# about_short

## Installation

    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

LB
LBPERF | LBORRES
--- | ---
preg_yn | preg_res

dataset
id | site | sex | preg_yn_e2 | preg_res_e2 | preg_yn_e3 | preg_res_e3
--- | --- | --- | --- | --- | --- | ---
01 | site 01 | f | y | neg | y | neg
02 | site 02 | m | y | neg | y | pos
03 | site 03 | f | y | neg | n | unnes

    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()
    #>   id    site sex LBPERF LBORRES    IDVAR VISIT
    #> 1 01 site 01   f      y     neg preg_res   _e2
    #> 2 01 site 01   f      y     neg preg_res   _e3
    #> 3 02 site 02   m      y     neg preg_res   _e2
    #> 4 02 site 02   m      y     pos preg_res   _e3
    #> 5 03 site 03   f      y     neg preg_res   _e2
    #> 6 03 site 03   f      n   unnes preg_res   _e3

### drug type

CM
CMTRT | CMDOSE
--- | ---
drug_type | drug_amount

dataset
id | e2_drug_type | e2_drug_amount | e3_drug_type | e3_drug_amount
--- | --- | --- | --- | ---
01 | type_one | 2 | type_one | 2
02 | type_two | 1 | type_two | 1
03 | type_one | 2 | type_one | 1

    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()
    #>   id    CMTRT CMDOSE     IDVAR VISIT
    #> 1 01 type_one      2 drug_type   e2_
    #> 2 01 type_one      2 drug_type   e3_
    #> 3 02 type_two      1 drug_type   e2_
    #> 4 02 type_two      1 drug_type   e3_
    #> 5 03 type_one      2 drug_type   e2_
    #> 6 03 type_one      1 drug_type   e3_

### vital functions

VS
VSTEST_HR | VSTEST_RESP
--- | ---
hr | respr

dataset
id | e2_hr | e2_respr | e3_hr | e3_respr
--- | --- | --- | --- | ---
01 | 60 | 12 | 65 | 13
02 | 70 | 15 | 71 | 14
03 | 76 | 16 | 86 | 18

    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()
    #>   id VSTEST_HR VSTEST_RESP IDVAR VISIT
    #> 1 01        60          12    hr   e2_
    #> 2 01        65          13    hr   e3_
    #> 3 02        70          15    hr   e2_
    #> 4 02        71          14    hr   e3_
    #> 5 03        76          16    hr   e2_
    #> 6 03        86          18    hr   e3_

### adverse events

AE
LBORRES | LBNRIND | LBCLSIG | LBTEST
--- | --- | --- | ---
ast | ast_norm | ast_cl | Aspartate transaminase

dataset
id | ast_e2 | ast_norm_e2 | ast_cl_e2 | ast_e3 | ast_norm_e3 | ast_cl_e3 | ae_yn_e5 | ae_desc_e5
--- | --- | --- | --- | --- | --- | --- | --- | ---
01 | 32 | norm | NA | 36 | norm | NA | no | NA
02 | 56 | no | no | 80 | no | yes | yes | abnormal ast
03 | 60 | no | yes | 32 | norm | NA | no | NA

    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()
    #>   id ae_yn_e5   ae_desc_e5 LBORRES LBNRIND LBCLSIG    IDVAR VISIT
    #> 1 01       no         <NA>      32    norm    <NA> ast_norm   _e2
    #> 2 01       no         <NA>      36    norm    <NA> ast_norm   _e3
    #> 3 02      yes abnormal ast      56      no      no ast_norm   _e2
    #> 4 02      yes abnormal ast      80      no     yes ast_norm   _e3
    #> 5 03       no         <NA>      60      no     yes ast_norm   _e2
    #> 6 03       no         <NA>      32    norm    <NA> ast_norm   _e3
    #>                   LBTEST
    #> 1 Aspartate transaminase
    #> 2 Aspartate transaminase
    #> 3 Aspartate transaminase
    #> 4 Aspartate transaminase
    #> 5 Aspartate transaminase
    #> 6 Aspartate transaminase