Automating incidence and prevalence analysis in open cohorts

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发表日期：

2024年7月4日

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Neil Cockburn,
Ben Hammond,
Illin Gani,
Samuel Cusworth,
Aditya Acharya,
Krishna Gokhale,
Rasiah Thayakaran,
Francesca Crowe,
Sonica Minhas,
William Parry Smith,
Beck Taylor,
Krishnarajah Nirantharakumar,
Joht Singh Chandan

摘要

Motivation

Data is increasingly used for improvement and research in public health, especially administrative data such as that collected in electronic health records. Patients enter and exit these typically open-cohort datasets non-uniformly; this can render simple questions about incidence and prevalence time-consuming and with unnecessary variation between analyses. We therefore developed methods to automate analysis of incidence and prevalence in open cohort datasets, to improve transparency, productivity and reproducibility of analyses.

Implementation

We provide both a code-free set of rules for incidence and prevalence that can be applied to any open cohort, and a python Command Line Interface implementation of these rules requiring python 3.9 or later.

General features

The Command Line Interface is used to calculate incidence and point prevalence time series from open cohort data. The ruleset can be used in developing other implementations or can be rearranged to form other analytical questions such as period prevalence.

Availability

The command line interface is freely available from https://github.com/THINKINGGroup/analogy_publication.