#!/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/")