pk_define {apmx}

Create definition file from published dataset

Description

Definition file table can be read into a template word document (.docx) or blank document if desired. Definitions are sourced from a variable list stored separately on your server. Please refer to apmx::variable_list_export() for a standard copy of the variable list.

Usage

pk_define(
  df,
  file = NULL,
  project,
  data,
  variable.list,
  template = NULL,
  font = "Times New Roman",
  size = 9,
  na = -999
)

Arguments

df

apmx analysis dataset

file

optional filepath for defintion file (.docx file)

project

project name

data

dataset name

variable.list

reference dataframe for variable definitions

template

optional filepath for definition file template (.docx file)

font

font for table contents

size

font size for table contents

na

value used for missing or na numeric covariates

Value

dataset definition file

Examples

## Simple ex domain with 1 subject and 1 dose
ex <- data.frame(STUDYID = "ABC101",
                 USUBJID = "ABC101-001",
                 EXSTDTC = "2000-01-01 10:00:00",
                 EXSTDY = 1,
                 EXTPTNUM = 0,
                 EXDOSE = 100,
                 CMT = 1,
                 EXTRT = "ABC",
                 EXDOSU = "mg",
                 VISIT = "Day 1",
                 EXTPT = "Dose",
                 EXDOSFRQ = "Once",
                 EXROUTE = "Oral")

## Simple pc domain with 1 subject and 3 observations
pc <- data.frame(USUBJID = "ABC101-001",
                 PCDTC = c("2000-01-01 09:40:00",
                           "2000-01-01 10:29:00",
                           "2000-01-01 12:05:00"),
                 PCDY = 1,
                 PCTPTNUM = c(0, ##Units of hours
                              0.021,
                              0.083),
                 PCSTRESN = c(NA,
                              469,
                              870),
                 PCLLOQ = 25,
                 CMT = 2,
                 VISIT = "Day 1",
                 PCTPT = c("Pre-dose",
                           "30-min post-dose",
                           "2-hr post-dose"),
                 PCTEST = "ABC",
                 PCSTRESU = "ug/mL")

## Create apmx dataset with pk_build()
df <- pk_build(ex, pc)

## Create variable definitions with variable_list_create()
vl <- variable_list_create()

## Create definition file
pk_define(df, variable.list = vl)