DALY-summarize: Load, Merge, and Summarize Results by (Sub)Region

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

Description

Functions to load, merge and summarize the number of incident cases, deaths, YLDs, YLLs or DALY of getDALY_per_region or getDALY_per_subregion objects.

Usage

## Get summary for 1 agent
summarize(x, what, rate = FALSE, age = c("all", "<5", "5+"), 
          denom = 1e+05, names = "all")

## Get summary for all agents 
summarize_all(agents, what = "daly", rate = F, by = "region",
              age = "all", fb = F)

## Load (fb) results per (sub)region
load_results(agent, by, fb)

## Get summary per (sub)region for 1 agent
get_total(agent, what = "daly", rate = FALSE,
          by = c("subregion", "region"), age = c("all", "<5", "5+"), fb = FALSE)

##
get_global(x, what, by_region = FALSE, denom = 1e+05, rate = FALSE, 
           names = "all", age = "all")

## Get DALY samples by (sub)region for 1 agent
get_samples(agent, what = c("daly", "yld", "yll", "incidence", "cases", "deaths"),
            by = c("subregion", "region"), fb = FALSE, ...)

## Get DALY samples by (sub)region for >1 agent
get_all_samples(agents, what = c("daly", "yld", "yll", "incidence", "cases", "deaths"),
                by = c("subregion", "region"), fb = FALSE, ...)

## Get all samples, per outcome
get_samples_per_outcome(agent, dir, date, denom = 1e+05,
                        by = c("subregion", "region"), outcomes)

Arguments

x	object generated by getDALY_per_region or getDALY_per_subregion
what	parameter to be summarized
rate	logical flag; should values be summarized per 100,000?
age	age group for which summary is made
denom	denominator used in rates
names	node name(s) for which summary is made
agent	vector of 4 elements: agent name, directory, date total burden, date foodborne burden
agents	list of agent vectors
by	which set of results to use: c("subregion", "region")
fb	logical flag; should foodborne results be used?
by_region	logical flag; should results be presented at (sub)regional level, or should they be aggregated at global level?
dir	agent directory
date	date burden estimation
outcomes	vector of outcomes to be used
...	other arguments to be passed to underlying functions

Value

The summarize functions return a data frame with the mean, median, 95% uncertainty interval, and standard deviation of the specified value(s) per (sub)region and globally. The get functions return a list of samples according to the arguments specified.

See Also

DALY_map, FERG_report

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