sleep

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-# Note: Deprecated alcohol functions removed in v3.0.0 modernization
 export(COPD_Emph_der_fun1)
 export(COPD_Emph_der_fun2)
 export(DPSDPP)
@@ -10,9 +9,7 @@ export(LBFA_31A)
 export(LBFA_31A_a)
 export(LBFA_31A_b)
 export(RACDPAL_fun)
-# Note: Deprecated smoking functions removed in v3.0.0 modernization
 export(SPS_5_fun)
-# Note: SPU25_fun deprecated and removed
 export(active_transport1_fun)
 export(active_transport2_fun)
 export(active_transport3_fun)
@@ -21,12 +18,12 @@ export(adl_score_5_fun)
 export(adl_score_6_fun)
 export(age_cat_fun)
 export(assess_adl)
-export(assess_binge_drinking)
-export(assess_drinking_risk_long)
-export(assess_drinking_risk_short)
 export(calculate_bmi)
 export(calculate_energy_expenditure)
-export(categorize_bmi)
+export(calculate_pack_years)
+export(calculate_smoke_simple)
+export(calculate_smoking_status)
+export(calculate_time_quit_smoking)
 export(diet_score_fun)
 export(diet_score_fun_cat)
 export(energy_exp_fun)
@@ -38,28 +35,16 @@ export(is_equal)
 export(merge_rec_data)
 export(multiple_conditions_fun1)
 export(multiple_conditions_fun2)
-# Note: Deprecated pack years functions removed in v3.0.0 modernization
 export(pct_time_fun)
 export(pct_time_fun_cat)
-# Note: All preprocess functions removed from exports in v3.0.0
-# These are now internal functions used within derived variable functions
-# - preprocess_cchs_missing_codes() -> internal use only
-# - preprocess_smoking_variable() -> internal use only
-# - Deprecated pattern functions removed completely
 export(rec_with_table)
 export(resp_condition_fun1)
 export(resp_condition_fun2)
 export(resp_condition_fun3)
 export(score_adl)
 export(score_adl_6)
 export(set_data_labels)
-# Modernized v3.0.0 smoking functions
-export(calculate_smoking_status)
-export(calculate_time_quit_smoking)
-export(calculate_pack_years)
-export(calculate_smoke_simple)
 export(standardise_csv)
-# Note: Deprecated time_quit_smoking functions removed in v3.0.0 modernization
 export(validate_missing_code_preprocessing)
 importFrom(dplyr,do)
 importFrom(dplyr,rowwise)
@@ -70,4 +55,3 @@ importFrom(sjlabelled,"set_label<-")
 importFrom(sjlabelled,set_label)
 importFrom(sjlabelled,set_labels)
 importFrom(stringr,str_match)
-# Note: Legacy functions (adl_fun, bmi_fun, binge_drinker_fun, etc.) moved to R/legacy/ - no longer exported

