title: "randomForest.ddR README" author: "Vishrut Gupta, Arash Fard, Winston Li, Matthew Saltz" date: "2015-10-22"

Start the parallel backend with 2 instances

library(ddR)
library(randomForest.ddR)
library(randomForest)
nInst = 2
useBackend(parallel,executors = nInst)

Generate some data:

K = 10 clusters, ncol = 10 features, nrow ~ 10000 observations

ncol = 10
nrow = 10000
nrow = as.integer(nrow/nInst)
K = 10

Generate centers of clusters

centers = 100*matrix(rnorm(K*ncol),nrow = K)

Generate observations of features

generateRFData <- function(id, centers, nrow, ncol) {
	offsets = matrix(rnorm(nrow*ncol),nrow = nrow,ncol = ncol)
	cluster_ids = sample.int(nrow(centers),nrow,replace = TRUE)
	feature_obs = centers[cluster_ids,] + offsets
	features <- data.frame(cluster_ids, feature_obs)
}
features <- dmapply(generateRFData,id = 1:nInst,
                MoreArgs = list(centers = centers, nrow = nrow, ncol = ncol),
		output.type = "dframe", 
		combine = "rbind", nparts = c(nInst,1))
colnames(features) <- paste("X",1:ncol(features),sep="")

Example of drandomForest function using formula interface on dframe data

cat("\nStarting drandomForest using formula interface on dframe:")
training <- system.time(model <- drandomForest(X1 ~ ., features,nExecutor = nInst))[3]
predicting <- system.time(predictions <- predict(model, features))[3]
cat("\n\ttraining model took: \t", training," seconds \n\tpredictions took: \t",predicting," seconds\n")

Reformatting data to match formula interface on data.frame data

features_local <- collect(features)

Example of drandomForest function using data.frame and formula interface

cat("\nStarting drandomForest using formula over data.frame interface:")
training <- system.time(model <- drandomForest(X1 ~ ., features_local,nExecutor = nInst))[3]
predicting <- system.time(predictions <- predict(model, features_local))[3]
cat("\n\ttraining model took: \t", training," seconds \n\tpredictions took: \t",predicting," seconds\n")

Reformatting data to match x,y interface on darray data

cat("\nStarting drandomForest using x,y interface on darrays")
features_x = dmapply(function(x) data.matrix(x)[,-1], parts(features),
		output.type = "darray", combine = "rbind", 
		nparts = nparts(features))
features_y = dmapply(function(x) matrix(x[,1],ncol = 1), parts(features),
		output.type = "darray", combine = "rbind", 
		nparts = nparts(features))

Example of drandomForest function using x,y interface on darrays

training <- system.time(model <- drandomForest(x = features_x, y = features_y,nExecutor = nInst))[3]
predicting <- system.time(predictions <- predict(model, features_x))[3]
cat("\n\ttraining model took: \t", training," seconds\n\tpredictions took: \t",predicting," seconds\n")

Reformatting data to match x,y interface on matrix data

cat("\nStarting drandomForest using x,y matrix interface")
features_x = collect(features_x)
features_y = collect(features_y)

Example of drandomForest function using x,y interface on matrix data

training <- system.time(model <- drandomForest(x = features_x, y = features_y,nExecutor = nInst))[3]
predicting <- system.time(predictions <- predict(model, features_x))[3]
cat("\n\ttraining model took: \t", training," seconds\n\tpredictions took: \t",predicting," seconds\n")

Comparison to randomForest function using data.frame and formula interface

cat("\nStarting randomForest using formula interface on data.frame")
training <- system.time(model <- randomForest(X1 ~ ., features_local))[3]
predicting <- system.time(predictions <- predict(model, features_local))[3]
cat("\n\ttraining model took: \t", training," seconds\n\tpredictions took: \t",predicting," seconds\n")

How to Contribute

You can help us in different ways:

1. Reporting issues.
2. Contributing code and sending a Pull Request.

In order to contribute the code base of this project, you must agree to the Developer Certificate of Origin (DCO) 1.1 for this project under GPLv2+:

By making a contribution to this project, I certify that:

(a) The contribution was created in whole or in part by me and I have the 
    right to submit it under the open source license indicated in the file; or
(b) The contribution is based upon previous work that, to the best of my 
    knowledge, is covered under an appropriate open source license and I 
    have the right under that license to submit that work with modifications, 
    whether created in whole or in part by me, under the same open source 
    license (unless I am permitted to submit under a different license), 
    as indicated in the file; or
(c) The contribution was provided directly to me by some other person who 
    certified (a), (b) or (c) and I have not modified it.
(d) I understand and agree that this project and the contribution are public and
    that a record of the contribution (including all personal information I submit 
    with it, including my sign-off) is maintained indefinitely and may be 
    redistributed consistent with this project or the open source license(s) involved.

To indicate acceptance of the DCO you need to add a Signed-off-by line to every commit. E.g.:

Signed-off-by: John Doe <john.doe@hisdomain.com>

To automatically add that line use the -s switch when running git commit:

$ git commit -s