Matter AI | Code Reviewer Documentation

R Anti-Patterns Overview

Growing Objects in a Loop

# Anti-pattern: Growing objects in a loop
result <- c()
for (i in 1:1000000) {
  result <- c(result, i)  # Inefficient: creates a new vector each time
}

# Better approach: Pre-allocate memory
result <- numeric(1000000)
for (i in 1:1000000) {
  result[i] <- i
}

# Even better: Use vectorization
result <- 1:1000000

Avoid growing objects incrementally in loops. Pre-allocate memory for the final object size or use vectorized operations instead.

Using apply() on Data Frames

# Anti-pattern: Using apply() on data frames
df <- data.frame(a = 1:10, b = 11:20, c = 21:30)
result <- apply(df, 2, mean)  # Converts to matrix, losing column types

# Better approach: Use lapply() or vapply() for data frames
result <- vapply(df, mean, numeric(1))

# Or use dplyr
library(dplyr)
result <- df %>% summarise_all(mean)

Avoid using apply() on data frames as it converts them to matrices, which can lead to unexpected results if columns have different types. Use lapply(), vapply(), or packages like dplyr instead.

Using $ and [[]] Inconsistently

# Anti-pattern: Inconsistent subsetting
df <- data.frame(a = 1:10, b = 11:20)
x <- df$a  # Using $
y <- df[['b']]  # Using [[]]

# Function that fails with $ notation
process_column <- function(data, col_name) {
  return(mean(data$col_name))  # This doesn't work as expected
}

# Better approach: Consistent use of [[]]
process_column <- function(data, col_name) {
  return(mean(data[[col_name]]))  # This works correctly
}

Be consistent with subsetting operators. Use [[]] when the column name is stored in a variable or when writing functions that take column names as parameters.

Using attach()

# Anti-pattern: Using attach()
df <- data.frame(x = 1:10, y = 11:20)
attach(df)
result <- x + y  # Seems convenient but dangerous
# What if we modify df or create new variables with the same names?
detach(df)

# Better approach: Use with() or explicit references
result <- with(df, x + y)

# Or use pipe operators
library(dplyr)
result <- df %>% mutate(sum = x + y) %>% pull(sum)

Avoid using attach() as it can lead to confusing scoping issues and hard-to-find bugs. Use with(), explicit references, or pipe operators instead.

Using row.names

# Anti-pattern: Using row.names for data
df <- data.frame(x = 1:3, y = 4:6)
row.names(df) <- c("A", "B", "C")

# Better approach: Use a proper column
df <- data.frame(id = c("A", "B", "C"), x = 1:3, y = 4:6)

Avoid using row.names() to store actual data. Instead, include the information as a proper column in your data frame.

Using for Loops Instead of Vectorization

# Anti-pattern: Using for loops for simple operations
x <- 1:1000
result <- numeric(length(x))
for (i in seq_along(x)) {
  result[i] <- x[i] * 2
}

# Better approach: Use vectorization
result <- x * 2

Avoid using for loops for operations that can be vectorized. R is optimized for vector operations, which are typically much faster.

Using global() and <<-

# Anti-pattern: Using global variables and <<-
counter <- 0
increment_counter <- function() {
  counter <<- counter + 1  # Modifies global variable
}

# Better approach: Pass and return values explicitly
increment_counter <- function(counter) {
  return(counter + 1)
}
counter <- increment_counter(counter)

Avoid using global variables and the <<- operator. Instead, pass values explicitly to functions and return modified values.

Not Using Proper Error Handling

# Anti-pattern: No error handling
process_file <- function(file_path) {
  data <- read.csv(file_path)  # Will error if file doesn't exist
  # Process data...
  return(result)
}

# Better approach: Use tryCatch
process_file <- function(file_path) {
  tryCatch({
    data <- read.csv(file_path)
    # Process data...
    return(result)
  }, error = function(e) {
    warning(paste("Error processing file:", e$message))
    return(NULL)
  })
}

Use proper error handling with tryCatch() to gracefully handle errors and provide meaningful error messages.

