Data Definitions

Data definitions for the pk.csv PK model data set.

yspec
data

Definitions table

The following table provides data definitions for the pk.csv data set which are used for the population PK analysis in this Expo.

VARIABLE LABEL TYPE CODES
C Commented rows character . = Not a comment, C = Comment for exclusion
NUM Row number numeric
ID NONMEM ID number numeric
TIME Time after first dose (unit: hour) numeric
SEQ Data type numeric 0 = Dose, 1 = Observation
CMT Compartment numeric 1 = Dose, 2 = Observation
EVID Event identifier numeric 0 = Observation event, 1 = Dosing event
AMT Dose amount (unit: mg) numeric
DV Dependent variable numeric
AGE Age (unit: years) numeric
WT Weight (unit: kg) numeric
HT Height (unit: cm) numeric
EGFR Estimated glomerular filtration rate (unit: mL/min/1.73m2) numeric
ALB Albumin (unit: g/dL) numeric
BMI Body mass index (unit: kg/m2) numeric
SEX Sex numeric 0 = Male, 1 = Female
AAG Alpha-1-acid glycoprotein (unit: mg/dL) numeric
SCR Serum creatinine (unit: mg/dL) numeric
AST Aspartate aminotransferase (unit: U/L) numeric
ALT Alanine aminotransferase (unit: U/L) numeric
CP Child-Pugh score numeric 0 = normal, 1 = score=1, 2 = score=2, 3 = score=3
TAFD Time after first dose (unit: hour) numeric
TAD Time after dose (unit: hour) numeric
LDOS Last dose amount (unit: mg) numeric
MDV Missing dependent variable numeric 0 = No, 1 = Yes
BLQ Below limit of quantification numeric 1 = Above QL, 0 = Below QL
PHASE Study phase indicator numeric values: 1
STUDYN Study number numeric values: 1, 2, 3, 4
DOSE Nominal dose amount numeric 5 = 5 mg, 10 = 10 mg, 25 = 25 mg, 50 = 50 mg, 75 = 75 mg, 100 = 100 mg, 150 = 150 mg, 200 = 200 mg
SUBJ Subject identifer character
USUBJID Unique subject identifier character
STUDY Study name character values: 101-DEMO-001, 101-DEMO-002, 201-DEMO-003, 201-DEMO-004
ACTARM Treatment arm character values: DEMO 5 mg, DEMO 10 mg, DEMO 10 mg qd x7, DEMO 25 mg, DEMO 25 mg qd x7, DEMO 50 mg qd x7, DEMO 75 mg qd x7, DEMO 100 mg, DEMO 100 mg qd x7, DEMO 150 mg, DEMO 200 mg
RF Renal function stage character norm = normal, mild, mod = moderate, sev = severe

Definitions object

The data definitions can be loaded into your R session using the yspec package. The following code snippet uses the ys_load() function and points to the yaml file where definitions are coded.

library(yspec)

spec <- ys_load(here("data/derived/pk.yml"))

head(spec)
.    name info  unit                 short source
. 1     C  cd-     .        Commented rows lookup
. 2   NUM  ---     .            Row number lookup
. 3    ID  ---     .      NONMEM ID number lookup
. 4  TIME  ---  hour Time after first dose lookup
. 5   SEQ  -d-     .             Data type lookup
. 6   CMT  -d-     .           Compartment lookup
. 7  EVID  -d-     .      Event identifier lookup
. 8   AMT  ---    mg           Dose amount lookup
. 9    DV  ---     .    Dependent variable lookup
. 10  AGE  --- years                   Age lookup

Define pdf document

We can render a more formal data definitions document in .pdf format to support a formal submission package.

The define.pdf document is a single listing of definitions for all data sets in the analysis. It is built from data definition objects for each analysis data set. Page one and two are provided as an example below. You won’t be able to click through the links as this content is hosted on a website. However, on page two under 1 Datasets, you’ll see the Description column links to the header of the particular data set, and Location links to the SASxport file (.xpt) on disk. In this example there was only one data set but if you have multiple data sets you’d see multiple rows to this table.

Page 1

Page 2