first commit

.Rbuildignore

+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

+Package: group5labbonus
+Type: Package
+Title: What the Package Does (Short Line)
+Version: 1.0
+Date: 2024-11-03
+Author: Who wrote it
+Maintainer: Who to complain to <yourfault@somewhere.net>
+Description: More about what it does (maybe more than one line).
+License: GPL-3 + file LICENSE
+RoxygenNote: 7.3.2
+Encoding: UTF-8
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(ridgereg)

R/ridgereg.R

+#' Ridge Regression Reference Class
+#'
+#' This class implements ridge regression with methods for initialization, coefficient extraction,
+#' prediction, and printing the model summary.
+#'
+#' @field formula_string A character string representing the regression formula.
+#' @field data_string A character string representing the data frame used.
+#' @field formula A formula specifying the relationship between dependent and independent variables.
+#' @field data A data frame containing the variables specified in the formula.
+#' @field lambda A numeric value for the ridge penalty parameter.
+#' @field coefficients A matrix containing the estimated ridge regression coefficients.
+#' @field fitted_values A matrix of the fitted (predicted) values.
+#' @field residuals A matrix of the residuals (difference between actual and fitted values).
+#'
+#' @param formula A formula specifying the model.
+#' @param data A data frame containing the variables in the formula.
+#' @param lambda The ridge penalty parameter.
+#'
+#' @export ridgereg
+ridgereg <- setRefClass(
+  "ridgereg",
+  fields = list(
+    formula_string = "character",
+    data_string = "character",
+    formula = "formula",
+    data = "data.frame",
+    lambda = "numeric",
+    coefficients = "matrix",
+    fitted_values = "matrix",
+    residuals = "matrix"
+  ),
+  methods = list(
+    initialize = function(formula, data, lambda) {
+      formula_string <<- deparse(formula)
+      data_string <<- deparse(substitute(data))
+      lambda <<- lambda
+
+      X <- model.matrix(formula, data)
+      y <- data[[all.vars(formula)[1]]]
+
+      X_norm <- scale(X[, -1])
+      X_norm <- cbind(1, X_norm)
+
+      I <- diag(ncol(X_norm))
+      I[1, 1] <- 0
+      beta_ridge <- solve(t(X_norm) %*% X_norm + lambda * I) %*% t(X_norm) %*% y
+      coefficients <<- beta_ridge
+
+      fitted_values <<- X_norm %*% beta_ridge
+      residuals <<- y - fitted_values
+    },
+    print = function() {
+      class_name <- class(.self)[1]
+      cat("Call:\n")
+      cat(class_name,"(formula = ",formula_string ,", data = ",data_string,",lambda = ",lambda,")","\n", sep = "")
+      cat("\nCoefficients:\n")
+      coef_names <- rownames(coefficients)
+      coef_values <- as.vector(coefficients)
+      names(coef_values) <- coef_names
+      print.default(coef_values)
+    },
+    pred = function() {
+      return(as.vector(fitted_values))
+    },
+    coef = function() {
+      named_coefs <- setNames(as.vector(coefficients), rownames(coefficients))
+      return(named_coefs)
+    }
+  )
+)
+
+# model <- ridgereg$new(Sepal.Length ~ Sepal.Width + Petal.Length, data = iris, lambda = 0.1)
+# model$print()
+# model$pred()
+# model$coef()

Read-and-delete-me

+* Edit the help file skeletons in 'man', possibly combining help files for
+  multiple functions.
+* Edit the package 'DESCRIPTION'.
+* Edit the exports in 'NAMESPACE', and add necessary imports.
+* Put any C/C++/Fortran code in 'src'.
+* If you have compiled code, add a useDynLib() directive to 'NAMESPACE'.
+* Run R CMD build to build the package tarball.
+* Run R CMD check to check the package tarball.
+
+Read "Writing R Extensions" for more information.

group5labbonus.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette

man/fun.Rd

+\name{fun}
+\alias{fun}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{
+A Capitalized Title (ideally limited to 65 characters)
+}
+\description{
+%%  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+fun()
+}
+%- maybe also 'usage' for other objects documented here.
+\details{
+%%  ~~ If necessary, more details than the description above ~~
+}
+\value{
+%%  ~Describe the value returned
+%%  If it is a LIST, use
+%%  \item{comp1 }{Description of 'comp1'}
+%%  \item{comp2 }{Description of 'comp2'}
+%% ...
+}
+\references{
+%% ~put references to the literature/web site here ~
+}
+\author{
+%%  ~~who you are~~
+}
+\note{
+%%  ~~further notes~~
+}
+
+%% ~Make other sections like Warning with \section{Warning }{....} ~
+
+\seealso{
+%% ~~objects to See Also as \code{\link{help}}, ~~~
+}
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or standard data sets, see data().
+
+## The function is currently defined as
+function () 
+print()
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory (show via RShowDoc("KEYWORDS")):
+% \keyword{ ~kwd1 }
+% \keyword{ ~kwd2 }
+% Use only one keyword per line.
+% For non-standard keywords, use \concept instead of \keyword:
+% \concept{ ~cpt1 }
+% \concept{ ~cpt2 }
+% Use only one concept per line.

