Growthcleanr

Module 1	Introduction	Unit 1 CODI Introduction
Module 2	Getting Started	Unit 1 How to Use this Toolbox
Module 3	Audiences/Roles	Unit 1 Researchers	Unit 2 Network partners	Unit 3 Legal	Unit 4 Implementers	Unit 5 Participants
Module 4	People & Processes	Unit 1 CODI Approach	Unit 2 CODI Roles & Scope	Unit 3 Clinical and Community Linkages Assessment	Unit 4 Governance Model
Module 5	Standards	Unit 1 Data Models	Unit 2 FHIR Implementation Guides
Module 6	Tools	Unit 1 Growthcleanr	Unit 2 GrowthViz	Unit 3 CODI Prevalence Queries	Unit 4 Privacy Preserving Record Linkage	Unit 5 CODI Use Cases
Module 7	Implementations	Unit 1 CODI Implementations
Module 8	Resources	Unit 1 CODI References	Unit 2 CODI Resources
Module 9	Appendices	Unit 1 Appendix A: CODI Downloads

Who should use growthcleanr?

Anyone who wants to clean height and weight data from electronic health record (EHR) systems should use growthcleanr.

These roles use growthcleanr:

What is growthcleanr?

It is an R package with programs for cleaning height and weight data collected from electronic health record (EHR) systems. The tools support cleaning anthropometric measures for individuals 2 to 65 years of age.⁶ Height and weight measurements are critical for the study of conditions that rely on understanding children’s overall growth pattern. Unfortunately, these measurements are subject to data errors including swapped values, incorrect units and misplaced decimal points. All can result in messy data that muddle the child’s actual growth trajectory over time. The growthcleanr method helps prepare height and weight data sets for secondary uses such as research or surveillance.

Why use growthcleanr?

growthcleanr takes a manual process that typically takes months and automates the process into something that takes minutes or hours depending on the data and compute power. In addition, height and weight datasets from EHRs are often used to facilitate growth research; however, measurement and recording errors can lead to misleading results. growthcleanr offers an automated method for identifying biologically implausible values in pediatric EHR growth data.⁷

How to use growthcleanr

Details on how to get started and advanced topics can be found on the growthcleanr GitHub page. Select the correct growthcleanr version for the age group you are working with. To start running growthcleanr, an R installation with a variety of additional packages is required, as is a growth measurement dataset prepared for use in growthcleanr. growthcleanr also comes with a sample synthetic data set which can be used to learn the package and test the code.

Growthcleanr R Package

growthcleanr R package contains code, data and documentation that can be installed by users of R. This package processes data to identify biologically implausible height and weight measurements. Results from growthcleanr include a flag for each measurement indicating whether it is to be included or excluded based on plausibility, of specific types of exclusions identified distinctly. To run growthcleanr, an R installation is required. growthcleanr also comes with a sample synthetic data set which can be used to learn the package and test the code. To read more about the specifics of the growthcleanr R package, visit GitHub.

User videos

Watch a demonstration with a subject matter expert (SME) that introduces growthcleanr, a free and open-source program used to clean height/weight values from EHR data for ages 2-65.

View instructions on how to install growthcleanr, prepare your data, run the program, and review your results.