table_1.27.rmd

---
title: "Untitled"
author: "Smriti karki"
date: "10/27/2020"
output: html_document
---

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

```{r}
library(haven)
library(pivottabler)
library(dplyr)
library(tidyr)
library(tidyverse)
library(magrittr)
library(pagedown)
```
```{r}
adsu <- read_sas("E:/Numeric mind/adam/New_Study-master/New_Study-master/adam/adsu.sas7bdat",NULL)

col2 <- adsu %>% filter(PARAM=="History of illicit non-IV drug use") %>%
   group_by(TRT01P) %>% 
  dplyr::count(AVALC)  %>% 
  pivot_wider(names_from = TRT01P, values_from = n)
col2$`DTG + RPV`[is.na(col2$`DTG + RPV`)] <- 0
col2$Q2M[is.na(col2$Q2M)]<- 0
col2 <- col2 %>% mutate(Total = `DTG + RPV`+ Q2M)
col2 <- col2 %>%
  mutate(dtg = paste0(round(`DTG + RPV` / sum(`DTG + RPV`) * 100), "%"))%>% 
  mutate(q2m = paste0(round(Q2M / sum(Q2M) * 100), "%")) %>% 
  mutate(total = paste0(round(Total / sum(Total) * 100), "%"))
col2$dtg <- assertive.base::parenthesise(col2$dtg)
col2$q2m <- assertive.base::parenthesise(col2$q2m)
col2$total <- assertive.base::parenthesise(col2$total)
col2 <- col2 %>% 
  unite("DTG + RPV", c(`DTG + RPV`,dtg),sep = "  ") %>% 
  unite("Q2M", c(Q2M,q2m),sep = "  ") %>% 
  unite("Total", c(Total,total),sep = "  ")
col2 <- col2 %>%  add_row(AVALC= "History of illicit non-IV drug use",`DTG + RPV`="",Q2M="",Total="", .before = 1,.after = NULL)
col2 <- col2 %>% add_row(AVALC="n",`DTG + RPV`="7",Q2M="90",Total="97",.before = 2)

# line2 <- data.frame("n",7,90,97) 
# names(line2) <- c("AVALC","DTG + RPV","Q2M","Total")
col2 <- col2 %>%  add_row(AVALC= "History of illicit IV drug use",`DTG + RPV`="",Q2M="",Total="")
col2 <- col2 %>% add_row(AVALC="n",`DTG + RPV`="7",Q2M="90",Total="97")


col3 <- adsu %>% filter(PARAM=="History of illicit IV drug use") %>%
   group_by(TRT01P) %>% 
  dplyr::count(AVALC) %>% 
  pivot_wider(names_from = TRT01P, values_from = n)
col3$`DTG + RPV`[is.na(col3$`DTG + RPV`)] <- 0
col3 <- col3 %>% mutate(Total = `DTG + RPV`+ Q2M)
x <- sum(col3$`DTG + RPV`)
y <- sum(col3$Q2M)
t <- sum(col3$Total)
col3 <- col3 %>%
  mutate(dtg = scales::percent(`DTG + RPV`/x)) %>% 
  mutate(q2m = scales::percent(Q2M/y)) %>% 
  
  mutate(total = scales::percent(Total/t))
col3$dtg <- assertive.base::parenthesise(col3$dtg)
col3$q2m <- assertive.base::parenthesise(col3$q2m)
col3$total <- assertive.base::parenthesise(col3$total)
col3 <- col3 %>% 
  unite("DTG + RPV", c(`DTG + RPV`,dtg),sep = "  ") %>% 
  unite("Q2M", c(Q2M,q2m),sep = "  ") %>% 
  unite("Total", c(Total,total),sep = "  ")
col3 <- col3 %>% add_row(AVALC="Current User",`DTG + RPV`="0",Q2M="0",Total="0", .before = 2, .after = NULL)

line1<- c("History of smoking use","","","")
line2 <- c("n",7,90,97)
col3 <- col3 %>% rbind(line1)
col3 <- col3 %>% rbind(line2)


col4 <- adsu %>% filter(PARAM=="History of smoking use") %>%
   group_by(TRT01P) %>% 
  dplyr::count(AVALC) %>% 
  pivot_wider(names_from = TRT01P, values_from = n)
col4$`DTG + RPV`[is.na(col4$`DTG + RPV`)] <- 0
col4 <- col4 %>% mutate(Total = `DTG + RPV`+ Q2M)
x <- sum(col4$`DTG + RPV`)
y <- sum(col4$Q2M)
col4 <- col4 %>%
  mutate(dtg = scales::percent(`DTG + RPV`/x)) %>% 
  mutate(q2m = scales::percent(Q2M/y)) %>% 
  mutate(total = paste0(round(Total / sum(Total) * 100), "%"))
col4$dtg <- assertive.base::parenthesise(col4$dtg)
col4$q2m <- assertive.base::parenthesise(col4$q2m)
col4$total <- assertive.base::parenthesise(col4$total)
col4 <- col4 %>% 
  unite("DTG + RPV", c(`DTG + RPV`,dtg),sep = "  ") %>% 
  unite("Q2M", c(Q2M,q2m),sep = "  ") %>% 
  unite("Total", c(Total,total),sep = "  ")
col4 <- col4[-c(1),] 
col4 <- col4%>%  add_row(AVALC="Former Smoker",`DTG + RPV` = "2  (29%)", Q2M = "18  (20%)", Total = "20  (21%)")
  
table_2 <- dplyr::bind_rows(col2, col3,col4) 


library(data.table)

# table_2 <- table_2 %>% 
#   setnames("",
#            paste0("Q2M <br/> (N = ",sum(is.numeric(table_2$Q2M)),")"),
#            paste0("DTG + RPV <br/> (N = ", sum(is.numeric(table_2$`DTG + RPV`)),")"),
#            paste0("Total <br/> (N = ",sum(is.numeric(table_2$Total)),")"))

table_2 <-setnames(table_2, "Q2M", "Q2M <br/>  (N= 90) ")
table_2 <-setnames(table_2, "DTG + RPV", "DTG + RPV  (N= 7) ")
table_2 <-setnames(table_2, "Total", "Total (N= 97) ")

title <- c("<center> Table 1.27 <br/> Summary of Substance Use at Entry </center> <br/>"=4 )
sidetitle <- c("Protocol: 209035 POLAR <br/>
Population: Intent-to-Treat Exposed <br/>"=4) 
footer <- paste("<br/><br/>","smritikarki:",getwd(),toupper(format(Sys.time(),format = "%d%b%Y %H:%M")))
kableExtra::kable(table_2,align = "l",escape = F, bootstrap_options = "basic") %>% 
  kable_minimal(full_width = T, html_font = "Courier New") %>% 
  kableExtra::add_header_above(header = title,escape = F,line = F) %>% 
  kableExtra::add_header_above(header = sidetitle,escape = F,line = F,align = "l")
rm(list = ls())

```