FERG2015-package: DALY Calculation Framework for WHO/FERG - 2015 revision

Description Details


The FERG2015 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 FERG2015 package is based on the DALY package.


Package: FERG2015
Type: Package
Version: 0.3.0
Date: 2018-01-04
Authors: Brecht Devleesschauwer, Scott McDonald
Maintainer: Brecht Devleesschauwer <[email protected]>
Depends: R (>= 3.4.0), methods
Imports: XLConnect, knitr, xtable, lme4, rjags, ggplot2, prevalence, rworldmap, RColorBrewer
SystemRequirements: JAGS (>= 4.2.0) (see http://mcmc-jags.sourceforge.net)
License: GPL (>= 2)
LazyData: yes

Available functions in the FERG2015 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.

brechtdv/FERG2015 documentation built on May 13, 2019, 5:05 a.m.