subset-naomi-output-package.R

#' This script is an example of the function subset_output_package() to load,
#' subset, and resave the Naomi output package.
#'
#' The arguments to the function are:
#'
#' * path:             file path to the output package.
#' * output_path:      file path to save the new subsetted package (end in .zip).
#' * area_id:          vector of area_ids to keep or drop.
#' * area_level:       vector of area_levels to keep or drop.
#' * sex:              vector of sexes to keep or drop.
#' * age_group:        vector of age_groups to keep or drop.
#' * calendar_quarter: vector of calendar quarters to keep or drop.
#' * indicator:        vector of indicators to keep or drop
#' * drop:             TRUE/FALSE whether to drop the specified stratifications.
#' * check_list:       TRUE/FALSE check whether specified values are found (optional).

library(tidyverse)
library(sf)
library(zip)

source("https://raw.githubusercontent.com/mrc-ide/naomi/subset-output/R/outputs.R")
source("https://raw.githubusercontent.com/mrc-ide/naomi/subset-output/R/utils.R")

#' Example

digest_path <- "naomi_spectrum_digest_d64a7.zip",
subset_digest_path <- "nigeria_coarse_age_subset.zip"

age_groups_drop <- c("00-04", "05-09", "10-14", "15-19", "20-24", "25-29", "30-34", 
                     "35-39", "40-44", "45-49", "50-54", "55-59", "60-64", "65-69", 
                     "70-74", "75-79", "80+", "00-00", "01-04")

subset_output_package(digest_path, subset_digest_path,
                      age_group = age_groups_drop,
                      drop = TRUE)

subset_digest_path <- "nigeria_four_age_subset.zip"
age_groups_keep <- c("00-14", "15-24", "15-49", "50+")

subset_output_package(digest_path, subset_digest_path,
                      age_group = age_groups_keep,
                      drop = FALSE)