In Epiconcept-Paris/STRAP-epiuf: Epiconcept Team Utility Functions for STRAP Project

knitr::opts_chunk$set(echo = TRUE)
options(knitr.kable.NA = '')
library(epiuf)
library(kableExtra)

Description

The aim of this function is to describe numeric variables or categorical variables (must be in factor) according or not to another variable in a table. For example : to describe age, sex, vaccination status according to the case or control status.

# create example dataset for testing
nbrecords <- 100
df <- data.frame(
  age = sample(c(0:110,NA), nbrecords, replace = TRUE),
  sex = factor(sample(c(0,1,NA), nbrecords, replace = TRUE), levels = c(0,1), labels = c("Female", "Male")),
  fluvaccany = factor(sample(c(0,1,NA), nbrecords, replace = TRUE), levels = c(0,1), labels = c("No", "Yes")),
  lab_flu = sample(c(0,1), nbrecords, replace = TRUE)
)
df$agegp4 <- cut(df$age, c(0, 4, 14, 64, max(df$age, na.rm = T)), include.lowest = TRUE, labels = c("0-4", "5-14", "15-64", "65 +"))

Testing the function

DescBy: descriptive table

# Test: no labels specified
table <- descBy(data = df, vars = c("age", "agegp4", "sex", "fluvaccany"))
kable(table)

# Example
table <- descBy(data = df, 
                vars = c("age", "agegp4", "sex", "fluvaccany"),
                labels = c("Age", "Age in group", "Sex", "Seasonal influenza vaccination"))
kable(table)

DescBy: descriptive table according to another variable

# Test: by is not a factor
try(
   table <- descBy(data = df, 
                   vars = c("age", "agegp4", "sex"), 
                   labels = c("Age", "Age in group", "Sex"), 
                   by = "lab_flu")
   )

# Test: by has not enough categories (minimum is 2)
df2 <- subset(df, lab_flu == 0)
df2$lab_flu <- factor(df2$lab_flu, levels = c(0), labels = c("Controls"))
try (
  table <- descBy(data = df2, 
                  vars = c("age", "agegp4", "sex"), 
                  labels = c("Age", "Age in group", "Sex"), 
                  by = "lab_flu")
)

# Test: no labels for the variables
df$lab_flu <- factor(df$lab_flu, levels = c(0,1), labels = c("Controls", "Cases"))
table <- descBy(data = df, 
                vars = c("age", "agegp4", "sex", "fluvaccany"), 
                by = "lab_flu")
kable(table)

# Example:
table <- descBy(data = df, 
                vars = c("age", "agegp4", "sex", "fluvaccany"), 
                labels = c("Age", "Age in group", "Sex", "Seasonal influenza vaccination"), 
                by = "lab_flu")
kable(table)

Epiconcept-Paris/STRAP-epiuf documentation built on Aug. 5, 2024, 3:41 a.m.