adlb1.Rmd

---
title: "adbl"
author: "Smriti karki"
date: "8/1/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

##loading library  
```{r}
library(haven)
library(tidyverse)
library(readr)
library(readxl)
library(dplyr)

```
##importing files
```{r}
lb <- read_sas("E:/Numeric mind/adam/New_Study-master/New_Study-master/sdtm/lb.sas7bdat",NULL)
adsl <- read_sas("E:/Numeric mind/adam/New_Study-master/New_Study-master/adam/adsl.sas7bdat",NULL)
adlb <- read_sas("E:/Numeric mind/adam/New_Study-master/New_Study-master/adam/adlb.sas7bdat",NULL)

```
##create adlb file
```{r}
adlb1 <- lb %>% select(STUDYID,USUBJID,LBSEQ,LBTESTCD,LBCAT,LBORRES,LBORRESU,LBSTRESC,LBSTRESN,LBSTRESU,LBSTNRLO,LBSTNRHI,LBBLFL,LBFAST,LBDY,VISIT,VISITNUM,LBDTC)
rm <- adsl %>%  select(USUBJID,SITEID,LTSUBJID,AGE,AGEU,RACE,SEX,COUNTRY,SAFFL,ITTEFL,SCRNFL,PPROTFL,ENRLFL,LTFUFL,TRT01P,TRT01PN,TRT01A,TRT01AN,MNTEDT,TRTSDT,TRTEDT)
adlb1 <- adlb1 %>% left_join(rm)
rm(rm)
```
##TRTP(20)
```{r}
adlb1 <- adlb1 %>% mutate(TRTP = TRT01P)
```
##TRTPN(21)
```{r}
adlb1 <- adlb1 %>% mutate(TRTPN = TRT01PN)
```
##TRTA(22)
```{r}
adlb1 <- adlb1 %>% mutate(TRTA = TRT01A)
```
##TRTAN(23)
```{r}
adlb1 <- adlb1 %>% mutate(TRTAN = TRT01AN)
```
##If time is collected then ADT=numeric date part of LB.LBDTC, else if time is not collected then ADT is the numeric version of LB.LBDTC.
##ADT(48)
```{r}
rm <- adlb1 %>% mutate(ADT = as.Date(LBDTC))
adlb1 <- adlb1 %>% full_join(rm)
rm(rm)
```
##If ADT>=ADSL.TRTSDT then ADT-ADSL.TRTSDT+1, else ADT-ADSL.TRTSDT.
##ADY(49)
```{r}
adlb1 <- adlb1 %>% mutate(ADY = case_when(
  ADT >= TRTSDT ~ ADT - TRTSDT + 1,
  TRUE ~ ADT - TRTSDT))
```
##PARCAT1(50)
```{r}
adlb1 <- adlb1 %>% mutate(PARCAT1 = LBCAT)
```
##PARCAT1N(51)
```{r}
adlb1 <- adlb1 %>% mutate(PARCAT1N = case_when(
  PARCAT1 == "CHEMISTRY" ~ 1,
  PARCAT1 == "COAGULATION" ~2,
  PARCAT1 == "DRUG SCREENING" ~3,
  PARCAT1 == "HEMATOLOGY" ~4,
  PARCAT1 == "IMMUNOLOGY" ~5,
  PARCAT1 == "URINALYSIS" ~6,
  PARCAT1 == "VIROLOGY" ~7))
```