rgeco: rgeco: R package for accessing the Generable API

In generable/rgeco: R package for accessing the Generable API

rgeco: R package for accessing the Generable API

Description

The Generable API is a HTTP REST API that provides access to data and inferences. The rgeco package provides convenient access to the information in the API in an R-friendly format.

Usage

xarray

Format

An object of class python.builtin.module (inherits from python.builtin.object) of length 0.

Setup

This package requires authentication to the Generable API before you can access data or inferences.

You can configure your login credentials as ENV variables by adding them to an .Renviron file in your project root.

The full list of ENV vars supported includes:

  GECO_API_USER=
  GECO_API_PASSWORD=
  GECO_API_URL=https://geco.generable.com
  GECO_API_PROJECT=
  GECO_API_PROJECT_VERSION=

However, only GECO_API_USER and GECO_API_PASSWORD are required.

Once your environment variables are set up, you can run login() to test authentication.

Data API

The data namespace provides access to study or project data stored in the Geco database.

Key methods for accessing these data are:

1. fetch_biomarkers: Fetch biomarkers data

2. fetch_subjects: Fetch subjects data

3. fetch_labs: Fetch labs data

4. fetch_pkpd: Fetch and format pkpd data from biomarkers data

5. list_biomarker_names: List biomarkers present in the data

Inference API

The inference namespace provides access to inferences from pre-computed model runs.

A model run is a model fit to a prepared analysis datasets.

Key methods for working with inferences are:

1. find_runs: List and search runs

2. fetch_dataset: Fetch analysis dataset (training data) used for the run

3. fetch_predicted_survival: Fetch inferences for predicted survival

4. fetch_predicted_biomarkers: Fetch inferences for predicted biomarkers

5. fetch_biomarker_params: Fetch inferences for biomarker-submodel parameters

6. fetch_hazard_betas: Fetch inferences for relative hazard according to covariates

7. fetch_predicted_hazard: Fetch inferences for predicted hazard over time

8. fetch_association_state: Fetch inferences for association state(s), linking biomarker model to hazard model

9. list_parameter_names: List and describe parameters available for a model run

10. list_predictive_names: List and describe predicted quantities available for a model run

11. fetch_draws: Fetch draws for any parameter or predicted quantity available for a model run

12. fetch_quantiles: Fetch quantiles for any parameter or predicted quantity available for a model run

generable/rgeco documentation built on Oct. 16, 2024, 2:45 a.m.