Pregnancy Exposure to Phenols and Anthropometric Measures in Gestation and at Birth

Article info

Repository contains reproducible analyses for the paper: Jedynak et al., 2022.

Analysis overview

Analyses depend on R (>= 4.2.0).

Code used to produce the files is found in the corresponding files: jedynak_pregnancy_2022_Epidemiology.Rmd and jedynak_pregnancy_2022_supplement_Epidemiology.Rmd (executable files).

The corresponding knitted files are: phenols_growth.html and phenols_growth.html (read-only files).

This analysis was performed under Windows 10 x64 (build 19041) using:

• R 4.2.2 (2022-11-01)
• renv 0.15.0 dependency management package

Packages

All packages used in the analyses are saved in the renv/library/R-4.2/x86_64-w64-mingw32 folder at the version used to produce these results, under control of the renv package manager. Re-running the analysis requires execution of renv::restore() which will upgrade/ downgrade user's packages to the versions used in the present study. This operation will modify the packages only locally (for the project), so it will not affect user's package library.

To run

Re-running the analysis requires an additional data/raw_data folder that is not shared here. These data can only be provided upon request and after approval by the SEPAGES consortium (contact: Sarah Lyon-Caen). Running two scripts: jedynak_pregnancy_2022_Epidemiology.Rmd and jedynak_pregnancy_2022_supplement_Epidemiology.Rmd will allow to fully reproduce the analysis.

Repo organization

data/raw_data folder

Analysis input data-files are not made available as they contain sensitive information. The analysis input data files would be:

• bdd_grossesse_v4_1.dta = dataset containing information on the anthropometric measures (digital ultrasound and measures collected at birth), n = 484
• phenols_phthalates_pregnancy_mr_2020-03-26_448.csv = dataset containing information on phenols exposure, n = 479
• tobaccopregnancy_ag_20201218_16_copy.dta = dataset containing information on smoking during pregnancy, n = 484
• donnees_echo_saisies_quest_mt1caj1.dta = dataset containing manual ultrasound data, n = 38
• limits_data_2022-01-24.csv = dataset containing information on LOD and LOQ values for each phenol

results/ folder

It contains figures and tables subfolders as well as results obtained in the main analyses

R/ folder

This folder contains all the source files and functions used for the analyses.

Session info

R version 4.2.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_Europe.utf8 
[2] LC_CTYPE=English_Europe.utf8   
[3] LC_MONETARY=English_Europe.utf8
[4] LC_NUMERIC=C                   
[5] LC_TIME=English_Europe.utf8    

attached base packages:
[1] stats     graphics  grDevices datasets 
[5] utils     methods   base     

other attached packages:
 [1] Hmisc_4.7-2     Formula_1.2-4  
 [3] survival_3.4-0  lattice_0.20-45
 [5] ggpubr_0.5.0    magrittr_2.0.3 
 [7] forcats_0.5.2   stringr_1.5.0  
 [9] dplyr_1.1.0     purrr_0.3.5    
[11] readr_2.1.3     tidyr_1.1.0    
[13] tibble_3.1.8    ggplot2_3.4.0  
[15] tidyverse_1.2.0

loaded via a namespace (and not attached):
 [1] colorspace_2.0-3    ggsignif_0.6.4     
 [3] deldir_1.0-6        ellipsis_0.3.2     
 [5] rprojroot_2.0.3     flextable_0.8.3    
 [7] htmlTable_2.4.1     base64enc_0.1-3    
 [9] rstudioapi_0.14     mice_3.15.0        
[11] farver_2.1.0        bit64_4.0.5        
[13] fansi_1.0.3         lubridate_1.9.0    
[15] xml2_1.3.3          splines_4.2.3      
[17] knitr_1.41          jsonlite_1.8.4     
[19] broom_0.8.0         cluster_2.1.4      
[21] png_0.1-8           compiler_4.2.3     
[23] httr_1.4.4          backports_1.4.1    
[25] Matrix_1.5-3        fastmap_1.1.0      
[27] cli_3.4.1           htmltools_0.5.3    
[29] tools_4.2.3         gtable_0.3.1       
[31] glue_1.6.2          Rcpp_1.0.8.3       
[33] carData_3.0-5       cellranger_1.1.0   
[35] vctrs_0.5.2         writexl_1.4.1      
[37] svglite_2.1.0       xfun_0.35          
[39] rvest_1.0.3         timechange_0.1.1   
[41] lifecycle_1.0.3     renv_0.15.0        
[43] rstatix_0.7.1       scales_1.2.1       
[45] vroom_1.6.0         ragg_1.2.5         
[47] hms_1.1.2           parallel_4.2.3     
[49] RColorBrewer_1.1-3  HardyWeinberg_1.7.5
[51] yaml_2.3.6          gridExtra_2.3      
[53] gdtools_0.2.4       rpart_4.1.19       
[55] latticeExtra_0.6-30 stringi_1.7.6      
[57] checkmate_2.1.0     zip_2.2.2          
[59] truncnorm_1.0-8     chron_2.3-58       
[61] rlang_1.0.6         pkgconfig_2.0.3    
[63] systemfonts_1.0.4   Rsolnp_1.16        
[65] evaluate_0.18       labeling_0.4.2     
[67] compareGroups_4.6.0 htmlwidgets_1.5.4  
[69] bit_4.0.5           tidyselect_1.2.0   
[71] here_1.0.1          R6_2.5.1           
[73] generics_0.1.2      pillar_1.8.1       
[75] haven_2.5.1         foreign_0.8-84     
[77] withr_2.5.0         abind_1.4-5        
[79] nnet_7.3-18         modelr_0.1.8       
[81] crayon_1.5.2        car_3.0-12         
[83] uuid_1.1-0          interp_1.1-3       
[85] utf8_1.2.2          tzdb_0.3.0         
[87] rmarkdown_2.18      officer_0.4.4      
[89] jpeg_0.1-10         grid_4.2.3         
[91] readxl_1.4.1        data.table_1.14.6  
[93] digest_0.6.30       webshot_0.5.4      
[95] textshaping_0.3.6   munsell_0.5.0      
[97] viridisLite_0.4.1   kableExtra_1.3.4