msf_dict: MSF data dictionaries and dummy datasets
In R4EPI/msfdict: Epidemiology data dictionaries and random data generators

View source: R/msf_dict.R

msf_dict

R Documentation

MSF data dictionaries and dummy datasets

Description

These function produces MSF OCA dictionaries based on DHIS2 (for outbreaks) and Kobo (for surveys) data sets defining the data element name, code, short names, types, and key/value pairs for translating the codes into human-readable format.

Usage

msf_dict(
  disease,
  name = "MSF-outbreak-dict.xlsx",
  tibble = TRUE,
  compact = TRUE,
  long = TRUE
)

msf_dict_survey(
  disease,
  name = "MSF-survey-dict.xlsx",
  tibble = TRUE,
  compact = TRUE,
  long = TRUE,
  template = TRUE
)

Arguments

`disease`	Specify which disease you would like to use. `msf_dict()` supports "AJS", "Cholera", "Measles", "Meningitis" `msf_dict_survey()` supports "Mortality", "Nutrition", "Vaccination_long" and "Vaccination_short" (only used in surveys if `template = TRUE`)
`name`	the name of the dictionary stored in the package. `msf_dict_survey()` supports Kobo dictionaries not stored within this package, to use these: specify `name`as path to .xlsx file and set the `template = False`
`tibble`	Return data dictionary as a tidyverse tibble (default is TRUE)
`compact`	if `TRUE` (default), then a nested data frame is returned where each row represents a single variable and a nested data frame column called "options", which can be expanded with `tidyr::unnest()`. This only works if `long = TRUE`.
`long`	If `TRUE` (default), the returned data dictionary is in long format with each option getting one row. If `FALSE`, then two data frames are returned, one with variables and the other with content options. @param template Only used for `msf_dict_survey()`. If `TRUE` (default) the returned data dictionary is a generic MSF OCA ERB pre-approved dictionary. If `FALSE` allows you to read in your own Kobo dictionary by defining a path in `name`.
`template`	(for survey dictionaries): if `TRUE` read in a generic dictionary based on the MSF OCA ERB pre-approved template. However you can also specify your own dictionary if this differs substantially, by setting `template = FALSE` and defining a path in `name`.

Examples


if (require("dplyr") & require("matchmaker")) {
  withAutoprint({
    # You will often want to use MSF dictionaries to translate codes to human-
    # readable variables. Here, we generate a data set of 20 cases:
    dat <- gen_data(
      dictionary = "Cholera",
      varnames = "data_element_shortname",
      numcases = 20,
      org = "MSF"
    )
    print(dat)

    # We want the expanded dictionary, so we will select `compact = FALSE`
    dict <- msf_dict(disease = "Cholera", long = TRUE, compact = FALSE, tibble = TRUE)
    print(dict)

    # Now we can use matchmaker to filter the data:
    dat_clean <- matchmaker::match_df(dat, dict,
      from = "option_code",
      to = "option_name",
      by = "data_element_shortname",
      order = "option_order_in_set"
    )
    print(dat_clean)
  })
}

R4EPI/msfdict documentation built on June 15, 2025, 6:33 a.m.