ceps/cep-005-sleep/.gitignore

@@ -0,0 +1 @@
+/.quarto/

ceps/cep-005-sleep/L0_documentation_assessment.md

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+# L0 Documentation assessment: Sleep variables
+
+## Overview
+
+This document assesses the documentation and source data for sleep harmonization variables in the CCHS, supporting PR #161.
+
+## Variables in scope
+
+| Variable | Label | Type | Description |
+|----------|-------|------|-------------|
+| SLP_02 | Trouble sleeping | Categorical | Frequency of trouble going to sleep or staying asleep |
+| SLP_02_A | Trouble sleeping | Categorical | 2001 version (different scale) |
+| SLP_03 | Sleep refreshing | Categorical | Frequency of finding sleep refreshing |
+| SLP_03_A | Sleep refreshing | Categorical | 2001 version (different scale) |
+| SLP_04 | Difficulty awake | Categorical | Frequency of difficulty staying awake |
+| SLP_04_A | Difficulty awake | Categorical | 2001 version (different scale) |
+| SLPG01 | Hours sleep | Categorical | Hours spent sleeping each night (grouped) |
+| SLPG01_A | Hours sleep | Categorical | 2001/2007-2008 version |
+| SLPG01_B | Hours sleep | Categorical | Master file 2011-2014 |
+| SLPG01_C | Hours sleep | Categorical | Master file 2001/2015-2016 |
+| SLPG01_cont | Hours sleep | Continuous | Hours sleeping (continuous) |
+
+## PUMF availability by cycle
+
+| Cycle | Sleep hours | Trouble sleeping | Sleep refreshing | Difficulty awake |
+|-------|-------------|------------------|------------------|------------------|
+| 2001 | GENA_03 | GENA_04 | GENA_05 | GENA_06 |
+| 2003 | **NOT AVAILABLE** | **NOT AVAILABLE** | **NOT AVAILABLE** | **NOT AVAILABLE** |
+| 2005 | **NOT AVAILABLE** | **NOT AVAILABLE** | **NOT AVAILABLE** | **NOT AVAILABLE** |
+| 2007-2008 | SLP_01 | SLP_02 | SLP_03 | SLP_04 |
+| 2009-2010 | **NOT AVAILABLE** | **NOT AVAILABLE** | **NOT AVAILABLE** | **NOT AVAILABLE** |
+| 2011-2012 | SLPG01 | SLP_02 | SLP_03 | SLP_04 |
+| 2013-2014 | SLPG01 | SLP_02 | SLP_03 | SLP_04 |
+| 2015-2016 | SLPG005 | SLP_010 | SLP_015 | SLP_020 |
+| 2017-2018 | SLPG005 | SLP_010 | SLP_015 | SLP_020 |
+
+## Critical finding: Missing cycles
+
+**Sleep variables are NOT available in 2003, 2005, and 2009-2010 PUMF files.**
+
+This was verified by searching the DDI XML files for all sleep-related variable names. The sleep module was an optional content module that was not included in these cycles.
+
+## Scale differences
+
+### 2001 scale (3-point)
+For trouble sleeping (GENA_04), sleep refreshing (GENA_05), difficulty awake (GENA_06):
+- 1 = Most of the time
+- 2 = Sometimes
+- 3 = Never
+- 6 = Not applicable
+- 7 = Don't know
+- 8 = Refusal
+- 9 = Not stated
+
+### 2007+ scale (5-point)
+For SLP_02, SLP_03, SLP_04 (and renamed versions):
+- 1 = None of the time / Never
+- 2 = A little of the time / Rarely
+- 3 = Some of the time / Sometimes
+- 4 = Most of the time
+- 5 = All of the time
+- 6 = Valid skip / Not applicable
+- 7 = Don't know
+- 8 = Refusal
+- 9 = Not stated
+
+**Important:** The 2001 scale cannot be directly mapped to the 2007+ scale because:
+- 2001 has 3 substantive categories (most/sometimes/never)
+- 2007+ has 5 substantive categories (none/little/some/most/all)
+
+This explains why there are separate _A variables for 2001 - they cannot be harmonized to the same scale.
+
+## Hours sleep variable encoding
+
+### 2001 (GENA_03) - Continuous-ish
+- 1 = < 2 hours
+- 2 = 2 - < 3 hours
+- ...
+- 12 = >= 12 hours
+- 96 = Not applicable
+- 97 = Don't know
+- 98 = Refusal
+- 99 = Not stated
+
+### 2007-2008 (SLP_01) - Grouped
+Uses similar categorical encoding.
+
+### 2011-2018 (SLPG01, SLPG005) - Grouped
+Similar categorical encoding with hour ranges.
+
+## PR #161 review
+
+### Scope
+PR adds master file cycles to existing sleep variables:
+- SLP_02, SLP_03, SLP_04: Adding cchs2011_2012_m, cchs2013_2014_m, cchs2015_2016_m
+- SLP_02_A, SLP_03_A, SLP_04_A: Adding cchs2001_m
+- SLPG01_A: Adding cchs2001_p (already has cchs2007_2008_p), cchs2015_2016_m
+- SLPG01_B: New variable for cchs2011_2012_m, cchs2013_2014_m
+- SLPG01_cont: Adding master cycles
+
+### Issues identified
+
+1. **SLPG01_C variableStart reference**: Uses `cchs2015_2016_m::SLP_009` but need to verify this is the correct Master file variable name (PUMF uses SLPG005).
+
+2. **Scale consistency**: The PR correctly maintains separate _A variables for 2001 due to the scale difference.
+
+3. **Database name format**: Need to verify all database names follow the correct format (e.g., `cchs2011_2012_m` not `cchs_2011_2012_m`).
+
+## Recommendations
+
+1. Verify SLPG01_C source variable for 2015-2016 Master file
+2. Document the scale incompatibility between 2001 and later cycles in variable notes
+3. Add coverage note about 2003, 2005, 2009-2010 being unavailable
+
+## Sources reviewed
+
+- [x] cchs_available_variables_list.csv
+- [x] CCHS 2001 DDI
+- [x] CCHS 2015-2016 DDI
+- [x] Existing variables.csv
+- [x] PR #161 diff

