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Set up the folders and load polio data for the desk review

init_dr.Rd

Prepares the folders and files required for the desk review. The function primarily serves to organize the files used for the desk review and set standardized environmental variables (i.e., Sys.getenv(), where values for x related to the desk review is prefixed with "DR") . The function only supports running one country at a time.

Usage

init_dr(
  country_name,
  start_date = NULL,
  end_date = NULL,
  local_dr_folder = getwd(),
  lab_data_path = NULL,
  iss_data_path = NULL,
  attach_spatial_data = T,
  branch = "main",
  source = F,
  data_folder = "GID/PEB/SIR/Data",
  polis_folder = "GID/PEB/SIR/POLIS",
  use_edav = TRUE
)

Arguments

country_name

str Name of the country. You may pass multiple countries as a vector of strings.

start_date

str Start date of the desk review. If NULL, defaults to four years from when the function was ran on January 1st.

end_date

str End date of the desk review. If NULL, defaults to six weeks from when the function is ran.

local_dr_folder

str Folder where the desk review code is located. Defaults to the current working directory.

lab_data_path

str Location of the lab data. Defaults to NULL.

iss_data_path

str Location of the ISS data. Defaults to NULL.

attach_spatial_data

logical Whether to include spatial data. Defaults to TRUE.

branch

str What branch to download the DR functions from GitHub. "main" is the default, which contains the official version of the package. Other branches, like "dev" may contain experimental features not yet available in the "main" branch.

source

logical Whether to source local functions or use sirfunctions. Defaults to FALSE.

data_folder

str Location of the data folder containing pre-processed POLIS data, spatial files, coverage data, and population data. Defaults to "GID/PEB/SIR/Data".

polis_folder

str Location of the POLIS folder. Defaults to "GID/PEB/SIR/POLIS".

use_edav

logical Build raw data list using EDAV files. Defaults to TRUE.

Value

list A list containing all dataframe for all polio data.

Examples

if (FALSE) { # \dontrun{
ctry.data <- init_dr("algeria", source = F) # Sets up folder in the current working directory
ctry.data <- init_dr("algeria", branch = "dev") # Use functions from the dev branch
ctry.data <- init_dr(c("algeria", "nigeria"), source = F) # Multiple countries.
} # }