Package: chmsflow 0.1.0

Rafidul Islam

chmsflow: Transforming and Harmonizing CHMS Variables

Harmonizes variables from the Canadian Health Measures Survey (CHMS) across cycles 1-6 (2007-2019), producing consistent, analysis-ready variables for use with CHMS data. Recoding is data-driven through metadata tables and applied with recodeflow::rec_with_table() from the 'recodeflow' package. The recoding approach builds on sjmisc::rec() from the 'sjmisc' package (Ludecke 2018) <doi:10.21105/joss.00754>.

Authors:Rafidul Islam [aut, cre, cph], Douglas Manuel [aut, cph], Therese Chan [ctb], The Ottawa Hospital Research Institute [cph]

chmsflow_0.1.0.tar.gz
chmsflow_0.1.0.tar.gz(r-4.7-any)chmsflow_0.1.0.tar.gz(r-4.6-any)
chmsflow_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
chmsflow/json (API)
NEWS

# Install 'chmsflow' in R:
install.packages('chmsflow', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/big-life-lab/chmsflow/issues

Pkgdown/docs site:https://big-life-lab.github.io

Datasets:
  • cycle1 - Canadian Health Measures Survey (CHMS) Cycle 1
  • cycle1_meds - Canadian Health Measures Survey (CHMS) Cycle 1 Medications
  • cycle2 - Canadian Health Measures Survey (CHMS) Cycle 2
  • cycle2_meds - Canadian Health Measures Survey (CHMS) Cycle 2 Medications
  • cycle3 - Canadian Health Measures Survey (CHMS) Cycle 3
  • cycle3_meds - Canadian Health Measures Survey (CHMS) Cycle 3 Medications
  • cycle4 - Canadian Health Measures Survey (CHMS) Cycle 4
  • cycle4_meds - Canadian Health Measures Survey (CHMS) Cycle 4 Medications
  • cycle5 - Canadian Health Measures Survey (CHMS) Cycle 5
  • cycle5_meds - Canadian Health Measures Survey (CHMS) Cycle 5 Medications
  • cycle6 - Canadian Health Measures Survey (CHMS) Cycle 6
  • cycle6_meds - Canadian Health Measures Survey (CHMS) Cycle 6 Medications
  • variable_details - Variable-details.csv
  • variables - Variables.csv

On CRAN:

Conda:

quarto

3.65 score 8 scripts 46 exports 37 dependencies

Last updated from:94ab7c7261. Checks:4 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK142
source / vignettesOK232
linux-release-x86_64OK148
wasm-releaseOK127

Exports:adjust_dbpadjust_sbpaggregate_meds_by_personcalculate_exercise_daily_avgcalculate_exercise_weeklycalculate_fv_daily_cycles1to2calculate_fv_daily_cycles3to6calculate_gfrcalculate_household_incomecalculate_nonhdlcalculate_pack_yearscalculate_waist_height_ratiocategorize_ckdcategorize_diet_qualitycategorize_exercisecategorize_income_quintilecategorize_nonhdlderive_alcohol_riskderive_alcohol_risk_detailedderive_cvd_family_historyderive_cvd_personal_historyderive_diabetes_statusderive_hypertensionderive_hypertension_adjderive_hypertension_controlderive_hypertension_control_adjis_ace_inhibitoris_ace_med_cycles1to2is_any_antihtn_medis_any_htn_med_cycles1to2is_bb_med_cycles1to2is_beta_blockeris_calcium_channel_blockeris_ccb_med_cycles1to2is_diab_med_cycles1to2is_diabetes_medis_diur_med_cycles1to2is_diureticis_lowest_income_quintileis_misc_htn_med_cycles1to2is_nsaidis_nsaid_med_cycles1to2is_other_antihtn_medrecode_after_medsrecode_meds_cycles1to2recode_meds_cycles3to6

Dependencies:bitbit64clicliprcpp11crayondatawizarddplyrforcatsgenericsgluehavenhmsinsightlifecyclemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrrecodeflowrlangsjlabelledstringistringrtibbletidyrtidyselecttzdbutf8vctrsvroomwithrXML

Analysis walkthrough: hypertension prevalence

Rendered fromanalysis_walkthrough.qmdusingquarto::htmlon Jun 08 2026.

Last update: 2026-06-08
Started: 2026-06-08

Derived variables

Rendered fromderived_variables.qmdusingquarto::htmlon Jun 08 2026.

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Get started

Rendered fromget_started.qmdusingquarto::htmlon Jun 08 2026.

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How to add variables to chmsflow

Rendered fromhow_to_add_variables.qmdusingquarto::htmlon Jun 08 2026.

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Methodology

Rendered frommethodology.qmdusingquarto::htmlon Jun 08 2026.

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Missing data (tagged_na)

Rendered fromtagged_na_usage.qmdusingquarto::htmlon Jun 08 2026.

