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Generate Directory Paths for the MOSAIC Project

Source: R/get_paths.R
get_paths.Rd

The get_paths() function generates a structured list of file paths for different data and document directories in the MOSAIC project, based on the provided root directory.

Usage

get_paths(root = NULL)

Arguments

root

A string specifying the root directory of the MOSAIC project; if NULL, getOption("root_directory") (see set_root_directory).

Value

A named list of paths, all built with file.path(root, ...):

ROOT

The root directory.

DATA_RAW, DATA_PROCESSED

MOSAIC-data/raw and MOSAIC-data/processed.

DATA_SCRAPE_WHO_VACCINATION

MOSAIC-data/raw/WHO/vaccination.

DATA_SCRAPE_WHO_WEEKLY, DATA_SCRAPE_GTFCC

WHO AWD and GTFCC scrapes under ees-cholera-mapping/data/cholera/.

DATA_DEM, DATA_EMDAT_RAW, DATA_IDMC_RAW

Raw inputs under MOSAIC-data/raw/ (DEM, EMDAT, IDMC).

DATA_SHAPEFILES, DATA_SIMILARITY_MATRIX, DATA_ELEVATION, DATA_ENSO, DATA_OAG, DATA_UNICEF, DATA_WORLD_BANK, DATA_DEMOGRAPHICS, DATA_WASH, DATA_SYMPTOMATIC, DATA_IMMUNITY, DATA_SUSPECTED, DATA_VACCINE_EFFECTIVENESS

Processed data under MOSAIC-data/processed/ (shapefiles, similarity_matrix, elevation, enso, OAG, UNICEF, world_bank, demographics, WASH, symptomatic, immunity, suspected_cases, vaccine_effectiveness).

DATA_CLIMATE, DATA_CLIMATE_DAILY

MOSAIC-data/processed/climate/weekly and .../climate/daily.

DATA_WHO_ANNUAL, DATA_WHO_WEEKLY, DATA_WHO_DAILY

MOSAIC-data/processed/WHO/ annual, weekly, daily.

DATA_JHU_WEEKLY, DATA_JHU_DAILY

MOSAIC-data/processed/JHU/weekly and .../daily.

DATA_SUPP_WEEKLY, DATA_SUPP_DAILY

Both MOSAIC-data/processed/SUPP/daily: the weekly supplemental file cholera_country_weekly_processed.csv is written and read there.

DATA_CHOLERA_WEEKLY, DATA_CHOLERA_DAILY, DATA_AI_WEEKLY

Combined surveillance under MOSAIC-data/processed/cholera/ (weekly, daily, ai/weekly).

DATA_GTFCC_VACCINATION

MOSAIC-data/processed/GTFCC/vaccination.

DATA_EMDAT, DATA_IDMC

MOSAIC-data/processed/EMDAT/weekly and .../IDMC/weekly.

ENSO_DATA_REPO, OPEN_METEO_REPO, AI_CHOLERA_REPO

Sibling repositories enso-data, open-meteo-pipeline, ai-cholera-data-mining.

MODEL_INPUT, MODEL_OUTPUT

MOSAIC-pkg/model/input and MOSAIC-pkg/model/output.

DOCS_FIGURES, DOCS_TABLES, DOCS_PARAMS

MOSAIC-docs/figures, tables, parameters.

Details

This function helps organize the directory structure for data and document storage in the MOSAIC project by generating paths for raw data, processed data, figures, tables, and parameters. The paths are returned as a named list and can be used to streamline the access to various project-related directories.

Examples

if (FALSE) { # \dontrun{
root_dir <- "/{full file path}/MOSAIC"
PATHS <- get_paths(root_dir)
print(PATHS$DATA_RAW)
} # }