Skip to main content
← Back to Software

setools

Time-Varying Data & Registries

Swedish registry toolkit (ICD expansion, migrations, MS progression, etc.)

. net install setools, from(...)
View on GitHub →

Version 1.2.1 | 2026-04-26

setools provides practical Stata commands for working with Swedish health registries. Instead of writing one-off data-management code for each new project, you get tested, documented building blocks for the steps that recur across register-based cohort studies: comorbidity scoring, procedure-code extraction, migration-based exclusions, and MS disability-progression endpoints.

The package covers three data shapes:

  1. Diagnosis-level data — cci_se computes the Swedish Charlson Comorbidity Index (ICD-7 through ICD-10).
  2. Procedure-level data — procmatch searches KVÅ procedure codes and extracts first-occurrence dates.
  3. Person-level cohort data — migrations applies migration-based exclusions and derives emigration censoring dates; sustainedss, cdp, and pira define MS disability-progression endpoints from repeated EDSS measurements.

Requirements

  • Stata 16 or later
  • Internet access if you want to run the _data/ example workflows below directly from GitHub

Installation

capture ado uninstall setools
net install setools, from("https://raw.githubusercontent.com/tpcopeland/Stata-Tools/main/setools") replace

Commands

Registry code utilities

Command Description
setools Package overview and command browser
cci_se Compute the Swedish Charlson Comorbidity Index from ICD-7 through ICD-10 data
procmatch Match KVÅ procedure codes and extract first-occurrence dates

Cohort construction

Command Description
migrations Apply migration-based exclusions and derive emigration censoring dates

Multiple sclerosis progression endpoints

Command Description
sustainedss Compute sustained EDSS threshold dates
cdp Compute confirmed disability progression dates from baseline EDSS
pira Classify confirmed progression as PIRA or relapse-associated worsening

How It Works

setools covers three distinct data shapes, and the right command depends on which one you have in memory:

  1. cci_se and procmatch work on long diagnosis-level or procedure-level registry data. cci_se can read one diagnosis variable or a list of diagnosis variables per row.
  2. migrations works on a person-level cohort in memory plus a separate migration file supplied in either wide in_#/out_# format or long event_date/event_type format.
  3. sustainedss, cdp, and pira work on repeated EDSS measurements, and pira also needs a relapse file.

Start with setools or setools, detail inside Stata if you want a menu-style overview before choosing a command.

Choosing the Right Command

If you need to... Use
Turn diagnosis codes into a Swedish Charlson score cci_se
Search one or more procedure variables for a KVÅ code set procmatch
Exclude people not resident in Sweden at study start and derive emigration censoring migrations
Find the first sustained EDSS threshold crossing sustainedss
Define confirmed disability progression from baseline EDSS cdp
Separate confirmed progression into PIRA versus relapse-associated worsening pira

Demo

Package overview

setools overview

Registry code utilities

cci_se — Swedish Charlson Comorbidity Index (click to expand)

cci_se output

procmatch — KVÅ procedure code matching (click to expand)

procmatch output

Cohort construction

migrations — migration exclusions and censoring (click to expand)

migrations output

MS disability progression

sustainedss — sustained EDSS progression (click to expand)

sustainedss output

cdp — confirmed disability progression (click to expand)

cdp output

pira — progression independent of relapse activity (click to expand)

pira output

Quick Start

Swedish Charlson Comorbidity Index

use "https://raw.githubusercontent.com/tpcopeland/Stata-Tools/main/_data/diagnoses.dta", clear
cci_se, id(id) icd(icd) date(visit_date) components noisily
summarize charlson

Use components to get individual comorbidity indicators alongside the total score. Use dates to also get the earliest diagnosis date per component.

Procedure code matching

use "https://raw.githubusercontent.com/tpcopeland/Stata-Tools/main/_data/procedures.dta", clear
procmatch match, codes("FNG02 FNG05") procvars(kva_code) generate(cardiac_proc) noisily
procmatch first, codes("FNG02 FNG05") procvars(kva_code) ///
    datevar(proc_date) idvar(id) generate(cardiac_ever) gendatevar(cardiac_dt)

Migration exclusions and censoring

migrations needs a local file path in migfile(). It accepts both wide in_#/out_# format and long event_date/event_type format. All date variables must be Stata daily dates with %td formats.

use "https://raw.githubusercontent.com/tpcopeland/Stata-Tools/main/_data/cohort.dta", clear
copy "https://raw.githubusercontent.com/tpcopeland/Stata-Tools/main/_data/migrations_wide.dta" "migrations_wide.dta", replace
migrations, migfile("migrations_wide.dta") startvar(study_entry) verbose

After migrations, excluded people are dropped and migration_out_dt is ready for use as a right-censoring date.

MS disability progression endpoints

use "https://raw.githubusercontent.com/tpcopeland/Stata-Tools/main/_data/relapses.dta", clear
sustainedss id edss edss_date, threshold(4) keepall
cdp id edss edss_date, dxdate(dx_date) keepall

pira requires a separate relapse file to classify progression as PIRA versus relapse-associated worsening:

copy "https://raw.githubusercontent.com/tpcopeland/Stata-Tools/main/_data/relapses_only.dta" "relapses_only.dta", replace
pira id edss edss_date, dxdate(dx_date) relapses("relapses_only.dta") keepall

Use confirmwindow() / confirmdays() when your study uses a different confirmation rule, and windowbefore() / windowafter() to adjust the relapse exclusion window.

Data Shape Notes

  • cci_se expects diagnosis-level long data with an ID, a date variable, and one or more diagnosis-code variables.
  • procmatch expects one or more procedure-code variables, and procmatch first also needs a date variable and subject ID.
  • migrations expects one row per person in memory plus a migration file in either wide in_#/out_# format or long event_date/event_type format.
  • sustainedss, cdp, and pira expect EDSS visits sorted within person by date.

References

  • Charlson ME, Pompei P, Ales KL, MacKenzie CR. A new method of classifying prognostic comorbidity in longitudinal studies: development and validation. Journal of Chronic Diseases. 1987;40(5):373-383.
  • Ludvigsson JF, Appelros P, Askling J, et al. Adaptation of the Charlson comorbidity index for register-based research in Sweden. Clinical Epidemiology. 2021;13:21-41.
  • Kappos L, et al. Inclusion of brain volume loss in a revised measure of no evidence of disease activity in relapsing-remitting multiple sclerosis. Multiple Sclerosis Journal. 2016;22(10):1297-1305.
  • Lublin FD, et al. Defining the clinical course of multiple sclerosis: the 2013 revisions. Neurology. 2014;83(3):278-286.

Version History

  • 1.2.1 (2026-04-26): Documentation improvements — richer help files for all Stata fluency levels, consistent cross-references across all commands, "Choosing the right command" guidance in the overview help file
  • 1.2.0 (2026-04-24): Added dates option to cci_se — generates earliest diagnosis date per comorbidity component alongside the binary indicators. Also includes the v1.1.0 Mata hash-table engine for faster ICD classification
  • 1.0.1 (2026-04-22): Added long-format migration-file support in migrations, enforced %td daily-date formats for migrations inputs, extended cci_se to accept multiple diagnosis variables in icd(), and expanded QA coverage for both features
  • 1.0.0 (2026-04-08): Initial Stata-Tools release of the Swedish registry toolkit

Author

Timothy P Copeland, Karolinska Institutet

License

MIT