Host a CRAN mirror using Docker

CRAN mirrors are the backbone to everyday common R usage. They provide the R website and most of the R packages today. Currently there are about 104 official CRAN mirrors. Hosting a CRAN mirror is one step to help the R community and is explained here.

To ease that process, at BNOSAC, we have created a Docker image which sets up a CRAN mirror.
That Docker image can be found and is available for download at the following docker registry: https://registry.hub.docker.com/u/bnosac/cran-mirror

For people who don't know Docker, it is basically a tool which allows developers to containerise an application. In this case, the application is to run a CRAN mirror.
How does it work. 3 steps:

1. Install Docker on your computer or server as explained here, if you haven't done this already.
2. Pull the docker image: docker pull bnosac/cran-mirror
3. Run the CRAN mirror: docker run -p 22:22 -p 80:80 -v /home/bnosac/CRAN/:/var/www/html -d bnosac/cran-mirror

That's it! It started synching CRAN on /home/bnosac/CRAN and will synch every day at 02h30 UTC. You can now go to 0.0.0.0 in your browser or find the ip address where it is running and go to that address in your browser to see the R website (see https://registry.hub.docker.com/u/bnosac/cran-mirror for more info).

Now what can you do with it?

• have a local CRAN mirror in your company
• install.packages("data.table", repos = "mylocalmirror")
• serve the community with another mirror if a closeby mirror is not readily available

Machine learning with R & Advanced R programming course

This year, BNOSAC offers 2 R courses in cooperation with the Leuven Statistics Research Center. The courses are part of the Leuven STATistics STATe of the Art Training Initiative and are given in Leuven (Belgium).

For R users and data scientists we offer a 2 short courses on R programming & statistical learning. Namely

* Advanced R programming topics (November 3-4, 2014)
* Statistical Machine Learning with R (November 27-28, 2014):

You can download the brochure with the courses here: http://lstat.kuleuven.be/training/HR_BRO_LSTAT_2014-2015.pdf

Interested? Registration can be done here.

RMOA package for running streaming classifcation & regression models now at CRAN

Last week, we released the RMOA package at CRAN (http://cran.r-project.org/web/packages/RMOA). It is an R package to allow building streaming classification and regression models on top of MOA.
MOA is the acronym of 'Massive Online Analysis' and it is the most popular open source framework for data stream mining which is being developed at the University of Waikato: http://moa.cms.waikato.ac.nz. Our RMOA package interfaces with MOA version 2014.04 and focusses on building, evaluating and scoring streaming classification & regression models on data streams.

Classification & regression models which are possible through RMOA are:

- Classification trees:
  * AdaHoeffdingOptionTree
  * ASHoeffdingTree
  * DecisionStump
  * HoeffdingAdaptiveTree
  * HoeffdingOptionTree
  * HoeffdingTree
  * LimAttHoeffdingTree
  * RandomHoeffdingTree
- Bayesian classification:
  * NaiveBayes
  * NaiveBayesMultinomial
- Active learning classification:
  * ActiveClassifier
- Ensemble (meta) classifiers:
  * Bagging
      + LeveragingBag
      + OzaBag
      + OzaBagAdwin
      + OzaBagASHT
  * Boosting
      + OCBoost
      + OzaBoost
      + OzaBoostAdwin
  * Stacking
      + LimAttClassifier
  * Other
      + AccuracyUpdatedEnsemble
      + AccuracyWeightedEnsemble
      + ADACC
      + DACC
      + OnlineAccuracyUpdatedEnsemble
      + TemporallyAugmentedClassifier
      + WeightedMajorityAlgorithm

- Regression modelling:
  * AMRulesRegressor
  * FadingTargetMean
  * FIMTDD
  * ORTO
  * Perceptron
  * RandomRules
  * SGD (Stochastic Gradient Descent)
  * TargetMean

Interfaces are implemented to model data in standard files (csv, txt, delimited), ffdf data (from the ff package), data.frames and matrices.

Documentation of MOA directed towards RMOA users can be found at http://jwijffels.github.io/RMOA
Examples on the use of RMOA can be found in the documentation, on github at https://github.com/jwijffels/RMOA or e.g. by viewing the showcase at http://bnosac.be/index.php/blog/16-rmoa-massive-online-data-stream-classifications-with-r-a-moa

If you need support on building streaming models on top of your large dataset. Get into contact.
 

RMOA: Massive online data stream classifications with R & MOA

1. It uses a limited amount of memory. So this means no RAM issues when building models.
2. Processes one example at a time, and will run over it only once
3. Works incrementally - so that a model is directly ready to be used for prediction purposes

1. Easy to set up data streams on data in RAM (data.frame/matrix), data in files (csv, delimited, flat table) as well as out-of memory data in an ffdf (ff package).
2. Easy to set up a MOA classification model 
3. There are 26 classification models available which range from
   1. Classification Trees (AdaHoeffdingOptionTree, ASHoeffdingTree, DecisionStump, HoeffdingAdaptiveTree, HoeffdingOptionTree, HoeffdingTree, LimAttHoeffdingTree, RandomHoeffdingTree)
   2. Bayes Rule (NaiveBayes, NaiveBayesMultinomial)
   3. Ensemble learning
      • Bagging (LeveragingBag, OzaBag, OzaBagAdwin, OzaBagASHT)
      • Boosting (OCBoost, OzaBoost, OzaBoostAdwin)
      • Stacking (LimAttClassifier)
      • Other (AccuracyUpdatedEnsemble, AccuracyWeightedEnsemble, ADACC, DACC, OnlineAccuracyUpdatedEnsemble, TemporallyAugmentedClassifier, WeightedMajorityAlgorithm)
   4. Active learning (ActiveClassifier)
4. Easy R-familiar interface to train the model on streaming data with a familiar formula interface as in trainMOA(model, formula, data, subset, na.action = na.exclude, ...)
5. Easy to predict new data alongside the model as in predict(object, newdata, type = "response", ...)

## 
## Installation from github
## 
library(devtools)
install.packages("ff")
install.packages("rJava")
install_github("jwijffels/RMOA", subdir="RMOAjars/pkg")
install_github("jwijffels/RMOA", subdir="RMOA/pkg")

## 
## HoeffdingTree example
## 
require(RMOA)
hdt <- HoeffdingTree(numericEstimator = "GaussianNumericAttributeClassObserver")
hdt
## Define a stream - e.g. a stream based on a data.frame
data(iris)
iris <- factorise(iris)
irisdatastream <- datastream_dataframe(data=iris)
  
## Train the HoeffdingTree on the iris dataset
mymodel <- trainMOA(model = hdt, 
  formula = Species ~ Sepal.Length + Sepal.Width + Petal.Length, 
  data = irisdatastream)
## Predict using the HoeffdingTree on the iris dataset
scores <- predict(mymodel, newdata=iris, type="response")
table(scores, iris$Species)
scores <- predict(mymodel, newdata=iris, type="votes")
head(scores)

## 
## Boosted set of HoeffdingTrees
## 
irisdatastream <- datastream_dataframe(data=iris)
mymodel <- OzaBoost(baseLearner = "trees.HoeffdingTree", ensembleSize = 30)
mymodel <- trainMOA(model = mymodel, 
  formula = Species ~ Sepal.Length + Sepal.Width + Petal.Length, 
  data = irisdatastream)
  
## Predict 
scores <- predict(mymodel, newdata=iris, type="response")
table(scores, iris$Species)
scores <- predict(mymodel, newdata=iris, type="votes")
head(scores)