In R4EPI/epidict: Epidemiology data dictionaries and random data generators

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There are four MSF outbreak dictionaries available:

• Cholera/Acute watery diarrhea ("Cholera")
• Meningitis ("Meningitis)
• Measles/Rubella ("Measles")
• Acute Jaundice Syndrome (often suspected to be Hepatitis E) ("AJS")

You can read more about the outbreak dictionaries at https://r4epis.netlify.com/outbreaks

Acute Jaundice Syndrome (AJS)

Variables in the dictionary

The AJS dictionary contains definitions for r nrow(epidict::msf_dict("AJS")) variables:

library(epidict)
ajs <- msf_dict("AJS")
names_desc <- ajs[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)

Option codes

The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

ajs_codes <- tidyr::unnest(ajs, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(ajs_codes)

Cholera

Variables in the dictionary

The Cholera dictionary contains definitions for r nrow(epidict::msf_dict("Cholera")) variables:

library(epidict)
cholera <- msf_dict("Cholera")
names_desc <- cholera[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)

Option codes

The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

cholera_codes <- tidyr::unnest(cholera, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(cholera_codes)

Measles

Variables in the dictionary

The Measles dictionary contains definitions for r nrow(epidict::msf_dict("Measles")) variables:

library(epidict)
measles <- msf_dict("Measles")
names_desc <- measles[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)

Option codes

The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

measles_codes <- tidyr::unnest(measles, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(measles_codes)

Meningitis

Variables in the dictionary

The Meningitis dictionary contains definitions for r nrow(epidict::msf_dict("Meningitis")) variables:

library(epidict)
meningitis <- msf_dict("Meningitis")
names_desc <- meningitis[c("data_element_formname", "data_element_shortname", "data_element_description", "data_element_valuetype")]
DT::datatable(names_desc)

Option codes

The dictionaries are exported using option codes that can be translated to human-readable format. This table shows how they are translated.

meningitis_codes <- tidyr::unnest(meningitis, cols = options)[c("data_element_shortname", "data_element_valuetype", "option_code", "option_name", "option_order_in_set")]
DT::datatable(meningitis_codes)

Exploring the dictionaries

You can explore the excel-formatted dictionaries with browseURL(system.file("extdata", "MSF-outbreak-dict.xlsx", package = "epidict")), but treat it as read-only.

R4EPI/epidict documentation built on Aug. 31, 2022, 5:34 a.m.