mcpbeat Sign in

R Oop Skill for Claude

R object-oriented programming guide for S7, S3, S4, and vctrs. Use when designing R classes or choosing an OOP system.

2k tokens
context cost
the whole folder, loaded on every use
1
files
instructions only
0
copies elsewhere
how many repositories repackaged it
188
stars on the repo
on the repository, not the skill itself

Install

one command, takes just this skill from the repository
npx skills add https://github.com/ab604/claude-code-r-skills --skill r-oop

The instruction itself

22 sections, as written by the author

R Object-Oriented Programming

*S7, S3, S4, and vctrs: choosing the right OOP system for your needs*

S7: Modern OOP for New Projects

  • S7 combines S3 simplicity with S4 structure
  • Formal class definitions with automatic validation
  • Compatible with existing S3 code
# S7 class definition
Range <- new_class("Range",
  properties = list(
    start = class_double,
    end = class_double
  ),
  validator = function(self) {
    if (self@end < self@start) {
      "@end must be >= @start"
    }
  }
)

# Usage - constructor and property access
x <- Range(start = 1, end = 10)
x@start  # 1
x@end <- 20  # automatic validation

# Methods
inside <- new_generic("inside", "x")
method(inside, Range) <- function(x, y) {
  y >= x@start & y <= x@end
}

OOP System Decision Matrix

S7 vs vctrs vs S3/S4 Decision Tree

Start here: What are you building?

1. Vector-like objects (things that behave like atomic vectors)

Use vctrs when:
- Need data frame integration (columns/rows)
- Want type-stable vector operations
- Building factor-like, date-like, or numeric-like classes
- Need consistent coercion/casting behavior
- Working with existing tidyverse infrastructure

Examples: custom date classes, units, categorical data

2. General objects (complex data structures, not vector-like)

Use S7 when:
- NEW projects that need formal classes
- Want property validation and safe property access (@)
- Need multiple dispatch (beyond S3's double dispatch)
- Converting from S3 and want better structure
- Building class hierarchies with inheritance
- Want better error messages and discoverability

Use S3 when:
- Simple classes with minimal structure needs
- Maximum compatibility and minimal dependencies
- Quick prototyping or internal classes
- Contributing to existing S3-based ecosystems
- Performance is absolutely critical (minimal overhead)

Use S4 when:
- Working in Bioconductor ecosystem
- Need complex multiple inheritance (S7 doesn't support this)
- Existing S4 codebase that works well

Detailed S7 vs S3 Comparison

| Feature | S3 | S7 | When S7 wins |

|---------|----|----|---------------|

| Class definition | Informal (convention) | Formal (new_class()) | Need guaranteed structure |

| Property access | $ or attr() (unsafe) | @ (safe, validated) | Property validation matters |

| Validation | Manual, inconsistent | Built-in validators | Data integrity important |

| Method discovery | Hard to find methods | Clear method printing | Developer experience matters |

| Multiple dispatch | Limited (base generics) | Full multiple dispatch | Complex method dispatch needed |

| Inheritance | Informal, NextMethod() | Explicit super() | Predictable inheritance needed |

| Migration cost | - | Low (1-2 hours) | Want better structure |

| Performance | Fastest | ~Same as S3 | Performance difference negligible |

| Compatibility | Full S3 | Full S3 + S7 | Need both old and new patterns |

Practical Guidelines

Choose S7 when you have

# Complex validation needs
Range <- new_class("Range",
  properties = list(start = class_double, end = class_double),
  validator = function(self) {
    if (self@end < self@start) "@end must be >= @start"
  }
)

# Multiple dispatch needs
method(generic, list(ClassA, ClassB)) <- function(x, y) ...

# Class hierarchies with clear inheritance
Child <- new_class("Child", parent = Parent)

Choose vctrs when you need

# Vector-like behavior in data frames
percent <- new_vctr(0.5, class = "percentage")
data.frame(x = 1:3, pct = percent(c(0.1, 0.2, 0.3)))  # works seamlessly

# Type-stable operations
vec_c(percent(0.1), percent(0.2))  # predictable behavior
vec_cast(0.5, percent())          # explicit, safe casting

Choose S3 when you have

# Simple classes without complex needs
new_simple <- function(x) structure(x, class = "simple")
print.simple <- function(x, ...) cat("Simple:", x)

