rabvRedcapProcessing

Tools for processing rabies metadata for REDCap upload

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Table of Contents

1. Introduction
2. Workflow
3. Installation
4. Bug Reports
5. Contributors

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Introduction

rabvRedcapProcessing is an R package designed to streamline the cleaning, validation, and formatting of rabies lab metadata before uploading to REDCap. It automates common curation tasks including:

• Matching data to a REDCap dictionary
• Handling common mismatches and blank fields
• Recoding labels to dictionary codes
• Creating REDCap-compatible repeat instruments (diagnostic and sequencing forms)

This ensures data consistency across multiple labs and minimizes manual formatting errors.

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Workflow

The typical workflow is illustrated below:

Function	Description	Input	Output
read_data()	Load and summarize input metadata	csv filePath	Data frame + duplicates report
read_and_parse_dict()	Load REDCap dictionary and extract coded lists	optional dictPath	List of mini dictionaries
compare_cols_to_dict()	Check for missing or extra columns vs REDCap dictionary	Data + optionaldictPath	Harmonized data frame
scan_mismatched_levels()	Scan for values that don’t match allowed dictionary codes	Data + col_to_check + dicts	Warnings to inform your manual processing (if necessary)
tidy_up_values()	Fix common value mismatches (e.g., typos, synonyms)	Data	Cleaned data
create_diagnostic_result_rule()	Derive final diagnostic result from test columns	Data	updated diagnostic_result(df)
recode_data()	Recode labels to dictionary codes	Data + dicts	Recoded data frame
final_processing()	Final formatting & generation of REDCap-ready forms	Data + optionaldictPath + access_group	Diagnostic + Sequencing forms

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Installation

Install directly from GitHub using devtools:

# install.packages("devtools") # if not already installed
devtools::install_github("RAGE-toolkit/rabvRedcapProcessing")
library(rabvRedcapProcessing)

Bug reports

Please report issues or suggest improvements via GitHub:

URL: https://github.com/RAGE-toolkit/rabvRedcapProcessing
BugReports: https://github.com/RAGE-toolkit/rabvRedcapProcessing/issues

Contributors

Martha M. Luka, Kirstyn Brunker