Adherence to Canada’s Food Guide and cardiovascular disease

This repository presents the analysis code for the study Greater adherence to the 2019 Canada’s Food Guide recommendations on healthy food choices reduces the risk of cardiovascular disease in adults: a prospective analysis of UK Biobank data published in the American Journal of Clinical Nutrition (Brassard et al., 2022a).

The general objective was to estimate the effect of adherence to Canada’s Food Guide recommendations on healthy food choices, measured using the HEFI-2019 (Brassard et al, 2022b, 2022c), on cardiovascular disease (CVD) risk in the UK Biobank prospective study.

1. Requirements and file structure

1.1 Data and software

The baseline covariate data (November 2020), original 24-h recall dietary intake data (July 2021), and outcome data (April 2021) of the UK Biobank were used, under application #25205.

The main analyses were executed in SAS (v9.4; maintenance release 9.04.01M7P08052020) in a Windows 10 64-bits environment. The manuscript file was successfully executed using RMarkdown and R (version 4.1.3) on macOS Big Sur 11.6.8 (64-bit; see complete session information details below).

1.2 SAS macros

SAS macros made by the National Cancer Institute (NCI) were used to perform measurement error correction (Zhang et al., 2011). The macros are available on the NCI website, but are included in the present repository in the /Macros/ folder.

• boxcox_survey.macro.v1.2.sas
• std_cov_boxcox24hr_conday_minamt_macro_v2.0.sas
• multivar_mcmc_macro_v2.1.sas
• multivar_distrib_macro_v2.1.sas
• percentiles_survey.macro.v1.1.sas

The HEFI-2019 scoring algorithm SAS macro hefi2019.scoring.macro.sas was used (available in a GitHub repository). Of note, the version in the present repository includes a very minor modification. Since beverages were reported in volume (ml) in the UK Biobank, the amount of unsweetened protein-rich beverages for 1 reference amount was set at 250 ml in the present study instead of 258g in the original macro (%let probev_gram_per_RA = 250; L143 of the modified macro).

1.3 Structure

Key steps of the main analysis are presented in separate .sas files. Each file would need to be executed in sequential order for successful execution. Raw UK Biobank file are not available publicly. However, the UK Biobank is an open access resource. Data described in the manuscript and code book are available upon request by registering and applying online (http://www.ukbiobank.ac.uk/register-apply).

In addition, summary statistics output of each step are provided. Thus, the 10_HEFI19CVD_Article.rmd RMarkdown file can be used to generate the manuscript including tables and figures based on summary statistics data. The 20_HEFI19CVD_OSM.rmd RMarkdown file generates the online supplementary material file.

Folders

• Macros: SAS macros (i.e., scripts) needed for main analysis based on .sas files 01 to 05;
• Manuscript: manuscript text, tables and figures generated by the RMarkdown files;
• NCI: results data generated by the NCI methods (see .sas files 01 to 05);
• Results: additional results data generated by various .sas codes (not shown) and manually-entered data for some supplementary tables.

2. Brief description

Complete details about analyses are provided in the article as well as in the online supplementary material.

Step 1. Distribution of HEFI-2019 score: estimation of population-level usual dietary intakes with the NCI multivariate methods to obtain distribution of HEFI-2019 score.

Step 2. Participant-level simulation: simulation of usual dietary intakes at the participant level with the NCI multivariate method to obtain measurement-error-corrected regression coefficients in outcome models.

Step 3. Inverse probability weighting: estimation of inverse probability of “treatment” weights, inverse probability of censoring weights, and combined weights to adjust for confounding and censoring.

Step 4. Outcome model: estimation of survival curves using energy-adjusted relationship between the total HEFI-2019 score based on usual intakes and incident CVD with Cox proportional hazards regression models.

Step 5. Bootstrap variance estimation: parametric bootstrap variance estimation using the 250 resampling to obtain confidence intervals.

10_HEFI19CVD_Article.Rmd: RMarkdown file to generate the text, tables and figures of the main manuscript. Tables and figures of the manuscript are generated in the /Manuscript/ folder.

20_HEFI19CVD_OSM.Rmd: RMarkdown file to generate the text, tables and figures of the online supplementary file. Tables and figures of the online supplementary file are generated in the /Manuscript/ folder.

3. References

Brassard D, Manikpurage HD, Thériault S, et al. Greater adherence to the 2019 Canada’s Food Guide recommendations on healthy food choices reduces the risk of cardiovascular disease in adults: a prospective analysis of UK Biobank data. Am J Clin Nutr 2022a. doi: 10.1093/ajcn/nqac256

Brassard D, Elvidge Munene LA, St-Pierre S, et al. Development of the Healthy Eating Food Index (HEFI)-2019 measuring adherence to Canada’s Food Guide 2019 recommendations on healthy food choices. Appl Physiol Nutr Metab 2022b;47:595-610. doi: 10.1139/apnm-2021-0415.

Brassard D, Elvidge Munene LA, St-Pierre S, et al. Evaluation of the Healthy Eating Food Index (HEFI)-2019 measuring adherence to Canada’s Food Guide 2019 recommendations on healthy food choices. Appl Physiol Nutr Metab 2022c;47(5):582-94. doi: 10.1139/apnm-2021-0416.

Zhang S, Midthune D, Guenther PM, et al. A New Multivariate Measurement Error Model with Zero-Inflated Dietary Data, and Its Application to Dietary Assessment. Ann Appl Stat 2011;5(2B):1456-87. doi: 10.1214/10-AOAS446.

Session Info

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## [1] "2022-09-19 10:54:22 EDT"

## R version 4.1.3 (2022-03-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur/Monterey 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] compiler_4.1.3  magrittr_2.0.3  fastmap_1.1.0   cli_3.3.0      
##  [5] tools_4.1.3     htmltools_0.5.3 rstudioapi_0.14 yaml_2.3.5     
##  [9] stringi_1.7.8   rmarkdown_2.16  knitr_1.40      stringr_1.4.1  
## [13] xfun_0.32       digest_0.6.29   rlang_1.0.4     evaluate_0.16