Using T and F Instead of TRUE and FALSE

# Anti-pattern: Using T and F
if (x > 10) {
  flag <- T
} else {
  flag <- F
}

# Better approach: Use TRUE and FALSE
if (x > 10) {
  flag <- TRUE
} else {
  flag <- FALSE
}

# Even better: Direct logical result
flag <- x > 10

Avoid using T and F as shortcuts for TRUE and FALSE. They are just variables that can be reassigned, potentially leading to confusing bugs.

Using stringsAsFactors=TRUE

# Anti-pattern: Letting strings be converted to factors
df <- read.csv("data.csv")  # By default, strings become factors

# Better approach: Be explicit about factor conversion
df <- read.csv("data.csv", stringsAsFactors = FALSE)

# Convert specific columns to factors as needed
df$category <- factor(df$category)

Avoid letting R automatically convert strings to factors. Be explicit about which columns should be factors. Note that in R 4.0.0 and later, the default changed to stringsAsFactors = FALSE.

Using rm(list=ls()) to Clean Environment

# Anti-pattern: Using rm(list=ls()) at the beginning of scripts
rm(list=ls())  # Clears the entire environment

# Better approach: Use separate R sessions or restart R
# Or be specific about what to remove
rm(temp_var, another_var)

Avoid using rm(list=ls()) to clean your environment, especially in scripts or functions. It can lead to unexpected behavior and makes code less reproducible. Instead, restart R or use separate R sessions.

Not Using Proper Package Management

# Anti-pattern: Loading packages without checking
library(dplyr)
library(ggplot2)
# What if these packages aren't installed?

# Better approach: Check and install if needed
if (!requireNamespace("dplyr", quietly = TRUE)) {
  install.packages("dplyr")
}
library(dplyr)

# Even better: Use pacman or similar
if (!requireNamespace("pacman", quietly = TRUE)) {
  install.packages("pacman")
}
pacman::p_load(dplyr, ggplot2, tidyr)

Use proper package management to check if packages are installed before loading them, and install them if needed.

Using setwd() in Scripts

# Anti-pattern: Using setwd() in scripts
setwd("/path/to/my/project")  # Not portable across different systems

# Better approach: Use here package or relative paths
library(here)
data <- read.csv(here("data", "mydata.csv"))

Avoid using setwd() in scripts as it makes them less portable. Use the here package or relative paths instead.

Not Using Proper Documentation

# Anti-pattern: No or minimal documentation
process_data <- function(data, threshold) {
  # Complex processing...
  return(result)
}

# Better approach: Use roxygen2 style documentation
#' Process data based on threshold
#'
#' @param data A data frame containing the input data
#' @param threshold Numeric threshold for filtering
#' @return A processed data frame
#' @examples
#' process_data(my_data, 0.5)
process_data <- function(data, threshold) {
  # Complex processing...
  return(result)
}

Document your functions and scripts properly, preferably using roxygen2-style comments for functions.

Using sapply() When Value Type Might Vary

# Anti-pattern: Using sapply() when return type might vary
result <- sapply(mixed_list, process_item)  # Might return list, vector, or matrix

# Better approach: Use vapply() with explicit return type
result <- vapply(mixed_list, process_item, numeric(1))

# Or use lapply() if you need a list
result <- lapply(mixed_list, process_item)

Avoid using sapply() when the return type might vary. Use vapply() with an explicit return type or lapply() instead.

Using Inefficient Data Structures

# Anti-pattern: Using data frames for simple lookups
lookup_df <- data.frame(key = c("A", "B", "C"), value = c(1, 2, 3))
get_value <- function(key) {
  lookup_df$value[lookup_df$key == key]  # Inefficient for large data
}

# Better approach: Use named vectors or environments
lookup_vec <- c(A = 1, B = 2, C = 3)
get_value <- function(key) {
  lookup_vec[key]  # Much faster
}

Choose appropriate data structures for your task. For lookups, named vectors or environments are often more efficient than data frames.

