ricu: download – R documentation

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download

Data download utilities

Description

Making a dataset available to ricu consists of 3 steps: downloading (download_src()), importing (import_src()) and attaching (attach_src()). While downloading and importing are one-time procedures, attaching of the dataset is repeated every time the package is loaded. Briefly, downloading loads the raw dataset from the internet (most likely in .csv format), importing consists of some preprocessing to make the data available more efficiently (by converting it to .fst format) and attaching sets up the data for use by the package.

Usage

download_src(x, data_dir = src_data_dir(x), ...)

## S3 method for class 'src_cfg'
download_src(
  x,
  data_dir = src_data_dir(x),
  tables = NULL,
  force = FALSE,
  user = NULL,
  pass = NULL,
  ...
)

Arguments

`x`	Object specifying the source configuration
`data_dir`	Destination directory where the downloaded data is written to.
`...`	Generic consistency
`tables`	Character vector specifying the tables to download. If `NULL`, all available tables are downloaded.
`force`	Logical flag; if `TRUE`, existing data will be re-downloaded
`user, pass`	PhysioNet credentials; if `NULL` and environment variables `RICU_PHYSIONET_USER`/`RICU_PHYSIONET_PASS` are not set, user input is required

Details

Downloads by ricu are focused data hosted by PhysioNet and tools are currently available for downloading the datasets MIMIC-III, eICU and HiRID (see data). While credentials are required for downloading any of the three datasets, demo dataset for both MIMIC-III and eICU are available without having to log in. Even though access to full dataset is credentialed, the datasets are in fact publicly available. For setting up an account, please refer to the registration form.

PhysioNet credentials can either be entered in an interactive session, passed as function arguments user/pass or as environment variables RICU_PHYSIONET_USER/RICU_PHYSIONET_PASS. For setting environment variables on session startup, refer to base::.First.sys() and for setting environment variables in general, refer to base::Sys.setenv() If the openssl package is available, SHA256 hashes of downloaded files are verified using openssl::sha256().

Demo datasets MIMIC-III demo and eiCU demo can either be installed as R packages directly by running

install.packages(
  c("mimic.demo", "eicu.demo"),
  repos = "https://septic-tank.github.io/physionet-demo"
)

or downloaded and imported using download_src() and import_src(). Furthermore, ricu specifies mimic.demo and eicu.demo as Suggests dependencies therefore, passing dependencies = TURE when calling install.packages() for installing ricu, this will automatically install the demo datasets as well.

While the included data downloaders are intended for data hosted by PhysioNet, download_src() is an S3 generic function that can be extended to new classes. Method dispatch is intended to occur on objects that inherit from or can be coerced to src_cfg. For more information on data source configuration, refer to load_src_cfg().

Value

Called for side effects and returns NULL invisibly.

Examples

## Not run: 

dir <- tempdir()
list.files(dir)

download_datasource("mimic_demo", data_dir = dir)
list.files(dir)

unlink(dir, recursive = TRUE)


## End(Not run)

ricu

Intensive Care Unit Data with R

v0.1.3

GPL-3

Authors

Nicolas Bennett [aut, cre], Drago Plecko [aut], Ida-Fong Ukor [aut]

Initial release