First look at the Tuberculosis data

Overview

In this vignette, we will explore the data set provided here in data(tb_clean), which is a data set originally collected and analyzed in Xie et al. (2018).

Exploratory Data Analysis

library(InfectionTrees)
library(tidyverse)
library(kableExtra)

The data tb_clean has 389 rows and 8 columns, where each row in the data corresponds to an individual with a detected case of Tuberculosis (TB).

The columns include demographic characteristics about the patients as well as two diagnostic tests of the disease, including a AFB sputum smear test, which we analyze here.

tb_sub <- tb_clean %>%
  mutate(cluster_id = group) %>%
  group_by(cluster_id) %>%
        mutate(cluster_size = n()) %>%
  ungroup()

This data has 158 clusters with the following distribution of cluster sizes:

sizes <- tb_sub %>% group_by(cluster_id) %>%
  summarize(cluster_size = n()) %>% 
  ungroup() %>%
  group_by(cluster_size) %>%
  summarize(freq = n()) 
  
  
sizes %>%
  kable() %>%
  kable_styling(bootstrap_options = c("condensed", "hover", "striped", "responsive"),
                full_width = FALSE, position = "center")

cluster_size	freq
1	75
2	41
3	20
4	5
5	4
6	3
7	3
8	2
9	1
10	1
16	1
17	1
25	1

This means that 47.5% of the clusters are singletons and 86.1% of the clusters have size at most 3.

A single cluster of individuals looks like the following:

tb_sub %>% filter(group == "27") %>%
  arrange(rel_time) %>%
  select(group, rel_time, everything()) %>%
   kable() %>%
  kable_styling(bootstrap_options = c("condensed", "hover", "striped", "responsive"),
                full_width = FALSE, position = "center")

group	rel_time	sex	county	race	spsmear	hivstatus	homeless	cluster_id	cluster_size
27	0 days	Male	MONTGOMERY	Black or African American	Positive	Negative	No	27	7
27	442 days	Female	MONTGOMERY	Black or African American	Positive	Negative	No	27	7
27	805 days	Female	MONTGOMERY	Black or African American	Positive	Negative	No	27	7
27	834 days	Female	MONTGOMERY	Black or African American	Positive	Negative	No	27	7
27	941 days	Male	PRINCE GEORGES	Black or African American	Positive	Negative	No	27	7
27	1015 days	Male	PRINCE GEORGES	Black or African American	Positive	Positive	No	27	7
27	1167 days	Male	PRINCE GEORGES	Black or African American	Positive	Negative	No	27	7

In our data set of 389 individuals, 56 or 14% of individuals are HIV+. In the clusters with more than 3 individuals, 37 of 172 or 22% of individuals are HIV+.