Package 'rCMA' reference manual

Title:	R-to-Java Interface for 'CMA-ES'
Description:	Tool for providing access to the Java version 'CMAEvolutionStrategy' of Nikolaus Hansen. 'CMA-ES' is the Covariance Matrix Adaptation Evolution Strategy, see <https://www.lri.fr/~hansen/cmaes_inmatlab.html#java>.
Authors:	Wolfgang Konen <[email protected]>, Nikolaus Hansen <hansen .AT. lri.fr>
Maintainer:	Wolfgang Konen <[email protected]>
License:	GPL (>= 3)
Version:	1.1.1
Built:	2024-11-19 06:46:22 UTC
Source:	CRAN

R interface to the Java CMA-ES of Niko Hansen

Description

CMA-ES R-to-Java interface

Details

Package:	rCMA
Type:	Package
Version:	1.1
Date:	2015-04-30
License:	GPL (>= 3)
LazyLoad:	yes

rCMA is a package to perform CMA-ES optimization, using the *Java* implementation by Niko Hansen [Hansen2009].
CMA-ES [HansOst96, Hansen13] is the Covariance Matrix Adapting Evolutionary Strategy for numeric black box optimization.
The main features of rCMA are:

Abiltiy to start the Java CMA-ES optimization with fitness functions defined in R.
Constraint handling: Arbitrary constraints can be incorporated, see function parameter isFeasible in cmaOptimDP.
Extensibility: Full access to all methods of the Java class CMAEvolutionStrategy through package rJava. New methods can be added easily. See the documentation of cmaEvalMeanX for further details, explanation of JNI types and a full example.
Test and Debug: The access of Java methods from R allows for easy debugging and test of programs using CMAEvolutionStrategy through R scripts without the necessity to change the underlying JAR file.

The main entry point functions are cmaNew, cmaInit and cmaOptimDP.

Note: To install rJava properly on some Unix systmes, it might be necessary to issue as root the command R CMD javareconf once, or, as normal user to issue the command R CMD javareconf -e prior to installing package rJava or prior to loading library rJava.

Author(s)

Wolfgang Konen ([email protected])

References

[HansOst96] Hansen, N. and Ostermeier, A.: Adapting arbitrary normal mutation distributions in evolution strategies: The covariance matrix adaptation. In Proceedings of the 1996 IEEE International Conference on Evolutionary Computation, pp. 312-317, 1996. PDF.
[Hansen09] https://www.lri.fr/~hansen/javadoc Nikolaus Hansen: Javadoc for CMA-ES Java package fr.inria.optimization.cmaes, 2009.
[Hansen13] https://www.lri.fr/~hansen/cmaesintro.html Nikolaus Hansen: The CMA Evolution Strategy Web Page, 2013.
[Urbanek13] http://cran.r-project.org/web/packages/rJava Urbanek, S.: rJava: Low-level R to Java interface, 2013.
[Oracle14] http://docs.oracle.com/javase/7/docs/technotes/guides/jni/spec/jniTOC.html Oracle: The Java Native Interface. Programmer's Guide and Specification, 2014.

Calculate the fitness of a population.

Description

The population is usually obtained by cmaSamplePopulation.

Usage

cmaCalcFitness(cma, popR, fitFunc)
cmaCalcFitness(cma, popR, fitFunc)

Arguments

`cma`	CMA-ES Java object, already initialized with `cmaInit`
`popR`	a (`dimension x popSize`) matrix from `cmaSamplePopulation`
`fitFunc`	a function to be minimized. Signature: accepts a vector `x`, returns a `double`.

Value

fitness, a vector of length cmaGetPopulationSize(cma) with the fitness of each individuum

Author(s)

Wolfgang Konen, FHK, 2013

Examples

cma <- cmaNew();
   cmaInit(cma,dimension=2,initialX=1.5);
   popR <- cmaSamplePopulation(cma);
   fitFunc <- function(x) {sum(x*x)};
   fitness <- cmaCalcFitness(cma,popR,fitFunc);
   cmaUpdateDistribution(cma,fitness);
cma <- cmaNew();
   cmaInit(cma,dimension=2,initialX=1.5);
   popR <- cmaSamplePopulation(cma);
   fitFunc <- function(x) {sum(x*x)};
   fitness <- cmaCalcFitness(cma,popR,fitFunc);
   cmaUpdateDistribution(cma,fitness);

Evaluate the meanX of the current population.

Description

After executing cmaOptimDP, there is a current population and a best-ever solution. Evaluate for the mean of the current population whether it is feasible and whether the mean is an even better solution. If so, update the best-ever solution.

