feat(smoking): Add smoking variable harmonization (CEP-002) #163
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Foundation for modular derived variable calculations: - clean_variables(): Step 1 & 3 preprocessing/validation - missing-data-functions.R: any_missing(), get_priority_missing() - missing-pattern-cache.R: Pattern detection for PUMF/Master codes - parse-range-notation.R: Range parsing for validation bounds - worksheet-getters.R: get_variable_details() metadata access - worksheet-loaders.R: load_worksheet_metadata() - file-sourcing.R: source_r_robust() for dependency loading - variable-discovery.R: Variable lookup utilities This infrastructure supports the new 3-step pattern: 1. clean_variables() - preprocess inputs 2. Domain logic - status-based calculations 3. clean_variables() - validate output bounds
Primary recommended variables using 3-step architecture: - smoking-status.R: calculate_SMKDSTY_A(), calculate_SMKDSTY_cat6() - smoke-start.R: calculate_age_start_smoking() - unified initiation age - smoking-cessation.R: calculate_time_quit_smoking() - years since quit - smoke-intensity.R: calculate_cigs_per_day() - routes SMK_204/SMK_208 - smoke-pack-years.R: calculate_pack_years() - cumulative exposure - smoke-stop.R: Supporting cessation logic - smoking-validation-constants.R: PACK_YEARS_CONSTANTS Key design decisions: - Single calculate_pack_years() works for both PUMF and Master - Unified feeders (age_start_smoking, cigs_per_day, time_quit_smoking) handle PUMF vs Master routing internally - PUMF has ~15-20% relative error due to midpoint estimation - Era-agnostic: handles 2001-2023 variable naming variations See ceps/cep-002-smoking/ for full specification.
Worksheets for smoking variable harmonization: - smoking_variables.csv: Variable definitions for smoking domain - smoking_variable_details.csv: Recoding rules and mappings Covers 5 subgroups: - 01-status: SMKDSTY_cat6 (6-category smoking status) - 02-initiation: age_start_smoking (age started daily) - 03-cessation: time_quit_smoking (years since quit) - 04-intensity: cigs_per_day (cigarettes per day) - 05-pack-years: pack_years_der (cumulative exposure) Supports all PUMF cycles 2001-2022.
Tests for primary recommended smoking variables: - test-age_start_smoking.R: Initiation age routing and bounds - test-cigs_per_day.R: Intensity routing by smoking status - test-pack_years.R: Cumulative exposure calculation - test-time_quit_smoking.R: Cessation timing validation Tests verify: - Correct routing based on SMKDSTY_A status - Valid output ranges per variable_details.csv bounds - Missing value handling (tagged_na vs numeric) - Universe validation (correct NA for out-of-scope respondents)
Quarto documentation for smoking variable harmonization: Main documents: - cep-002-smoking.qmd: Methodology and rationale - 00-variable-summary.qmd: Variable overview and recommendations - derived-functions.qmd: DV function specifications Subgroup specifications (QMD + worksheet CSVs): - 01-status: SMKDSTY_cat6 (6-category smoking status) - 02-initiation: age_start_smoking - 03-cessation: time_quit_smoking - 04-intensity: cigs_per_day - 05-pack-years: pack_years_der Rendered site: https://dmanuel.quarto.pub/cep-002-smoking-variables
Updates variables.csv and variable_details.csv with smoking harmonization: - 34 existing smoking variables updated with v3 definitions - 19 new smoking variables added - Extends coverage to 2022-2023 Master files - Adds unified feeder variables (age_start_smoking, cigs_per_day, etc.) Removes separate smoking_*.csv files (now merged into main worksheets). Variables: 360 → 379 (+19 new) Variable details: 3468 → 3678 (+210 net, replacing 500 with 710 improved rows)
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Pull request overview
This PR adds comprehensive smoking variable harmonization for CCHS cycles 2001-2023, implementing CEP-002. It introduces 19 new variables and updates 34 existing ones, extending coverage to Master files and establishing a new 3-step derived variable architecture.
Changes:
- New smoking variables across 5 subgroups (status, initiation, cessation, intensity, pack-years)
- Extended cycle coverage to PUMF 2001-2023 and Master 2001-2023
- New unified derived variable functions with standardized architecture
- Comprehensive test suite for derived variables
- Full CEP documentation in Quarto format
Reviewed changes
Copilot reviewed 38 out of 42 changed files in this pull request and generated no comments.
