---

Installation | Syntax | Examples | Feedback | Change log | Roadmap

---

Codefinder for Stata

(v1.00, 14 Jun 2024)

This repository contains the code required to install and run codefinder, a package that uses multiprocessing, associative arrays and optimised Mata functions to speed up many-to-many string matching in Stata. This can be used to identify the presence of lists of codes (e.g. ICD, SNOMED-CT, Read, Emis, etc) in variables containing data in string format. At present, codefinder has only been tested on Windows (10 and 11).

Installation

The package can be installed from GitHub using net install:

net install codefinder, from("https://raw.githubusercontent.com/jonathanbatty/stata-codefinder/main/installation/") replace

Syntax

Codefinder should be used with no data open in Stata. The syntax for codefinder is as follows:

codefinder varstosearch, dataset() codefiles() id() [options]

[options] = n_cores() summary

See the help file using help codefinder for full details of each option.

The basic usage is as follows:

codefinder dx*, dataset(".\data\patient_data.dta") codefiles("hypertension.txt diabetes.txt") id(id_var) n_cores(16)

Whereby the variables dx* (e.g. dx1, dx2, dx3, ... , dx_n) present in patient_data.dta will be searched for the diagnosis codes (strings) present in hypertension.txt and diabetes.txt (one code per line in each file). Each row of data should be identified using a unique identifier, id_var. Codefinder will run the string matching procedure using 16 CPU cores i this case. It will return a dataset in memory that includes id_var and a variable to indicate the presence of one or more codes from each text file in each initial observation (i.e. dx* in this case).

Examples

Examples of running codefinder using a simulated, synthetic dataset is provided in ./examples/.

Feedback

Please open an issue to report errors, suggest feature enhancements, and/or make any other requests.

Change Log

v1.01 (16/06/24)

• Minor bug fixes: installation now works with a single command.

v1.00 (14/06/24)

• Initial release.

Roadmap

• Test on Windows / Mac machines.
• Improvements in error reporting functionality: workers to flag errors to main Stata instance, which should handle these appropriately.
• Further incremental improvements to speed and stability.

Acknowledgements

JB received funding from the Wellcome Trust 4ward North Clinical Research Training Fellowship (227498/Z/23/Z; R127002).

Suggested Citation

Batty, J. A. (2024). Stata package ``codefinder'': efficient many-to-many string searching in Stata using multiprocessing (Version 1.0) [Computer software]. https://github.com/jonathanbatty/stata-codefinder