---
title: "about_short"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{about_short}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

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

## Installation
```{r setup, eval = FALSE}
library(dmtools)
```

## Overview

The `short()` can be useful for validation, if you need to reshape the dataset. You also need to create the excel document, where the name and number of columns can be any. If you have common columns, pass them to a parameter `common_cols` of `short()`. Notice, don't write common columns in the excel document. If you have the extra information e.g. the understandable name of an analysis, pass it to a parameter `extra`. 

## Usage

Some examples, where you can use `short()`.

### pregnancy test
```{r preg_table, echo = FALSE, result = 'asis', warning = FALSE, message = FALSE}
library(knitr)
library(dmtools)
library(dplyr)

preg <- system.file("preg.xlsx", package = "dmtools")
table <- readxl::read_xlsx(preg)
kable(table, caption = "LB")
```

```{r preg_dataset, echo = FALSE, result = 'asis'}

id <- c("01", "02", "03")
site <- c("site 01", "site 02", "site 03")
sex <- c("f", "m", "f")
preg_yn_e2 <- c("y", "y", "y")
preg_res_e2 <- c("neg", "neg", "neg")
preg_yn_e3 <- c("y", "y", "n")
preg_res_e3 <- c("neg", "pos", "unnes")

df <- data.frame( 
       id, site, sex,
       preg_yn_e2, preg_res_e2,
       preg_yn_e3, preg_res_e3,
       stringsAsFactors = FALSE)

kable(df, caption = "dataset")
```

```{r preg}
preg <- system.file("preg.xlsx", package = "dmtools")
obj_short <- short(preg, id, "LBORRES", c("site", "sex"))

obj_short <- obj_short %>% check(df)
obj_short %>% get_result()
```

### drug type
```{r drug_table, echo = FALSE, result = 'asis', warning = FALSE, message = FALSE}
drug <- system.file("drug.xlsx", package = "dmtools")
table <- readxl::read_xlsx(drug)
kable(table, caption = "CM")
```

```{r drug_dataset, echo = FALSE, result = 'asis'}

id <- c("01", "02", "03")
e2_drug_type <- c("type_one", "type_two", "type_one")
e2_drug_amount <- c(2, 1, 2)
e3_drug_type <- c("type_one", "type_two", "type_one")
e3_drug_amount <- c(2, 1, 1)

df <- data.frame( 
       id, e2_drug_type, e2_drug_amount,
       e3_drug_type, e3_drug_amount,
       stringsAsFactors = FALSE)

kable(df, caption = "dataset")
```

```{r drug}
drug <- system.file("drug.xlsx", package = "dmtools")
# parameter is_post has value FALSE because a dataset has a prefix in the names of variables
obj_short <- short(drug, id, "CMTRT", is_post = F)

obj_short <- obj_short %>% check(df)
obj_short %>% get_result()
```

### vital functions
```{r vf_table, echo = FALSE, result = 'asis', warning = FALSE, message = FALSE}
vf <- system.file("vf.xlsx", package = "dmtools")
table <- readxl::read_xlsx(vf)
kable(table, caption = "VS")
```

```{r vf_dataset, echo = FALSE, result = 'asis'}

id <- c("01", "02", "03")
e2_hr <- c(60, 70, 76)
e2_respr <- c(12, 15, 16)
e3_hr <- c(65, 71, 86)
e3_respr <- c(13, 14, 18)

df <- data.frame( 
       id, e2_hr, e2_respr,
       e3_hr, e3_respr, 
       stringsAsFactors = FALSE)

kable(df, caption = "dataset")
```

```{r vf}
vf <- system.file("vf.xlsx", package = "dmtools")
obj_short <- short(vf, id, "VSTEST_HR", is_post = F)

obj_short <- obj_short %>% check(df)
obj_short %>% get_result()
```

### adverse events
```{r ae_table, echo = FALSE, result = 'asis', warning = FALSE, message = FALSE}
ae <- system.file("ae.xlsx", package = "dmtools")
table <- readxl::read_xlsx(ae)
kable(table, caption = "AE")
```

```{r ae_dataset, echo = FALSE, result = 'asis'}

id <- c("01", "02", "03")
ast_e2 <- c(32, 56, 60)
ast_norm_e2 <- c("norm", "no", "no")
ast_cl_e2 <- c(NA, "no", "yes")
ast_e3 <- c(36, 80, 32)
ast_norm_e3 <- c("norm", "no", "norm")
ast_cl_e3 <- c(NA, "yes", NA)
ae_yn_e5 <- c("no", "yes", "no")
ae_desc_e5 <- c(NA, "abnormal ast", NA)

df <- data.frame( 
       id, ast_e2, ast_norm_e2, ast_cl_e2,
       ast_e3, ast_norm_e3, ast_cl_e3,
       ae_yn_e5, ae_desc_e5,
       stringsAsFactors = FALSE)

kable(df, caption = "dataset")
```

```{r ae}
ae <- system.file("ae.xlsx", package = "dmtools")
obj_short <- short(ae, id, "LBNRIND", common_cols = c("ae_yn_e5", "ae_desc_e5"), extra = "LBTEST")

obj_short <- obj_short %>% check(df)
obj_short %>% get_result()
```