Standard tables and figures

In eudract: Creates Safety Results Summary in XML to Upload to EudraCT, or ClinicalTrials.gov

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

library(eudract)
library(knitr)

We can easily produce some of the standard reports needed for most clinical trials, as well as producing the xml files needed to upload to EudraCT or ClinicalTrials.gov. See the other vignette

We first ensure the data is in the correct format, column names to produce a basic safety object

head(safety)
safety_statistics <- safety_summary(safety,exposed=c("Control"=99, "Experimental"=101))

A top level table is the $GROUP data frame with slightly improved column names

df <- safety_statistics$GROUP
names(df) <- c("Arm", "SAE count", "Non Serious AE count", "Death from AE count", "N", "All cause deaths count")
kable(df, caption = "Total Adverse Events")

Next we provide an incidence table

incidence <-  incidence_table(safety_statistics, type ="serious")
kable(incidence, caption="SAE incidence")
incidence <-  incidence_table(safety_statistics, type ="non_serious")
kable(incidence, caption="Non-serious AE incidence")

A table of relative risk can be given

rr <- relative_risk_table(safety_statistics, type="serious")
kable(rr, caption="SAE relative risks")

rr <- relative_risk_table(safety_statistics, type="non_serious")
kable(rr, caption="Non-serious AE relative risks")

Finally a set of dot-plots to show graphically and compare, using functions from patchwork to add titles

dot_plot(safety_statistics, type="serious", base=4)

dot_plot(safety_statistics, type="non_serious", base=4)

If you want to modify, then access the two elements $left.panel and $right.panel to modify as standard ggplot objects. The print and plot methods glue them back together within the framework of the patchwork package. Or you can dissect, edit, save, and use however you want.

fig <- dot_plot(safety_statistics, type="non_serious", base=4)
fig$left.panel <- fig$left.panel + ggplot2::labs(title="Absolute Risk")
fig

Should you wish to save to a file, then using the workflow below will work, using a graphics device such as, png, jpeg, pdf, svg. You will need to explicitly call the print(fig) function, and just fig on its own may not work.

temp <- tempfile(fileext=".png")
png(filename = temp)
print(fig)
dev.off()

Further filtering and refinements to the labels may be provided using the relative_risk and order_filter functions. See help pages for more details.

eudract documentation built on Sept. 11, 2024, 8:08 p.m.