Not Using Proper Subsetting

# Anti-pattern: Inefficient subsetting
df <- data.frame(id = 1:1000, value = rnorm(1000))
subset_df <- df[df$id %in% target_ids, ]  # Creates a copy

# Better approach: Use data.table or dplyr
library(data.table)
dt <- as.data.table(df)
subset_dt <- dt[id %in% target_ids]  # More efficient

# Or with dplyr
library(dplyr)
subset_df <- df %>% filter(id %in% target_ids)

Use efficient subsetting methods, especially for large datasets. Consider using packages like data.table or dplyr for better performance.

Not Using Proper Naming Conventions

# Anti-pattern: Inconsistent or unclear naming
x <- 10
procesData <- function(d) { /* ... */ }
calc.result <- procesData(x)

# Better approach: Consistent, descriptive naming
temperature_celsius <- 10
process_data <- function(data) { /* ... */ }
calculated_result <- process_data(temperature_celsius)

Use consistent, descriptive naming conventions for variables and functions. The most common convention in R is snake_case (words separated by underscores).

Not Using Proper Testing

# Anti-pattern: No testing
calculate_mean <- function(x) {
  sum(x) / length(x)  # What if x is empty or contains NA?
}

# Better approach: Use testthat or similar
library(testthat)

test_that("calculate_mean works correctly", {
  expect_equal(calculate_mean(c(1, 2, 3)), 2)
  expect_equal(calculate_mean(c(1, NA, 3), na.rm = TRUE), 2)
  expect_error(calculate_mean(numeric(0)))
})

# And fix the function
calculate_mean <- function(x, na.rm = FALSE) {
  if (length(x) == 0) stop("Cannot calculate mean of empty vector")
  sum(x, na.rm = na.rm) / sum(!is.na(x) | !na.rm)
}

Write tests for your functions to ensure they work correctly in different scenarios. Use packages like testthat for structured testing.

Using print() for Debugging

# Anti-pattern: Using print() for debugging
process_data <- function(data) {
  print("Processing data...")
  result <- some_calculation(data)
  print(result)
  return(result)
}

# Better approach: Use logging packages
library(logger)

process_data <- function(data) {
  log_info("Processing data...")
  result <- some_calculation(data)
  log_debug("Calculation result: {result}")
  return(result)
}

Avoid using print() statements for debugging. Use proper logging packages like logger or futile.logger instead.

Not Using Proper Memory Management

# Anti-pattern: Creating large intermediate objects
process_large_data <- function(data) {
  temp1 <- expensive_operation1(data)  # Large intermediate object
  temp2 <- expensive_operation2(temp1)  # Another large object
  result <- final_calculation(temp2)
  return(result)
}

# Better approach: Clean up intermediate objects
process_large_data <- function(data) {
  temp1 <- expensive_operation1(data)
  temp2 <- expensive_operation2(temp1)
  rm(temp1)  # Remove when no longer needed
  gc()  # Suggest garbage collection
  result <- final_calculation(temp2)
  return(result)
}

Be mindful of memory usage, especially when working with large datasets. Remove large objects when they’re no longer needed and consider using packages like data.table or ff for out-of-memory processing.

Using Default Arguments Incorrectly

# Anti-pattern: Mutable default arguments
add_to_list <- function(item, my_list = c()) {
  my_list <- c(my_list, item)
  return(my_list)
}
# This works as expected in R, unlike Python, but is still confusing

# Better approach: Initialize inside the function
add_to_list <- function(item, my_list = NULL) {
  if (is.null(my_list)) my_list <- c()
  my_list <- c(my_list, item)
  return(my_list)
}

Be careful with default arguments, especially when they are complex objects. Initialize them inside the function if needed.

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