29 lines
1.2 KiB
R
29 lines
1.2 KiB
R
#!/usr/bin/Rscript
|
|
getwd()
|
|
setwd("~/git/mosaic_2020/")
|
|
getwd()
|
|
########################################################################
|
|
# TASK: read data
|
|
########################################################################
|
|
# load libraries, packages and local imports
|
|
source("Header_TT.R")
|
|
########################################################################
|
|
# TODO: turn this to a repo
|
|
all_df <- read.csv("/home/pub/Work/MOSAIC/MOSAIC_from_work/MASTER/MOSAIC_2015_MASTER_Aki_stata_20150721/Mosaic_master_file_from_stata.csv"
|
|
, fileEncoding='latin1')
|
|
#hc_data<-
|
|
# meta data columns
|
|
meta_data_cols = c("mosaic", "gender", "age", "adult", "flustat", "type"
|
|
, "obesity", "obese2", "height", "height_unit", "weight"
|
|
, "weight_unit", "visual_est_bmi", "bmi_rating")
|
|
|
|
# check if these columns to select are present in the data
|
|
meta_data_cols%in%colnames(all_df)
|
|
all(meta_data_cols%in%colnames(all_df))
|
|
|
|
metadata_all = all_df[, meta_data_cols]
|
|
########################################################################
|
|
#
|
|
#outdir =
|
|
#outdir_plots =
|
|
outdir_stats = paste0("~/git/mosaic_2020/output/stats/")
|