Formatting and Combining Labs, Non-Labs, and Encounters

After you have done the preliminary operations, complete the following to work to with these on your computer.

1)format all three files - FLOWSHEETVALUEFACT files, labs, and encounters. (Formatting.R)
  a) format your FLOWSHEETVALUEFACT table
  b) format your labs table
  c) format your encounters table
  d) add Non_LONICs to labs
  e) parse as different patients
    i) there are some problems with reading the names.
    ii) sometimes they are read in scientific notation.
    iii) this is < 2% of the labs. None of the non-LOINCed values have this problem.
  f) now everything is combined.
  
  
Examples:

var_key <- read.csv("FLOWSHEETROWDIM.txt copy2.txt",sep ='!')
tp <- read.csv("Pts 726 to 750.csv")
tp <- format_plate(tp)
tp <- tbl_df(tp$plate)
directory <- getwd()
setwd("/Volumes/Sam's Drive/BOLA Study/USB20FD DUMP 5:22:19/LABS for 1 - 1000")
tp_labs <- read.csv("LABS for Pts 726 to 750.csv")
tp_labs <- format_lab_plate(tp_labs)
tp_labs <- tbl_df(tp_labs)
setwd(directory)
tp_enc <- filter(encounters1, Patient_ID %in% unique(tp$patient_ID))
tp_labs <- prune_lab_plates(tp_labs)
tp_total <- add_vitals_labs(tp,tp_labs)
tpe_total <- parse_as_different_patients(tp_total, tp_enc)