Show a summary per file
| File | Description |
|---|---|
| tests/testthat/test-time_quit_smoking.R | Unit tests for cessation timing calculation (337 lines) |
| tests/testthat/test-pack_years.R | Unit tests for pack-years derivation (386 lines) |
| tests/testthat/test-cigs_per_day.R | Unit tests for cigarettes per day routing (632 lines) |
| tests/testthat/test-age_start_smoking.R | Unit tests for initiation age calculation (353 lines) |
| ceps/cep-002-smoking/derived-functions.qmd | Function reference documentation (448 lines) |
| ceps/cep-002-smoking/cep-002-smoking.qmd | Main methodology and rationale (598 lines) |
| ceps/cep-002-smoking/05-pack-years.qmd | Pack-years variable documentation (276 lines) |
| ceps/cep-002-smoking/04-intensity.qmd | Intensity variable documentation (497 lines) |
| ceps/cep-002-smoking/03-cessation.qmd | Cessation variable documentation (555 lines) |
| ceps/cep-002-smoking/02-initiation.qmd | Initiation variable documentation (808 lines) |
| ceps/cep-002-smoking/00-variable-summary.qmd | Variable summary table (266 lines) |
| CSV worksheets (multiple) | Variable definitions and recoding rules |
| R/smoking-validation-constants.R | Validation constants for smoking functions |
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Jan 24, 2026
| "REP_5A","Repetitive strain injury - walking","Repetitive strain injury - type of activity - walking","Categorical","cchs2009_2010_p, cchs2010_p, cchs2011_2012_p, cchs2012_p, cchs2013_2014_p, cchs2014_p, cchs2015_2016_p, cchs2017_2018_p, cchs2009_s, cchs2010_s, cchs2012_s","cchs2015_2016_p::INJ_020A, cchs2017_2018_p::INJ_020A, [REP_5A]","Repetitive strain injury","Health status","N/A",NA,"","2.2.0","2025-06-30","Variable metadata completed","",NA,"active",NA | ||
| "REP_5B","Repetitive strain injury - sport/physical activity","Repetitive strain injury - type of activity - sports or physical exercise","Categorical","cchs2001_p, cchs2003_p, cchs2005_p, cchs2007_2008_p, cchs2009_2010_p, cchs2010_p, cchs2011_2012_p, cchs2012_p, cchs2013_2014_p, cchs2014_p, cchs2015_2016_p, cchs2017_2018_p, cchs2009_s, cchs2010_s, cchs2012_s","cchs2001_p::REPA_4A, cchs2003_p::REPC_4A, cchs2005_p::REPE_4A, cchs2007_2008_p::REP_4A, cchs2015_2016_p::INJ_020B, cchs2017_2018_p::INJ_020B, [REP_5B]","Repetitive strain injury","Health status","N/A",NA,"","2.2.0","2025-06-30","Variable metadata completed","",NA,"active",NA | ||
| "REP_5C","Repetitive strain injury - leisure/hobby","Repetitive strain injury - type of activity - leisure or hobby","Categorical","cchs2001_p, cchs2003_p, cchs2005_p, cchs2007_2008_p, cchs2009_2010_p, cchs2010_p, cchs2011_2012_p, cchs2012_p, cchs2013_2014_p, cchs2014_p, cchs2015_2016_p, cchs2017_2018_p, cchs2009_s, cchs2010_s, cchs2012_s","cchs2001_p::REPA_4B, cchs2003_p::REPC_4B, cchs2005_p::REPE_4B, cchs2007_2008_p::REP_4B, cchs2015_2016_p::INJ_020C, cchs2017_2018_p::INJ_020C, [REP_5C]","Repetitive strain injury","Health status","N/A",NA,"","2.2.0","2025-06-30","Variable metadata completed","",NA,"active",NA | ||
| "REP_5D","Repetitive strain injury - |
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SMK_09C (Years since stopped smoking daily - former daily) available as SMK_090 for 2015-2016 and 2017-2018
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Summary
Adds smoking variable harmonization for CCHS cycles 2001-2023, extending coverage to Master files and introducing unified derived variable functions using a new 3-step architecture.
Variables added (19 new)
cigs_per_day,SMK_202,SMK_203,SMK_207SMK_09A,SMK_10_gate,SMK_10A_A,SMK_10A_B,SMK_10A_cont,quit_pathwaySMKDSTY,SMKDGSTP,SMKDGSTP_cont,SMKDVSTPSMK_01C,SMK_040,SMK_06C,SMK_09C,SMKG09C_contVariables updated (34 existing)
variableStartmappings for era-specific source variable namespack_years_cat,pack_years_der,time_quit_smoking,SMKDSTY_A,SMKDSTY_B,SMKDSTY_cat3,SMKDSTY_cat5,SMKG040,SMKG040_cont,SMKG203_A/B/cont,SMKG207_A/B/cont,SMK_005,SMK_01A,SMK_030,SMK_05B,SMK_05C,SMK_05D,SMK_06A_A/B/cont,SMK_09A_A/B/cont,SMK_204,SMK_208,SMKG01C_A/B/cont,SMKG06C,SMKG09CCycle coverage
3-step derived variable architecture
New modular pattern for derived variables:
clean_variables()preprocesses and validates inputsSupporting infrastructure added:
R/clean-variables.R,R/missing-data-functions.R,R/missing-pattern-cache.RR/worksheet-getters.R,R/worksheet-loaders.R,R/variable-discovery.RTests added
test-age_start_smoking.Rtest-cigs_per_day.Rtest-pack_years.Rtest-time_quit_smoking.RDocumentation
Full specification: CEP-002 Smoking Variables
Source QMD files included in
ceps/cep-002-smoking/Test plan
R CMD checktestthat::test_file("tests/testthat/test-pack_years.R")