ceps/cep-005-sleep/PR-notes.qmd

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+---
+title: "PR #161 review notes"
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)
+```
+
+## Summary
+
+PR #161 adds Master file cycles for sleep variables. The review found **no critical errors** requiring fixes. The worksheets correctly:
+1. Exclude cycles without sleep data (2003, 2005, 2009-2010)
+2. Handle scale incompatibility between 2001 (3-point) and 2007+ (5-point)
+3. Map era-specific source variable names correctly
+
+## Sleep variable availability
+
+| Cycle | PUMF sleep data | Notes |
+|-------|-----------------|-------|
+| 2001 | Yes | GENA_03-06; 3-point scale |
+| 2003 | **No** | Not in PUMF |
+| 2005 | **No** | Not in PUMF |
+| 2007-2008 | Yes | SLP_01-04; 5-point scale |
+| 2009-2010 | **No** | Not in PUMF |
+| 2011-2012 | Yes | SLPG01, SLP_02-04 |
+| 2013-2014 | Yes | SLPG01, SLP_02-04 |
+| 2015-2016 | Yes | SLPG005, SLP_010-020 |
+| 2017-2018 | Yes | SLPG005, SLP_010-020 |
+
+## Scale incompatibility
+
+The worksheets correctly handle the scale difference:
+
+- **2001 (3-point):** Most of the time / Sometimes / Never → harmonized to `SLP_02_A`, `SLP_03_A`, `SLP_04_A`
+- **2007+ (5-point):** None / A little / Some / Most / All → harmonized to `SLP_02`, `SLP_03`, `SLP_04`
+
+## Variable naming verified
+
+| Era | Hours | Trouble | Refreshing | Awake |
+|-----|-------|---------|------------|-------|
+| 2001 | GENA_03 | GENA_04 | GENA_05 | GENA_06 |
+| 2007-2008 | SLP_01 | SLP_02 | SLP_03 | SLP_04 |
+| 2011-2014 | SLPG01 | SLP_02 | SLP_03 | SLP_04 |
+| 2015-2018 | SLPG005 | SLP_010 | SLP_015 | SLP_020 |
+
+## Verification notes
+
+1. **SLPG01_C source variable (SLP_009):** The worksheet references `cchs2015_2016_m::SLP_009` for Master files. This is consistent with ICES naming conventions where individual hour categories use sequential SLP_XXX codes (SLP_007 = 3-4h, SLP_008 = 4-5h, SLP_009 = 5-6h, etc.), different from PUMF's grouped SLPG005 variable.
+
+2. **Missing cycles:** Verified via DDI XML grep that 2003, 2005, and 2009-2010 PUMF files do not contain sleep variables. The worksheets correctly exclude these cycles.
+
+## Recommendation
+
+**Approve and merge PR #161.** No worksheet fixes required.

