combined_contingency_2x2_functions: Contingency Table and Statistical Test Functions

In AntonioJBT/episcout: Quickly Clean, Explore and Visualise Large Epidemiological Datasets

Contingency Table and Statistical Test Functions

Description

A comprehensive set of functions to:

• Generate contingency tables and summary tables.

• Perform 2x2 contingency table significance tests.

Usage

epi_stats_contingency_2x2_df(df, x_var, y_var)

epi_stats_contingency_2x2_tables(df, x_var)

rename_contingency_2x2_cols(contingency_2x2_list, df, x_var)

epi_stats_contingency_2x2_test(
  df,
  target_var,
  other_var,
  test_type = "fisher.test"
)

epi_stats_contingency_2x2_cols(df, min_unique = 2)

epi_stats_contingency_2x2_all(df, target_var, test_type = "fisher.test")

Arguments

df	A data frame containing the data to analyze.
x_var	A string or numeric index specifying the independent variable (column in df).
y_var	A string or numeric index specifying the dependent variable (column in df).
target_var	The name of the target variable (e.g., dependent variable) as a string.
other_var	The name of the other variable to test against the target variable.
test_type	The type of test to perform. Either "fisher.test" (default) or "chisq.test".
min_unique	Minimum number of unique values required to include a column for testing (default: 2).
output_file	(Optional) File path to save the aggregated test results.

Details

These functions include:

• epi_stats_contingency_2x2_df(): Creates a raw contingency table between two variables.

• epi_stats_contingency_2x2_tables(): Generates a named list of contingency tables for a target variable and all other variables.

• epi_stats_rename_contingency_2x2_cols(): Renames columns in a list of contingency tables for clarity.

• epi_stats_contingency_2x2_test(): Performs a statistical test (Fisher's exact or Chi-squared) on a 2x2 table.

• epi_stats_contingency_2x2_cols(): Selects suitable columns for contingency table tests.

• epi_stats_contingency_2x2_all(): Iteratively applies the tests and aggregates results into a data frame.

Value

• epi_stats_contingency_2x2_df(): A data frame representing the contingency table with raw frequencies.

• epi_stats_contingency_2x2_tables(): A named list of data frames, each representing a contingency table.

• epi_stats_rename_contingency_2x2_cols(): A list of data frames with renamed columns.

• epi_stats_contingency_2x2_test: A tidy data frame with test results for a single 2x2 table.

• epi_stats_contingency_2x2_cols(): A character vector of column names that meet the criteria for testing.

• epi_stats_contingency_2x2_all(): A data frame containing test results for all selected columns.

Examples

# Example dataset
set.seed(42)
col_facts <- data.frame(
  State = sample(c("Active", "Inactive"), 100, replace = TRUE),
  Gender = sample(c("Male", "Female"), 100, replace = TRUE),
  Something = sample(c("Yes", "No"), 100, replace = TRUE),
  Another = sample(c("Yes", "No", "Unknown"), 100, replace = TRUE),
  Type = sample(c("Type1", "Type2", "Type3"), 100, replace = TRUE),
  SingleValue = rep("Same", 100)
)

# Generate a contingency table for two variables
contingency_2x2_df <- epi_stats_contingency_2x2_df(col_facts, x_var = "State", y_var = "Gender")
print(contingency_2x2_df)

# Generate contingency tables for all variables
contingency_2x2_list <- epi_stats_contingency_2x2_tables(col_facts, x_var = "State")
print(contingency_2x2_list[[1]])

# Rename columns in contingency tables
renamed_list <- rename_contingency_2x2_cols(contingency_2x2_list, col_facts, x_var = "State")
print(renamed_list[[1]])

# Perform a single 2x2 test
result <- epi_stats_contingency_2x2_test(col_facts, "State", "Gender")
print(result)

# Select columns for testing
testable_columns <- epi_stats_contingency_2x2_cols(col_facts)
print(testable_columns)

# Run tests on all testable columns
results_df <- epi_stats_contingency_2x2_all(col_facts, "State")
print(results_df)

# Save results
write.table(results_df, "fishers_results.txt", sep = "\t", row.names = FALSE, quote = FALSE)

AntonioJBT/episcout documentation built on Feb. 20, 2025, 12:46 a.m.