study_ethnicity: Self-report Ethnicity Study Parameters

In icj/mecfun: MEC Microbiome Helpers

Description

Set global variables for the MEC Ethnicity paper

Usage

study_ethnicity(main_var = "Q1_eth",
  main_var_cols = viridis::viridis(5), main_cont = "",
  dir_out = "Output/Ethnicity", dir_dta = file.path(dir_out, "Data"),
  dir_dwn = file.path(dir_out, "Downloads"),
  dir_fig = file.path(dir_out, "Figures"), dir_tab = file.path(dir_out,
  "Tables"), study_filter = "mGWAS", study_title = "Ethnicity",
  sg = "ethnicity", q_cut = c(phylum = 0.05, genera = 0.05),
  zhern_cols = viridis::viridis(10), zhern_names = c("Demographics",
  "Alcohol", "Anthropometric measures", "Special diet",
  "Cultural foods & dietary components", "Dietary quality index",
  "Medical conditions", "Medications", "Physical activity", "Smoking"),
  run_code = FALSE, download_files = TRUE)

Arguments

main_var	Main study categorical variable
main_var_cols	Colors for main study varible
main_cont	Main study continuous variable
dir_out	Output directory
dir_dta	Output directory for data objects
dir_dwn	Output directory for downloadable files
dir_fig	Output directory for figures
dir_tab	Output directory for tables
study_filter	Study indicator for filtering to appropriate samples
study_title	Formal study title
sg	Lowercase study group name
q_cut	FDR cutoffs for phylum and genera
zhern_cols	Colors for Zhernakova categories
zhern_names	Names of Zhernakova categories
run_code	Run scripts during book build
download_files	Create downloadable file links

Value

Variables are saved to the global environment.

icj/mecfun documentation built on Nov. 4, 2019, 1:54 p.m.