OHDSI/BigKnn

Name: BigKnn

Owner: Observational Health Data Sciences and Informatics

Description: An R package implementing a large scale k-nearest neighbor classifier using the Lucene search engine

Created: 2016-02-04 13:56:34.0

Updated: 2017-03-14 17:22:56.0

Pushed: 2017-05-19 17:28:55.0

Homepage: null

Size: 4022

Language: R

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README

BigKnn

Introduction

An R package implementing a large scale k-nearest neighbor (KNN) classifier using the Lucene search engine.

Features

• Build KNN classifiers of arbitrary scale (up to millions of rows, millions of features)
• Fast classification performance due to use of highly optimized search engine (Lucene)
• Supports both weighted and unweighted KNN

Examples

riates <- data.frame(rowIds = c(1,1,1,2,2,3),
                     covariateIds = c(10,11,12,10,11,12),
                     covariateValues = c(1,1,1,1,1,1))

omes <- data.frame(rowIds = c(1,2,3),
                   y = c(1,0,0))

xFolder <- "s:/temp/lucene"

dKnn(outcomes = ff::as.ffdf(outcomes),
     covariates = ff::as.ffdf(covariates),
     indexFolder = indexFolder)

iction <- predictKnn(covariates = ff::as.ffdf(covariates),
                     indexFolder = indexFolder,
                     k = 10,
                     weighted = TRUE)

Technology

BigKnn is an R package using the Java based Lucene search engine. The data for the KNN is stored in a folder on the local file system.

System Requirements

Requires R. Also requires Java 1.7 or higher (Oracle Java is recommended) .

Dependencies

Please note that this package requires Java to be installed. If you don't have Java already intalled on your computed (on most computers it already is installed), go to java.com to get the latest version.

BigKnn also depends on the OHDSI Cyclops and OhdsiRTools packages.

Getting Started

Use the following commands in R to install the BigKnn package:

all.packages("drat")
::addRepo("OHDSI")
all.packages("BigKnn")

Getting Involved

• Package manual: BigKnn manual
• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

BigKnn is licensed under Apache License 2.0. Lucene fall under its own Apache License 2.0.

Development

BigKnn is being developed in R Studio and Eclipse

Development status

Under development. Use at your own risk.