rgeco

R client package for access to Generable compute (Geco) API. The API gives you access to the same data, inferences, and analytical summaries displayed in the application.

You must have a user account with Generable to use this package. See https://generable.com for more info or to request a demo.

Quick start for data

Install the package via remotes:

library(remotes)
remotes::install_github('generable/rgeco')

This package requires that Python be installed on your system, along with a Python library (xarray).

You can install these from R using reticulate:

For example:

reticulate::install_miniconda()
reticulate::py_install('xarray')

Note: if you're having trouble installing or configuring Python for R on your system, you might try the rminiconda package.

Now, we can login with your Generable credentials:

library(rgeco)
rgeco::login(user = 'user@email.com', password = 'yourpassword')

You can also save credentials in environment variables (GECO_API_USER and GECO_API_PASSWORD) for more reusable scripts.

List projects available:

projects <- list_projects()

Read subjects or biomarkers data for a project (replace demo with the name of a project you have access to)

subjects <- fetch_subjects(project = 'demo')
biomarkers <- fetch_biomarkers(project = 'demo', measurement_name = 'sld')

Read dosing data

doses <- fetch_doses(project = 'demo')

Read formatted PKPD data

measures <- list_biomarker_names(project = 'demo')
pkpd <- fetch_pkpd(project = 'demo', pd_measure = 'name_of_pd_measure', pk_measure = 'concentration')

List versions available for a project:

versions <- list_project_versions(project = 'demo')