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Recoding CHMS medication variables

Rendered fromrecoding_medications.qmdusingquarto::htmlon Jun 08 2026.

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Using chmsflow at an RDC

Rendered fromusing_chmsflow_at_an_rdc.qmdusingquarto::htmlon Jun 08 2026.

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Variable schema reference

Rendered fromvariables_and_variable_details.qmdusingquarto::htmlon Jun 08 2026.

Last update: 2026-06-08
Started: 2026-06-08

Readme and manuals

Help Manual

Help pageTopics
Adjusted diastolic blood pressureadjust_dbp
Adjusted systolic blood pressureadjust_sbp
Aggregate medication variables to one row per personaggregate_meds_by_person
Average daily minutes of moderate-to-vigorous physical activity (MVPA) from accelerometer datacalculate_exercise_daily_avg
Weekly minutes of moderate-to-vigorous physical activity (MVPA) from daily averagecalculate_exercise_weekly
Daily fruit and vegetable consumption in a year - cycles 1-2calculate_fv_daily_cycles1to2
Daily fruit and vegetable consumption in a year - cycles 3-6calculate_fv_daily_cycles3to6
Estimated glomerular filtration rate (GFR)calculate_gfr
Adjusted total household incomecalculate_household_income
Non-HDL cholesterol levelcalculate_nonhdl
Smoking pack-yearscalculate_pack_years
Waist-to-height ratio (WHtR)calculate_waist_height_ratio
Chronic kidney disease (CKD) derived variablecategorize_ckd
Categorical diet indicatorcategorize_diet_quality
Categorical weekly moderate-to-vigorous physical activity (MVPA) indicatorcategorize_exercise
Categorical adjusted household incomecategorize_income_quintile
Categorical non-HDL cholesterol levelcategorize_nonhdl
Canadian Health Measures Survey (CHMS) Cycle 1cycle1
Canadian Health Measures Survey (CHMS) Cycle 1 Medicationscycle1_meds
Canadian Health Measures Survey (CHMS) Cycle 2cycle2
Canadian Health Measures Survey (CHMS) Cycle 2 Medicationscycle2_meds
Canadian Health Measures Survey (CHMS) Cycle 3cycle3
Canadian Health Measures Survey (CHMS) Cycle 3 Medicationscycle3_meds
Canadian Health Measures Survey (CHMS) Cycle 4cycle4
Canadian Health Measures Survey (CHMS) Cycle 4 Medicationscycle4_meds
Canadian Health Measures Survey (CHMS) Cycle 5cycle5
Canadian Health Measures Survey (CHMS) Cycle 5 Medicationscycle5_meds
Canadian Health Measures Survey (CHMS) Cycle 6cycle6
Canadian Health Measures Survey (CHMS) Cycle 6 Medicationscycle6_meds
Low risk drinking scorederive_alcohol_risk
Low risk drinking score - former/never categoriesderive_alcohol_risk_detailed
Cardiovascular Disease (CVD) family historyderive_cvd_family_history
Cardiovascular disease (CVD) personal historyderive_cvd_personal_history
Diabetes derived variablederive_diabetes_status
Hypertension derived variablederive_hypertension
Hypertension derived variable with adjusted blood pressuresderive_hypertension_adj
Controlled hypertension derived variablederive_hypertension_control
Controlled hypertension derived variable with adjusted blood pressuresderive_hypertension_control_adj
ACE inhibitorsis_ace_inhibitor
ACE inhibitors - cycles 1-2is_ace_med_cycles1to2
Any anti-hypertensive medicationsis_any_antihtn_med
Any anti-hypertensive medications - cycles 1-2is_any_htn_med_cycles1to2
Beta blockers - cycles 1-2is_bb_med_cycles1to2
Beta blockersis_beta_blocker
Calcium channel blockersis_calcium_channel_blocker
Calcium channel blockers - cycles 1-2is_ccb_med_cycles1to2
Diabetes medications - cycles 1-2is_diab_med_cycles1to2
Diabetes medicationsis_diabetes_med
Diuretics - cycles 1-2is_diur_med_cycles1to2
Diureticsis_diuretic
Lowest income quintile indicatoris_lowest_income_quintile
Other anti-hypertensive medications - cycles 1-2is_misc_htn_med_cycles1to2
Non-steroidal anti-inflammatory drugs (NSAIDs)is_nsaid
Non-steroidal anti-inflammatory drugs (NSAIDs) - cycles 1-2is_nsaid_med_cycles1to2
Other anti-hypertensive medicationsis_other_antihtn_med
Recode variables that depend on derived medication variable inputsrecode_after_meds
Recode medication variables for cycles 1-2 (wide format)recode_meds_cycles1to2
Recode medication variables for cycles 3-6 (long format)recode_meds_cycles3to6
variable-details.csvvariable_details
variables.csvvariables