Apply proportion foodborne.
`get_global`	Get global results.

FERG Results :: helper functions
`load_results`	Load (fb_)results_per_region/subregion.
`get_total`	Get summary per (sub)region for 1 agent.
`get_samples`	Get DALY samples by (sub)region for 1 agent.
`get_all_samples`	Get DALY samples by (sub)region for >1 agent.
`get_samples_per_outcome`	Get all samples per outcome.
`summarize`	Summarize 'DALYrun_region' object.
`summarize_all`	Get summary for all agents.

FERG Results :: plot functions
`line_plot`	Median and UI, per agent.
`full_barplot`	Median rate, per agent & region.
`region_barplot`	YLD/YLL, ages, scaled to 100%, per agent.
`scatter_plot`	DALY/case ~ DALY/100,000, per agent.