ceps/cep-005-sleep/PR_NOTES.md

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+# PR #161 review notes: Sleep variables
+
+**Review date:** 2026-01-26
+**PR:** [#161 - Sleep variables](https://github.com/big-life-lab/cchsflow/pull/161)
+**Status:** Ready for merge
+
+## Summary
+
+PR #161 adds Master file cycles for sleep variables. The review found **no critical errors** requiring fixes. The worksheets correctly:
+
+1. Exclude cycles without sleep data (2003, 2005, 2009-2010)
+2. Handle scale incompatibility between 2001 (3-point) and 2007+ (5-point)
+3. Map era-specific source variable names correctly
+
+## Key findings
+
+### Sleep variable availability
+
+| Cycle | PUMF sleep data | Notes |
+|-------|-----------------|-------|
+| 2001 | Yes | GENA_03-06; 3-point scale |
+| 2003 | **No** | Not in PUMF |
+| 2005 | **No** | Not in PUMF |
+| 2007-2008 | Yes | SLP_01-04; 5-point scale |
+| 2009-2010 | **No** | Not in PUMF |
+| 2011-2012 | Yes | SLPG01, SLP_02-04 |
+| 2013-2014 | Yes | SLPG01, SLP_02-04 |
+| 2015-2016 | Yes | SLPG005, SLP_010-020 |
+| 2017-2018 | Yes | SLPG005, SLP_010-020 |
+
+### Scale incompatibility
+
+The worksheets correctly handle the scale difference:
+- **2001 (3-point):** Most of the time / Sometimes / Never → harmonized to `SLP_02_A`, `SLP_03_A`, `SLP_04_A`
+- **2007+ (5-point):** None / A little / Some / Most / All → harmonized to `SLP_02`, `SLP_03`, `SLP_04`
+
+### Variable naming verified
+
+| Era | Hours | Trouble | Refreshing | Awake |
+|-----|-------|---------|------------|-------|
+| 2001 | GENA_03 | GENA_04 | GENA_05 | GENA_06 |
+| 2007-2008 | SLP_01 | SLP_02 | SLP_03 | SLP_04 |
+| 2011-2014 | SLPG01 | SLP_02 | SLP_03 | SLP_04 |
+| 2015-2018 | SLPG005 | SLP_010 | SLP_015 | SLP_020 |
+
+## Verification notes
+
+1. **SLPG01_C source variable (SLP_009):** The worksheet references `cchs2015_2016_m::SLP_009` for Master files. This is consistent with ICES naming conventions where individual hour categories use sequential SLP_XXX codes (SLP_007 = 3-4h, SLP_008 = 4-5h, SLP_009 = 5-6h, etc.), different from PUMF's grouped SLPG005 variable.
+
+2. **Missing cycles:** Verified via DDI XML grep that 2003, 2005, and 2009-2010 PUMF files do not contain sleep variables. The worksheets correctly exclude these cycles.
+
+## Recommendation
+
+**Approve and merge PR #161.** No worksheet fixes required.
+
+## Related documentation
+
+- [L0_documentation_assessment.md](L0_documentation_assessment.md) - Detailed DDI review
+- [integration-test.qmd](integration-test.qmd) - rec_with_table() validation

ceps/cep-005-sleep/_publish.yml

@@ -0,0 +1,4 @@
+- source: project
+  quarto-pub:
+    - id: d4fca22b-634c-4b2a-b380-88696b5dc838
+      url: https://dmanuel.quarto.pub/cep-005-sleep-variables

ceps/cep-005-sleep/_quarto.yml

@@ -0,0 +1,22 @@
+project:
+  type: website
+  output-dir: _site
+
+website:
+  title: "CEP-005: Sleep variables"
+  navbar:
+    left:
+      - href: index.qmd
+        text: Home
+      - href: availability-matrix.qmd
+        text: Availability matrix
+      - href: integration-test.qmd
+        text: Integration test
+      - href: PR-notes.qmd
+        text: PR notes
+
+format:
+  html:
+    theme: cosmo
+    toc: true
+    code-fold: true