man/group5labbonus-package.Rd

+\name{group5labbonus-package}
+\alias{group5labbonus-package}
+\alias{group5labbonus}
+\docType{package}
+\title{
+\packageTitle{group5labbonus}
+}
+\description{
+\packageDescription{group5labbonus}
+}
+\details{
+%%  ~~ An overview of how to use the package, ~~
+%%  ~~ including the most important functions ~~
+}
+\author{
+\packageAuthor{group5labbonus}
+
+Maintainer: \packageMaintainer{group5labbonus}
+}
+\references{
+%%  ~~ Literature or other references for background information ~~
+}
+\keyword{package}
+
+%% Uncomment below to imitate parts of library(help = group5labbonus)
+%\section{The \file{DESCRIPTION} File}{\packageDESCRIPTION{group5labbonus}}
+%\section{Documentation Index}{\packageIndices{group5labbonus}}
+
+\seealso{
+%%  ~~ Optional links to other man pages, e.g. ~~
+%%  ~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
+}
+\examples{
+%%  ~~ Optional simple examples of the most important functions ~~
+}

man/ridgereg-class.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ridgereg.R
+\docType{class}
+\name{ridgereg-class}
+\alias{ridgereg-class}
+\alias{ridgereg}
+\title{Ridge Regression Reference Class}
+\arguments{
+\item{formula}{A formula specifying the model.}
+
+\item{data}{A data frame containing the variables in the formula.}
+
+\item{lambda}{The ridge penalty parameter.}
+}
+\description{
+This class implements ridge regression with methods for initialization, coefficient extraction,
+prediction, and printing the model summary.
+}
+\section{Fields}{
+
+\describe{
+\item{\code{formula_string}}{A character string representing the regression formula.}
+
+\item{\code{data_string}}{A character string representing the data frame used.}
+
+\item{\code{formula}}{A formula specifying the relationship between dependent and independent variables.}
+
+\item{\code{data}}{A data frame containing the variables specified in the formula.}
+
+\item{\code{lambda}}{A numeric value for the ridge penalty parameter.}
+
+\item{\code{coefficients}}{A matrix containing the estimated ridge regression coefficients.}
+
+\item{\code{fitted_values}}{A matrix of the fitted (predicted) values.}
+
+\item{\code{residuals}}{A matrix of the residuals (difference between actual and fitted values).}
+}}
+
+

tests/testthat.R

+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(group5labbonus)
+
+test_check("group5labbonus")

tests/testthat/test_ridgereg.R

+library(testthat)
+
+test_that("ridgereg initializes correctly", {
+  model <- ridgereg$new(Sepal.Length ~ Sepal.Width + Petal.Length, data = iris, lambda = 0.1)
+
+  # Check if coefficients are initialized correctly
+  expect_true(is.matrix(model$coefficients))
+  expect_equal(ncol(model$coefficients), 1)
+
+  # Check if fitted values and residuals are matrices
+  expect_true(is.matrix(model$fitted_values))
+  expect_true(is.matrix(model$residuals))
+})
+
+test_that("ridgereg predicts correctly", {
+  model <- ridgereg$new(Sepal.Length ~ Sepal.Width + Petal.Length, data = iris, lambda = 0.1)
+
+  # Test if predictions return a numeric vector
+  preds <- model$pred()
+  expect_true(is.numeric(preds))
+  expect_equal(length(preds), nrow(iris))
+})
+
+test_that("ridgereg coefficients extraction works", {
+  model <- ridgereg$new(Sepal.Length ~ Sepal.Width + Petal.Length, data = iris, lambda = 0.1)
+
+  # Test if coefficients are returned as a named numeric vector
+  coefs <- model$coef()
+  expect_true(is.numeric(coefs))
+  expect_true(!is.null(names(coefs)))
+})
+
+test_that("ridgereg print method displays correctly", {
+  model <- ridgereg$new(Sepal.Length ~ Sepal.Width + Petal.Length, data = iris, lambda = 0.1)
+
+  # Capture the print output
+  output <- capture.output(model$print())
+
+  # Check if the output contains relevant information
+  expect_true(any(grepl("Call:", output)))
+  expect_true(any(grepl("Coefficients:", output)))
+  expect_true(any(grepl("Sepal.Width", output)))
+})