The raw data files are available in data/raw/. These files have a variety of formats between studies.
The cleaned data files are available in data/clean/. These files are consistently formatted across studies.
The rest of this document describes how to reproduce the data analysis and figures.
All data go into subfolders of this folder.
Open R/source_all.R and install all of the packages listed there.
Open make_paper.R. Assuming the working directory is the same as the directory containing this file, the file paths will all be correct. To reproduce the analysis, source make_paper.R. This will run code to:
It will take a while to run.
Questions? smhughes@uw.edu
data/ contains all of the data. The raw/ sub-directory contains the raw files and the clean/ subdirectory contains the files after processing. required_files/ contains other necessary files that are not data.figures/images contains the figuresmake_paper.R runs all the code necessary to reproduce the analysis and generate the functionsR/ contains code files
clean_*.R load and clean raw datamodel_data.R runs the mixed modelsmeta_analysis.R cleans the data from the other studies, runs the models on them, and performs the meta-analysisfigures.R generates the figuresgenerate_supplement.R creates the supplementary tablesget_data.R and functions_*.R load helper functionssource_all.R loads all the packages and helper functionstables.Rmd creates statistical tables used in writing the paperplot_each_analyte_meta-analysis_separately.Rmd creates several plots for each meta-analysisThe analysis for the paper was run using the following versions of R and the packages:
## - Session info -----------------------------------------------------------------------------------
## setting value
## version R version 4.0.0 (2020-04-24)
## os Windows 10 x64
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate English_United States.1252
## ctype English_United States.1252
## tz America/Los_Angeles
## date 2022-08-05
##
## - Packages ---------------------------------------------------------------------------------------
## package * version date lib source
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0)
## backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0)
## beeswarm 0.2.3 2016-04-25 [1] CRAN (R 4.0.0)
## boot 1.3-24 2019-12-20 [2] CRAN (R 4.0.0)
## broom 0.7.8 2021-06-24 [1] CRAN (R 4.0.5)
## cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.0)
## cli 3.0.0 2021-06-30 [1] CRAN (R 4.0.5)
## colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0)
## CompQuadForm 1.4.3 2017-04-12 [1] CRAN (R 4.0.0)
## crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0)
## DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0)
## dbplyr 1.4.3 2020-04-19 [1] CRAN (R 4.0.0)
## digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0)
## dplyr * 1.0.7 2021-06-18 [1] CRAN (R 4.0.5)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.5)
## evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0)
## fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0)
## forcats * 0.5.0 2020-03-01 [1] CRAN (R 4.0.0)
## fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.5)
## generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.5)
## ggbeeswarm * 0.6.0 2017-08-07 [1] CRAN (R 4.0.0)
## ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.0.5)
## glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0)
## gtsummary * 1.3.0 2020-04-17 [1] CRAN (R 4.0.0)
## haven 2.2.0 2019-11-08 [1] CRAN (R 4.0.0)
## here * 0.1 2017-05-28 [1] CRAN (R 4.0.0)
## hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0)
## htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.5)
## httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.5)
## janitor * 2.0.1 2020-04-12 [1] CRAN (R 4.0.0)
## jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.0.0)
## knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0)
## lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.0)
## lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.5)
## lme4 * 1.1-23 2020-04-07 [1] CRAN (R 4.0.0)
## lmerTest * 3.1-2 2020-04-08 [1] CRAN (R 4.0.0)
## lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.0.0)
## magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0)
## MASS 7.3-51.5 2019-12-20 [2] CRAN (R 4.0.0)
## mathjaxr 1.4-0 2021-03-01 [1] CRAN (R 4.0.5)
## Matrix * 1.3-4 2021-06-01 [1] CRAN (R 4.0.5)
## meta * 5.0-1 2021-10-20 [1] CRAN (R 4.0.5)
## metafor 3.0-2 2021-06-09 [1] CRAN (R 4.0.5)
## minqa 1.2.4 2014-10-09 [1] CRAN (R 4.0.0)
## modelr 0.1.7 2020-04-30 [1] CRAN (R 4.0.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0)
## nlme 3.1-147 2020-04-13 [2] CRAN (R 4.0.0)
## nloptr 1.2.2.1 2020-03-11 [1] CRAN (R 4.0.0)
## numDeriv 2016.8-1.1 2019-06-06 [1] CRAN (R 4.0.0)
## pander * 0.6.3 2018-11-06 [1] CRAN (R 4.0.0)
## patchwork * 1.0.0 2019-12-01 [1] CRAN (R 4.0.0)
## pillar 1.6.1 2021-05-16 [1] CRAN (R 4.0.5)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0)
## purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.0.0)
## R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0)
## Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.0.5)
## readr * 1.3.1 2018-12-21 [1] CRAN (R 4.0.0)
## readxl * 1.3.1 2019-03-13 [1] CRAN (R 4.0.0)
## reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.0)
## rlang 0.4.11 2021-04-30 [1] CRAN (R 4.0.5)
## rmarkdown * 2.1 2020-01-20 [1] CRAN (R 4.0.0)
## rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0)
## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.5)
## rvest 0.3.5 2019-11-08 [1] CRAN (R 4.0.0)
## scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.0)
## sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0)
## snakecase 0.11.0 2019-05-25 [1] CRAN (R 4.0.0)
## statmod 1.4.34 2020-02-17 [1] CRAN (R 4.0.0)
## stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0)
## stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.0)
## tibble * 3.1.2 2021-05-16 [1] CRAN (R 4.0.5)
## tidyr * 1.1.3 2021-03-03 [1] CRAN (R 4.0.5)
## tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.0)
## tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 4.0.0)
## utf8 1.1.4 2018-05-24 [1] CRAN (R 4.0.0)
## vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.0.5)
## vipor 0.4.5 2017-03-22 [1] CRAN (R 4.0.0)
## withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.5)
## xfun 0.13 2020-04-13 [1] CRAN (R 4.0.0)
## xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.0)
## yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0)
##
## [1] C:/Users/smhughes/Documents/R/win-library/4.0
## [2] C:/Program Files/R/R-4.0.0/library