Summarising Clinicopathological Data

ClinicoPathDescriptives Team

This vignette focuses on the functions that generate tables and textual summaries.

Continuous Variables

summarydata() provides descriptive statistics (mean, median, quartiles) for numeric variables.

summarydata(
  data = histopathology,
  vars = vars(Age, TumorSize)
)

Categorical Variables

reportcat() summarises categorical variables with counts and percentages.

reportcat(
  data = histopathology,
  vars = vars(Sex, Grade)
)

Cross Tables

Use crosstable() to create cross tabulations with statistical tests. The group argument defines the column variable.

crosstable(
  data = histopathology,
  vars = vars(Sex, Grade),
  group = "PreinvasiveComponent",
  sty = "nejm",
  excl = TRUE
)

Table One for Publications

tableone() creates publication-ready tables of baseline characteristics.

tableone(
  data = histopathology,
  vars = vars(Sex, PreinvasiveComponent, LVI, PNI, Grade, Age),
  sty = "t3",
  excl = TRUE
)

These functions output results objects that contain tables which can be converted to data frames for further customisation.