# Maximum performance needs (rare)
# Existing S3 ecosystem contributions

S3 Patterns

Basic S3 Class

# Constructor
new_person <- function(name, age) {
  stopifnot(is.character(name), length(name) == 1)
  stopifnot(is.numeric(age), length(age) == 1)

  structure(
    list(name = name, age = age),
    class = "person"
  )
}

# Print method
print.person <- function(x, ...) {
  cat("Person:", x$name, "(age", x$age, ")\n")
  invisible(x)
}

# Generic + method
greet <- function(x) UseMethod("greet")
greet.person <- function(x) {
  cat("Hello, my name is", x$name, "\n")
}
greet.default <- function(x) {
  cat("Hello!\n")
}

S3 Inheritance

# Child class
new_employee <- function(name, age, company) {
  obj <- new_person(name, age)
  obj$company <- company
  class(obj) <- c("employee", class(obj))
  obj
}

# Method with inheritance
print.employee <- function(x, ...) {
  NextMethod()  # Call parent print method
  cat("Works at:", x$company, "\n")
  invisible(x)
}

S7 Patterns

Basic S7 Class

library(S7)

# Define class
Person <- new_class("Person",
  properties = list(
    name = class_character,
    age = class_numeric
  ),
  validator = function(self) {
    if (self@age < 0) {
      "@age must be non-negative"
    }
  }
)

# Create instance
bob <- Person(name = "Bob", age = 30)
bob@name  # "Bob"
bob@age <- 31  # Validated assignment

S7 Methods

# Define generic
greet <- new_generic("greet", "x")

# Add method
method(greet, Person) <- function(x) {
  cat("Hello, my name is", x@name, "\n")
}

# Default method
method(greet, class_any) <- function(x) {
  cat("Hello!\n")
}

S7 Inheritance

Employee <- new_class("Employee",
  parent = Person,
  properties = list(
    company = class_character
  )
)

# Override method
method(greet, Employee) <- function(x) {
  super(x, Person)@greet()  # Call parent method
  cat("I work at", x@company, "\n")
}

S7 Multiple Dispatch

# Generic with multiple dispatch
combine <- new_generic("combine", c("x", "y"))

# Method for specific combination
method(combine, list(Person, Person)) <- function(x, y) {
  cat(x@name, "meets", y@name, "\n")
}

method(combine, list(Person, class_character)) <- function(x, y) {
  cat(x@name, "receives message:", y, "\n")
}

Migration Strategy

  • S3 -> S7: Usually 1-2 hours work, keeps full compatibility
  • S4 -> S7: More complex, evaluate if S4 features are actually needed
  • Base R -> vctrs: For vector-like classes, significant benefits
  • Combining approaches: S7 classes can use vctrs principles internally

Migration Example: S3 to S7

# Original S3
new_person_s3 <- function(name, age) {
  structure(list(name = name, age = age), class = "person")
}

# Migrated S7
Person <- new_class("Person",
  properties = list(
    name = class_character,
    age = class_numeric
  )
)

# S7 is backwards compatible with S3 generics
# Existing S3 methods still work

When NOT to Use OOP

Sometimes simpler approaches are better:

# Don't create a class for simple data
# BAD
Point <- new_class("Point", properties = list(x = class_double, y = class_double))

# GOOD - just use a named list or vector
point <- c(x = 1.5, y = 2.3)

# Don't create classes for one-off operations
# Use functions instead
distance <- function(p1, p2) {
  sqrt((p1["x"] - p2["x"])^2 + (p1["y"] - p2["y"])^2)
}

Other skills for the same job

different authors, same section of the catalogue
Protocolsio Integration
by christophacham
×4

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

16k tokens
Tailored Resume Generator
by frostant
×4

Analyzes job descriptions and generates tailored resumes that highlight relevant experience, skills, and achievements to maximize interview chances

3k tokens
Excalidraw Diagram Generator
by github
vendor ×3

Generate Excalidraw diagrams from natural language descriptions. Use when asked to "create a diagram", "make a flowchart", "visualize a process", "draw a system architecture", "create a mind map", or "generate an Excalidraw file". Supports flowcharts, relationship diagrams, mind maps, and system architecture diagrams. Outputs .excalidraw JSON files that can be opened directly in Excalidraw.

36k tokens scripts
Expo Dev Client
by openai
vendor ×3

Build and distribute Expo development clients locally or via TestFlight

961 tokens
Executing Plans
by ZhanlinCui
×3

Use when you have a written implementation plan to execute in a separate session with review checkpoints

542 tokens
Anndata
by christophacham
×3

Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.

16k tokens
Benchling Integration
by christophacham
×3

Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

14k tokens
Biopython
by christophacham
×3

Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.

24k tokens

How to use it

Copy the folder

Take ab604/r-oop from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.