Calling R

Introduction

R language is one of powerful data mining tools, and its community is very large in the world (See the website: http://www.r-project.org/). Adding the R language into GAMA is our strong endeavors to accelerate many statistical, data mining tools into GAMA.

RCaller 2.0 package (Website: http://code.google.com/p/rcaller/) is used for GAMA 1.6.1.

Table of contents

• Introduction
  • Configuration in GAMA
  • Calling R from GAML
    • Calling the built-in operators
      • Example 1
    • Calling R codes from a text file (.txt) WITHOUT the parameters
      • Example 2
      • Correlation.R file
    • Output
      • Example 3
      • RandomForest.R file
• Load the package:
• Read data from iris:
• Build the decision tree:
• Build the random forest of 50 decision trees:
• Predict the acceptance of test set:
• Calculate the accuracy: * Output * Calling R codes from a text file (.R, .txt) WITH the parameters * Example 4 * Mean.R file * Output * Example 5 * AddParam.R file * Output

Configuration in GAMA

1) Install R language into your computer.

2) In GAMA, select menu option: Edit/Preferences.

3) In “Config RScript’s path”, browse to your “Rscript” file (R language installed in your system).

Notes: Ensure that install.packages(“Runiversal”) is already applied in R environment.

Calling R from GAML

Calling the built-in operators

Example 1

model CallingR

global {
	list X <- [2, 3, 1];
	list Y <- [2, 12, 4]; 

	list result;
	
	init{
		write corR(X, Y); // -> 0.755928946018454
		write meanR(X); // -> 2.0
	}
}

Calling R codes from a text file (.R,.txt) WITHOUT the parameters

Using R_compute(String RFile) operator. This operator DOESN’T ALLOW to add any parameters form the GAML code. All inputs is directly added into the R codes. Remarks: Don’t let any white lines at the end of R codes. R_compute will return the last variable of R file, this parameter can be a basic type or a list. Please ensure that the called packages must be installed before using.

Example 2

model CallingR

global
{
	list result;

	init{
		result <- R_compute("C:/YourPath/Correlation.R");
		write result at 0;
	}
}

Above syntax is deprecated, use following syntax with R_file instead of R_compute:

model CallingR

global
{
	file result;

	init{
		result <- R_file("C:/YourPath/Correlation.R");
		write result.contents;
	}
}

Correlation.R file

x <- c(1, 2, 3)

y <- c(1, 2, 4)

result <- cor(x, y, method = "pearson")

Output

result::[0.981980506061966]

Example 3

model CallingR

global
{
	list result;

	init{
		result <- R_compute("C:/YourPath/RandomForest.R");

		write result at 0;
	}
}

RandomForest.R file

# Load the package:

library(randomForest)

# Read data from iris:

data(iris)

nrow<-length(iris[,1])

ncol<-length(iris[1,])

idx<-sample(nrow,replace=FALSE)

trainrow<-round(2*nrow/3)

trainset<-iris[idx[1:trainrow],]

# Build the decision tree:

trainset<-iris[idx[1:trainrow],]

testset<-iris[idx[(trainrow+1):nrow],]

# Build the random forest of 50 decision trees:

model<-randomForest(x= trainset[,-ncol], y= trainset[,ncol], mtry=3, ntree=50)

# Predict the acceptance of test set: 

pred<-predict(model, testset[,-ncol], type="class")

# Calculate the accuracy:

acc<-sum(pred==testset[, ncol])/(nrow-trainrow)

Output

acc::[0.98]

Calling R codes from a text file (.R, .txt) WITH the parameters

Using R_compute_param(String RFile, List vectorParam) operator. This operator ALLOWS to add the parameters from the GAML code.

Remarks: Don’t let any white lines at the end of R codes. R_compute_param will return the last variable of R file, this parameter can be a basic type or a list. Please ensure that the called packages must be installed before using.

Example 4

model CallingR

global
{
	list X <- [2, 3, 1];
	list result;

	init{
		result <- R_compute_param("C:/YourPath/Mean.R", X);
		write result at 0;
	}
}

Mean.R file

result <- mean(vectorParam)

Output

result::[3.33333333333333]

Example 5

model CallingR

global {
	list X <- [2, 3, 1];
	list result;
	
        init{
		result <- R_compute_param("C:/YourPath/AddParam.R", X);
		write result at 0;
	}
}

AddParam.R file

v1 <- vectorParam[1]

v2<-vectorParam[2]

v3<-vectorParam[3]

result<-v1+v2+v3

Output

result::[10] //: # (endConcept|call_r)