The Pandemic PACT monitors and analyses global funding and research evidence related to diseases with pandemic potential, as well as broader research preparedness efforts, and is equipped to pivot in response to outbreaks. It collects, curates, codes, and analyses data in alignment with WHO priority diseases and other selected illnesses, including pandemic influenza, mpox, and plague. Pandemic PACT aims to guide policy and decision-making for research funders, policymakers, researchers, multilateral agencies. The Pandemic PACT data is publicly available for download from its website and from Figshare. This package provides an application programming interface (API) to both the research programme’s Figshare repository and website data download facility to provide programmatic access to its publicly available tracker data along with its other data products.
What does {pactr} do?
pactr provides functions to interface programmatically with Pandemic PACT’s data products either through its Figshare repository or its website.
The functions for Figshare interface are wrappers to specific
functions of the {deposits}
package which provides the underlying universal interface to various
online research data deposition services including Figshare. Current
Figshare-specific functionalities available in pactr
are:
Listing of outputs/assets available from the Panedmic PACT Figshare repository (experimental);
Downloading of outputs/assets available from the Pandemic PACT Figshare repository (experimental);
Reading of dataset outputs/assets available from the Pandemic PACT Figshare repository (experimental); and,
Processing of Pandemic PACT data (experimental).
The functions for interfacing with the data available from the Pandemic PACT website allow for downloading, reading, and processing. Current website data-specific functionalities available in pactr are:
Downloading of Pandemic PACT dataset available from the website (stable);
Reading of Pandemic PACT dataset available from the website (stable); and,
Processing of Pandemic PACT dataset available from the website (experimental).
Why develop {pactr}?
The main motivation for the development of pactr is to create a standardised programmatic interface to Pandemic PACT’s data for those performing research or investigation relevant to Pandemic PACT’s objectives. Standardised programmatic interface, in turn, allows for reproducible scientific workflows that use the Pandemic PACT dataset.
The Pandemic PACT research programme is described as a “living mapping review” or LMR with a plan for six-monthly updates to the dataset. Robust analytical tools that enforces standardised and reproducible steps in interfacing (reading, processing, and analysing) with this dataset ensures comparability and consistency of outputs across various types of potential research and investigations using this dataset. Such tooling also contributes to reducing the time between research ideas to research insights and discovery.
The overall vision is that the pactr package development project will foster a community of researchers who primarily use R for their research analysis and who are or plan to work on and use the Pandemic PACT funding tracker dataset for their current or future research. In turn, the hope is that this community of researchers will engage in the package development through the following pathways:
-
Use of the pactr package in their research work and through the process:
- identify lacking functionalities; and/or,
- report bugs and errors that come up during use.
Contribute code to improve current functionalities and/or add new functionalities.
Contribute documentation of use cases and application of the package.
Host/initiate training sessions, discussions, and/or seminars on the use of the package in relation to research related to the Pandemic PACT funding tracker dataset.