about_short"
In dmtools: Tools for Clinical Data Management

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

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

library(knitr)
library(dmtools)
library(dplyr)

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

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")

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

drug <- system.file("drug.xlsx", package = "dmtools")
table <- readxl::read_xlsx(drug)
kable(table, caption = "CM")

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")

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

vf <- system.file("vf.xlsx", package = "dmtools")
table <- readxl::read_xlsx(vf)
kable(table, caption = "VS")

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")

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

ae <- system.file("ae.xlsx", package = "dmtools")
table <- readxl::read_xlsx(ae)
kable(table, caption = "AE")

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")

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()