This data comes from a hypothetical study where the inhibition of factor Xa (FXa) following a single dose was studied in 72 patients consisting of 34 male and 38 female participants. For each subject, drug concentration and FXa inhibition were measured pre-dose and at 15 time points ranging from 5 minutes to 24 hours post-dose where doses ranged from 1.25 mg to 80 mg.
Shown here, the pmtables package generates data summary tables for age and weight stratified by dose level.
data %>%
distinct(ID, weight, age, sex, dose) %>%
mutate(dose = as.factor(dose)) %>%
pmtables::pt_cont_wide(by = "dose",
cols = "age,weight",
units = yspec::ys_get_unit(spec)) %>%
pmtables::stable() %>%
pmtables::st_as_image()
Exploratory analysis shows a concentration profile with a peak around 2 hours and then a slow elimination. The inhibition of FXa demonstrates a similar pattern where the greatest inhibition occurs several hours after the dose and greater inhibition is observed with larger doses. Also, a clear exposure-response relationship with near complete inhibition is observed at concentrations above 500 ng/mL.
data %>%
ggplot(aes(x=time, y=cobs, group=ID)) +
geom_point() +
geom_line() +
facet_wrap(~dose) +
scale_y_log10(name=ys_get_short_unit(spec)$cobs) +
scale_x_continuous(name=ys_get_short_unit(spec)$time,
breaks=c(2,4,8,12,24))
data %>%
ggplot(aes(x=time, y=fxa.inh, group=ID)) +
geom_point() +
geom_line() +
facet_wrap(~dose) +
scale_y_continuous(name=ys_get_short_unit(spec)$fxa.inh) +
scale_x_continuous(name=ys_get_short_unit(spec)$time,
breaks=c(2,4,8,12,24))
data %>%
ggplot(aes(x=cobs, y=fxa.inh, group=ID)) +
geom_point() +
geom_line() +
facet_wrap(~dose) +
scale_y_continuous(name=ys_get_short_unit(spec)$fxa.inh) +
scale_x_continuous(name=ys_get_short_unit(spec)$cobs)
These are the data definitions for the exdata3.csv data set which are used for the exposure-response analysis in this Expo.
| VARIABLE | LABEL | TYPE | CODES |
|---|---|---|---|
| ID | Subject ID | numeric | |
| weight | Body weight (unit: kg) | numeric | |
| age | Age (unit: year) | numeric | |
| sex | Sex | numeric | 1 = Male, 2 = Female |
| time | Time (unit: hours) | numeric | |
| dose | Dose (unit: mg) | numeric | |
| cobs | Concentration (unit: ng/mL) | numeric | |
| fxa.inh | FXa Inhibition (unit: percent) | numeric |
The data definitions can be loaded into your R session using the yspec package. We use the ys_load() function and point to the yaml file where definitions are coded. These data definitions will be used for axis labels, table headers, and captions in the subsequent analysis scripts.
library(yspec)
spec <- ys_load(here("data/derived/exdata3.yml"))
head(spec). name info unit short source
. 1 ID --- . Subject ID .
. 2 weight --- kg Body weight .
. 3 age --- year Age .
. 4 sex -d- . Sex .
. 5 time --- hours Time .
. 6 dose --- mg Dose .
. 7 cobs --- ng/mL Concentration .
. 8 fxa.inh --- percent FXa Inhibition .We can render a more formal data definitions document in .pdf format to support a more formal submission package. For more information, see the help files for the package yspec.