---
title: "Align-Columns-for-TLF-Reporting"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Align-Columns-for-TLF-Reporting}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Vignette Build Datetime

```{r built}
message(paste0('Datetime: ',Sys.Date(),':',Sys.time()))
```

## Load Libraries

```{r setup, message=FALSE}
library(repfun)
library(dplyr)
library(kableExtra)
```

## Set Up the Reporting Environment

```{r envir}
tmpdr <- tempdir()
datdir <- file.path(gsub("\\","/",tmpdr,fixed=TRUE),"datdir")
dir.create(datdir,showWarnings=FALSE)
repfun::copydata(datdir)
repfun::rs_setup(D_POP="SAFFL",D_POPLBL="Safety",D_POPDATA=repfun::adsl %>% 
           dplyr::filter(SAFFL =='Y'), D_SUBJID=c("STUDYID","USUBJID"), R_ADAMDATA=datdir)
repfun:::rfenv$G_POPDATA %>% dplyr::mutate(TRT01AN=ifelse(TRT01A=='Placebo',1,ifelse(TRT01A=='Xanomeline Low Dose',2,3))) %>% 
              repfun::ru_labels(varlabels=list('TRT01AN'='Actual Treatment for Period 01 (n)')) -> G_POPDATA
```

## Read in ADAE and Apply Population

```{r update1}
adae <- repfun:::rfenv$adamdata$adae.rda() %>% select(-SAFFL) %>% 
  repfun::ru_getdata(G_POPDATA, c("STUDYID", "USUBJID"), keeppopvars=c("TRT01AN", "TRT01A"))
```

## Generate Counts and Percents for AE Body System and Preferred Term

```{r cntper1}
aesum <- repfun::ru_freq(adae,
                 dsetindenom=G_POPDATA,
                 countdistinctvars=c('STUDYID','USUBJID'),
                 groupbyvarsnumer=c('TRT01AN','TRT01A','AEBODSYS','AEDECOD'),
                 anyeventvars = c('AEBODSYS','AEDECOD'),
                 anyeventvalues = c('ANY EVENT','ANY EVENT'),
                 groupbyvarsdenom=c('TRT01AN'),
                 resultstyle="NUMERPCT",
                 totalforvar=c('TRT01AN'),
                 totalid=99,
                 totaldecode='Total',
                 codedecodevarpairs=c("TRT01AN", "TRT01A"),
                 varcodelistpairs=c(""),
                 codelistnames=list(),
                 resultpctdps=0)
```

## Denormalize the AE Counts and Percents Data Set

```{r denorm1}
aesum_t <- aesum %>% repfun::ru_denorm(varstodenorm=c("tt_result", "PERCENT"), 
                               groupbyvars=c("tt_summarylevel", "AEBODSYS", "AEDECOD"), 
                               acrossvar="TRT01AN",
                               acrossvarlabel="TRT01A", acrossvarprefix=c("tt_ac", "tt_p"))
```

## Align the Columns for TLF Reporting

```{r align1}
aesum_t_a <- repfun::ru_align(aesum_t, "tt_ac:") %>% 
  select(-c('tt_p01','tt_p02','tt_p03','tt_p99','tt_summarylevel'))
```

## Display the Aligned AE Counts and Percents Data Set

```{r results1}
print("Aligned Reporting Data Set for AE Counts and Percents")
print(head(aesum_t_a,10))
```

## Generate Counts and Percents for Baseline Characteristics Data

```{r cntper2}
demstats <- repfun::ru_sumstats(G_POPDATA,
                          analysisvars=c("AGE","TRTDURD"),
                          groupbyvars=c("STUDYID","TRT01AN"),
                          codedecodevarpairs=c("TRT01AN", "TRT01A"),
                          totalforvar="TRT01AN", totalid=99,
                          totaldecode="Total",
                          statsinrowsyn = "Y",
                          analysisvardps=list("AGE"=1,"TRTDURD"=2),
                          statslist=c("n", "mean", "median", "sd", "min", "max"))
```

## Denormalize the Baseline Characteristics Summary Statistics Data

```{r denorm2}
demstats_t <- demstats %>% repfun::ru_denorm(varstodenorm=c("tt_result"), 
                                     groupbyvars=c("tt_avid", "tt_avnm", "tt_svid", "tt_svnm"),                                                                              acrossvar="TRT01AN", acrossvarlabel="TRT01A", 
                                     acrossvarprefix=c("tt_ac"))
```

## Align the Columns for TLF Reporting

```{r align2}
demstats_t_a <- repfun::ru_align(demstats_t, "tt_ac:")
```

## Display the Aligned Baseline Characteristics Summary Statistics Data Set

```{r results2}
print("Aligned Reporting Data Set for Baseline Characteristics Summary Stats")
print(head(demstats_t_a,10))
```