inst/doc/diseasystore-ecdc-respiratory-viruses.R

In diseasystore: Feature Stores for the 'diseasy' Framework

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(diseasystore)

## ----hidden_options, include = FALSE------------------------------------------
if (rlang::is_installed("withr")) {
  withr::local_options(
    "tibble.print_min" = 5,
    "diseasystore.verbose" = FALSE,
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.pull" = FALSE
  )
} else {
  opts <- options(
    "tibble.print_min" = 5,
    "diseasystore.verbose" = FALSE,
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.pull" = FALSE
  )
}

# We have a "hard" dependency for duckdb to render parts of this vignette
suggests_available <- rlang::is_installed("duckdb")
not_on_cran <- interactive() || identical(Sys.getenv("NOT_CRAN"), "true") ||
  identical(Sys.getenv("CI"), "true")

## ----download_data, eval = FALSE----------------------------------------------
# # First we set the path we want to use as an option
# options(
#   "diseasystore.DiseasystoreEcdcRespiratoryViruses.source_conn" =
#     file.path("local", "path")
# )
# 
# # Ensure folder exists
# source_conn <- diseasyoption("source_conn", "DiseasystoreEcdcRespiratoryViruses")
# if (!dir.exists(source_conn)) {
#   dir.create(source_conn, recursive = TRUE, showWarnings = FALSE)
# }
# 
# # Clone the repository
# system2(
#   "git",
#   args = c(
#     paste("-C", source_conn),
#     "clone https://github.com/EU-ECDC/Respiratory_viruses_weekly_data"
#   ),
#   stdout = TRUE
# )

## ----download_data_hidden, include = FALSE, eval = not_on_cran----------------
# In practice, it is best to make a local copy of the data which is
# stored in the "vignette_data" folder.
# This folder can either be in the package folder
# (preferred, please create the folder) or in the tempdir().
local_conn <- purrr::detect(
  "vignette_data",
  checkmate::test_directory_exists,
  .default = tempdir()
)

if (rlang::is_installed("withr")) {
  withr::local_options(
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.source_conn" = local_conn,
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.n_max" = 1000
  )
} else {
  opts <- c(
    opts,
    options(
      "diseasystore.DiseasystoreEcdcRespiratoryViruses.source_conn" = local_conn,
      "diseasystore.DiseasystoreEcdcRespiratoryViruses.n_max" = 1000
    )
  )
}

# Define the ECDC file to download
test_file <- "data/snapshots/2023-11-24_ILIARIRates.csv"

# Create folder and download file
dir.create(
  dirname(file.path(local_conn, test_file)),
  recursive = TRUE,
  showWarnings = FALSE
)

if (!file.exists(file.path(local_conn, test_file))) {
  remote_file <- source_conn_github(
    diseasyoption("remote_conn", "DiseasystoreEcdcRespiratoryViruses"),
    test_file
  )

  readr::read_csv(
    remote_file,
    n_max = 1000,
    show_col_types = FALSE,
    progress = FALSE
  ) |>
    readr::write_csv(file.path(local_conn, test_file))
}

# Check that the files are available after attempting to download
files_missing <- purrr::some(
  test_file,
  ~ !checkmate::test_file_exists(file.path(local_conn, .))
)
if (files_missing) {
  data_available <- FALSE
} else {
  data_available <- TRUE
}

## ----configure_diseasystore, eval = FALSE-------------------------------------
# # We define target_conn as a function that opens a DBIconnection to the DB
# target_conn <- \() DBI::dbConnect(duckdb::duckdb())
# options(
#   "diseasystore.DiseasystoreEcdcRespiratoryViruses.target_conn" = target_conn
# )

## ----configure_diseasystore_hidden, include = FALSE, eval = not_on_cran && suggests_available && data_available----
target_conn <- \() DBI::dbConnect(duckdb::duckdb())
if (rlang::is_installed("withr")) {
  withr::local_options(
    "diseasystore.DiseasystoreEcdcRespiratoryViruses.target_conn" = target_conn
  )
} else {
  opts <- c(
    opts,
    options(
      "diseasystore.DiseasystoreEcdcRespiratoryViruses.target_conn" = target_conn
    )
  )
}

## ----initializing_diseasystore, eval = not_on_cran && suggests_available && data_available----
ds <- DiseasystoreEcdcRespiratoryViruses$new()

## ----using_diseasystore_example_1, eval = not_on_cran && suggests_available && data_available----
# We can see all the available features in the feature store
ds$available_features

## ----using_diseasystore_example_2, eval = FALSE-------------------------------
# # Manually update the repository
# system2(
#   "git",
#   args = paste(
#     "-C",
#     diseasyoption("source_conn", "DiseasystoreEcdcRespiratoryViruses")
#   ),
#   stdout = TRUE
# )
# 
# # Disable automatic pulls
# options("diseasystore.DiseasystoreEcdcRespiratoryViruses.pull" = FALSE)

## ----using_diseasystore_example_3, eval = not_on_cran && suggests_available && data_available----
# And then retrieve a feature from the feature store
ds$get_feature(
  feature = "iliari_rates",
  start_date = as.Date("2023-01-01"),
  end_date = as.Date("2023-03-01")
)

## ----cleanup, include = FALSE-------------------------------------------------
if (exists("ds")) rm(ds)
gc()
if (!rlang::is_installed("withr")) {
  options(opts)
}