Example of how to perform a survival analysis

survival-analysis-example.R

# Load necessary libraries
library(tidyverse)      # For data manipulation
library(survival)       # For survival analysis
library(survminer)      # For survival visualization

# Load TidyTuesday data for the 5th week of 2023
data <- tidytuesdayR::tt_load(2023, week = 05)

# Extract relevant datasets
cats_uk <- data$cats_uk
data_reference <- data$cats_uk_reference

# Merge datasets based on tag_id
df <- cats_uk |> 
  inner_join(data_reference, by = "tag_id")

# Prepare data for survival analysis
surv_df <- df |>
  select(timestamp, hunt, animal_sex) |>
  filter(!is.na(hunt)) |>
  mutate(
    animal_sex = ifelse(animal_sex == "m", 1, 2),   # Convert animal_sex to numeric
    hunt = ifelse(hunt == "FALSE", 0, 1),           # Convert hunt to numeric
    timestamp = as.POSIXct(timestamp, format = "%Y-%m-%d %H:%M:%S"),  # Convert timestamp to POSIXct
    day = as.Date(timestamp, "%Y-%m-%d %H:%M:%S", tz = "GMT")          # Extract day from timestamp
  )

# Calculate date range
range(surv_df$day)

# Define start and end dates for analysis
start_date <- as.Date("2017-06-03")
end_date <- as.Date("2017-11-30")
date_seq <- seq(start_date, end_date, by = "day")

# Group data by day and calculate time elapsed from start date
cat_hz <- surv_df |> 
  group_by(day) |> 
  mutate(time = as.numeric(day - start_date) + 1) |>   # Calculate time elapsed
  arrange(time)                                       # Arrange data by time

# Perform survival analysis
fit <- survfit(Surv(time, hunt) ~ animal_sex, data = cat_hz)

# Generate survival plot
ggsurv <- ggsurvplot(fit,
  data = cat_hz,
  censor.shape = "|",
  censor.size = 4,
  risk.table = TRUE,
  submain = "Hazards Distribution and Sex Differences in Hunting Risk",
  caption = "Based on Kaplan-Meier estimates\nDataSource: #TidyTuesday 2023 Week5 Pet Cats UK"
)

# Customize plot appearance
ggsurv$plot %+%
  ggthemes::scale_colour_fivethirtyeight(labels = c("Male", "Female")) %+%
  labs(title = "Survival of UK Cats") %+%
  theme_survminer(
    base_family = "Roboto Condensed",
    font.main = c(18, "bold"),
    font.submain = c(14, "bold.italic"),
    font.caption = c(11, "plain"),
    font.x = c(12, "bold.italic"),
    font.y = c(12, "bold.italic"),
    font.tickslab = c(12, "plain")
  ) %+%
  theme(
    plot.background = element_rect(fill = "grey90", color = "grey90"),
    panel.background = element_rect(fill = "grey90", color = "grey90"),
    legend.background = element_blank()
  )