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eider

eider is an R package for extracting machine learning features from tabular data, in particular health records, in a declarative manner.

Features are specified as JSON objects which contain all the necessary information required to perform a given calculation. For example, the following calculates the number of total rows per patient id in the table labelled ae2 (details on how to specify this table are in the function documentation).

{
  "source_table": "ae2",
  "transformation_type": "COUNT",
  "grouping_column": "id",
  "absent_default_value": 0,
  "output_feature_name": "total_ae_attendances"
}

The output of this is a column named total_ae_attendances, containing the number of rows per patient, and with a value of 0 for any patients who do not appear in the ae2 table.

This declarative approach provides an alternative to traditional, imperative-style, dplyr pipelines which can be more difficult to reason about, especially when a series of features is being extracted and merged together. As features are specified without reference to a specific programming language or paradigm, it also encourages code that is concise, easy to read, and maintainable.

eider is a collaboration between The Alan Turing Institute, Public Health Scotland, and the Universities of Edinburgh and Durham. It grew out of a desire to generalise the feature extraction process for health data, specifically the SPARRA (Scottish Patients At Risk of Readmission and Admission) project (GitHub repo), and to allow similar analyses to be carried out in different contexts.

Installation

Install via CRAN:

Alternatively, install eider from its source code on GitHub using:

install.packages("devtools")
devtools::install_github("alan-turing-institute/eider", build_vignettes = TRUE)

Documentation

The package documentation is available online. In particular, the package articles contain a series of vignettes which provide detailed guidance on the package and its features.

Development

If you are making changes to the library itself, first clone the repository:

git clone git@github.com:alan-turing-institute/eider.git

You will need to install the lintr, pkgdown, devtools R packages to build documentation, run tests, and lint. Then, from the repository root, you can use the following commands:

  • make doc generates all function documentation, and also generates the README.md file from README.rmd
  • make lint lints the project directory
  • make test runs all tests

You can also use pre-commit to run all of these before committing, to ensure that you do not commit incomplete code. Firstly, install pre-commit according to the instructions on the webpage above. Then run pre-commit install.

What about vignettes? Well, building vignettes is slightly more complicated. You can perform a one-time build from the R console using pkgdown::build_site(), but running this every time you edit a file gets tiring quickly. To automate this, first install the package with make install, and install a working version of Python and also entr (the latter is available on Homebrew via brew install entr). Then run make vig: this will monitor your vignette RMarkdown files, rebuild the vignettes any time they are changed, and launch a HTTP server on port 8000 to view the files. If you change any library code you will have to run make install again before rerunning make vig.