thealgorithms/r

Collection of various algorithms implemented in R.

The Algorithms - R

R is a programming language and free software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing. The R language is widely used among statisticians and data miners for developing statistical software and data analysis. Polls, data mining surveys and studies of scholarly literature databases show substantial increases in popularity in recent years. As of November 2019, R ranks 16th in the TIOBE index, a measure of popularity of programming languages. (Wikipedia)

All algorithms can be found in the DIRECTORY.md file ordered by folder.

Contribution Guidelines

Please ensure to follow the points stated below if you would like to contribute:

• If your proposing a new algorithm or making changes to an existing one, make sure your code works. Reviewers or the general user must be able to directly emplace it in an R environment and get the desired output.
• Add an example to showcase the use of an algorithm proposed. It can be commented.
• Follow proper naming convention for variables (use . or _ to seperate terms, such as results.df for a data frame containing some results) and filenames (follow the convention that has been followed for files under the directory your committing to).
• Feel free to add links here to the newly added file(s), but ensure that they do not result in a merge conflict with different versions of this readme under previous pull requests.

r's Issues

Organise the files in a better way.

Put similar algorithms under an umbrella directory and make the files more organised.

Missing dependencies in .R files?

Hello,

I am having problems running some of the algorithms because they seem to expect me to have certain variables or methods loaded that I do not have.

For example, for DecisionTree.R:

library(rpart)
x <- cbind(x_train,y_train)
# grow tree 
fit <- rpart(y_train ~ ., data = x,method="class")
summary(fit)
# Predict Output 
predicted= predict(fit,x_test)

When I attempt to run this script in RStudio, I get the following errors:

Error in cbind(x_train, y_train) : object 'x_train' not found
> # grow tree 
> fit <- rpart(y_train ~ ., data = x,method="class")
Error in is.data.frame(data) : object 'x' not found
> summary(fit)
Error in object[[i]] : object of type 'closure' is not subsettable
> # Predict Output 
> predicted= predict(fit,x_test)
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "function"
> predicted= predict(fit,x_test)
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "function"

Are there other R files or packages that the user is expected to have installed, aside from the packages already included?

I am using a fresh RStudio install (version 1.1.463) on Ubuntu 16.04 with R version 3.2.3.

Where are the sample datasets?

I want to run the code in Rstudio, but all the data are not found.
Anyone can tell me where to download the datasets?

Thank you

Yg

Ggg

Create binary search algorithm in R

We can add a binary search algorithm in R under the searches folder.

Add documentation in the code (something similar to Doxygen)

Something similar to an issue in the Julia repository. See TheAlgorithms/Julia#7.

Improve Readme

Many new algorithms were added. The readme file can be updated with those new algorithms.
something like https://github.com/TheAlgorithms/Python/blob/master/README.md

Create Tim Sort Program

We can add a Tim Sort program in sorting_algorithms folder.

Establish Naming Conventions

• Folders names should be of the form A-Descriptive-Name
• Filenames should be of the form filename.ext

Duplicate files in documentation directory, only differing in case

When cloning the repo to my Windows machine, I received the following warning message:

Cloning into 'Algorithms-in-R'...
remote: Enumerating objects: 984, done.
remote: Counting objects: 100% (984/984), done.
remote: Compressing objects: 100% (424/424), done.
remote: Total 984 (delta 532), reused 984 (delta 532), pack-reused 0
Receiving objects: 100% (984/984), 927.20 KiB | 27.27 MiB/s, done.
Resolving deltas: 100% (532/532), done.
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

  'documentation/ANN.md'
  'documentation/ann.md'
  'documentation/K_Folds.md'
  'documentation/k_folds.md'
  'documentation/kmeans_raw_R.md'
  'documentation/kmeans_raw_r.md'
  'documentation/KNN.md'
  'documentation/knn.md'
  'documentation/linearRegressionRawR.md'
  'documentation/linearregressionrawr.md'
  'documentation/SVM.md'
  'documentation/svm.md'

Peter@bolide MINGW64 /c/repos/Learn/Algorithms
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So it seems to me these files are duplicated and only differing in case. However from each pair, one of them has a newer commit. So you might want to check these changes to see whether they have been applied to the right files, or correct the case of the most recent file and delete the older other one.

These changes are mostly from #88 it seems.

T

idk

ajaja

Update contribution guidelines

Once we figure exactly what the standard should be and overhaul all algorithms according to this standard.

print ("xyecoc")

add more Data Science and Data Analysis related algorithms

Multiple sequence alignment using R

myAlignment<- msaClustalW("mydata", type = "dna")
use default substitution matrix
Error in convertAlnRows(result$msa, type) : There is an invalid aln file!

I'm facing issue using the above code. I want to perform multiple sequence alignment on csv or fasta file. but getting this error. please help me to solve it.

Add Gitpod Setup

Description

Setup Gitpod environment for running the repository in Gitpod.

Add Gitpod ready to code Badge to the README.md file.

Other repos like Python and Java in TheAlgorithms use gitpod.

Screenshots

I have worked on silimar issue TheAlgorithms/PHP#130

I would like to work on this issue

R

Create searching algorithm in R

We can create a folder for searching algorithm in R language, and add certain searching algorithms such as linear search and binary search.

Reproducible code

I think as a standard all scripts should be completely independent and reproducible. I.e. people should be able to copy and paste code in their R REPL session without errors. This is currently not the case with many scripts in this repo. Instead of supplying example data, many algorithms are written as "templates" where one has to input their own data. However, there's no information what the data structure should even be.

R has many built in datasets, so these can be used to run algorithms with. If the script is just a function definition, then there should be an example usage of the function.

I could list here all scripts that need to be written this way.

What do you think?

Create Cocktail Sort program

We can add a Cocktail Sort program in sorting_algorithms folder.

Adding Quantitative finance algorithms

It will involve implementation of various financial algorithms in R

Add more algorithms

Everyone is welcome to add more algorithms to this project. This repo is new so we need contributions from all.

MSA problem in R Studio

Hi! I'm working for my midterms and I need answers ASAP

I downloaded sequences from NCBI (Complete Record > Fasta) and I installed necessary packages. By the time I reached using msa, the error appears. I don't know what to do anymore. Help! This is the codes by the way.

AlignNeeded = TRUE # The program reads fasta file and aligns it
if (AlignNeeded) {

file <- readDNAStringSet(fname)#for reading multiple DNA sequences from msa package
file
}

cb<- msa(file) # multiple sequence alignment from msa package
cb # aligned the 120 sequences in the file

use default substitution matrix
Error in convertAlnRows(result$msa, type) : There is an invalid aln file!

AFTER READING A SOLUTION HERE, I TRIED IT OUT, HERE'S THE PROBLEM

cb<- msa(file) # multiple sequence alignment from msa package
use default substitution matrix
Error in convertAlnRows(result$msa, type) : There is an invalid aln file!
library(Biostrings)
file_path <- "sequence-5.fasta"
cb <- msa(file_path, filetype = "sequence-5.fasta", type = "DNA")
Error in msaFun(inputSeqs = inputSeqs, cluster = cluster, gapOpening = gapOpening, :
The following parameters are not known
(or have been specifiedmore often than once):
filetype

PLEASE HELP ME