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 lookupDefine 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