Usage

cmaEvalMeanX(cma, fitFunc, isFeasible = function(x) TRUE)
cmaEvalMeanX(cma, fitFunc, isFeasible = function(x) TRUE)

Arguments

`cma`	CMA-ES Java object, already initialized with `cmaInit`
`fitFunc`	a function to be minimized. Signature: accepts a vector x, returns a double.
`isFeasible`	[`function(x){TRUE}`] a Boolean function checking the feasibility of the vector `x`. The default is to return always `TRUE`.

Details

The code of this function is also instructive as a full example for the extensibility of the rJava interface to CMA-ES. See the full code in demo/demoEvalMeanX. Some example rJava-calls are:

   rJava::.jcall(cma,"[D","getMeanX");
   bestSolutionObj =
     rJava::.jcall(cma,"Lfr/inria/optimization/cmaes/CMASolution;","setFitnessOfMeanX",fitFunc(meanX));
   rJava::.jcall(bestSolutionObj,"J","getEvaluationNumber");

Every direct method of classes in the CMA-ES Java package cmaes (see [Hansen09] for the complete Javadoc and [Hansen13] for an overview on CMA-ES in total) can be accessed with the .jcall-mechanism of the rJava R package:

     rJava::.jcall(obj,returnType,method,...)

where ... stands for the calling parameter(s) of method.
returnType is a string following the JNI type convention (see, e.g. [Oracle14])

	Field Descriptor	Java Language Type
	Z	boolean
	C	char
	I	int
	J	long
	F	float
	D	double
	[I	int[]
	[[D	double[][]
	Ljava/langString;	java.lang.String
	S	java.lang.String
	T	short

(Note: (a) the terminating ";" in "Ljava/langString;" (!) and (b) "S" is a short hand for "Ljava/langString;" and "T" is the re-mapped code for short. )

The calling parameters in ... have to be matched exactly. In R, numeric vectors are stored as doubles, so the calling syntax

          bestSolutionObj = .jcall(cma,rType,"setFitnessOfMeanX",fitFunc(meanX));

is just right for the Java method setFitnessOfMeanX(double[]) . In other cases, the calling R variable x has to be cast explicitly:

	Cast	Java Language Type
	.jbyte(x)	byte
	.jchar(x)	char
	as.integer(x)	int
	.jlong(x)	long
	.jfloat(x)	float

Value

bestSolution, a list with entries:

`bestX`	a vector of length `dimension` containing the best-ever solution, including `meanX`
`meanX`	a vector of length `dimension` containing the mean of the current (last) population in `cma`
`bestFitness`	the best-ever fitness value, including the evaluation of meanX
`bestEvalNum`	the function evaluation count where `bestFitness` occured
`lastEvalNum`	the total function evaluation count. If `bestEvalNum==lastEvalNum` then the best-ever fitness occured in the evaluation of `meanX`.

Author(s)

Wolfgang Konen, FHK, 2013-2015

References

[Hansen09] https://www.lri.fr/~hansen/javadoc Nikolaus Hansen: Javadoc for CMA-ES Java package fr.inria.optimization.cmaes, 2009.
[Hansen13] https://www.lri.fr/~hansen/cmaesintro.html Nikolaus Hansen: The CMA Evolution Strategy, 2013.
[Oracle14] http://docs.oracle.com/javase/7/docs/technotes/guides/jni/spec/jniTOC.html Oracle: The Java Native Interface. Programmer's Guide and Specification. Chapter 3 (JNI types), Sec. 'Type Signatures', 2014.

Examples

## Not run: 
   ## just to show the syntax, without calling cmaOptimDP
   fitFunc <- function(x) {  sum(x*x); }
   isFeasible <- function(x) {  TRUE;  }
   cma <- cmaNew(propFile="CMAEvolutionStrategy.properties");
   cmaInit(cma,dimension=2,initialX=1.5);
   bestSolution=cmaEvalMeanX(cma,fitFunc,isFeasible);
   str(bestSolution);
   
## End(Not run)
## Not run: 
   ## just to show the syntax, without calling cmaOptimDP
   fitFunc <- function(x) {  sum(x*x); }
   isFeasible <- function(x) {  TRUE;  }
   cma <- cmaNew(propFile="CMAEvolutionStrategy.properties");
   cmaInit(cma,dimension=2,initialX=1.5);
   bestSolution=cmaEvalMeanX(cma,fitFunc,isFeasible);
   str(bestSolution);
   
## End(Not run)

Initialize a CMA-ES Java object.

Description

Initialize a CMA-ES Java object.

Usage

cmaInit(cma, seed = NULL, dimension = NULL, initialX = NULL,
  initialStandardDeviations = NULL)
cmaInit(cma, seed = NULL, dimension = NULL, initialX = NULL,
  initialStandardDeviations = NULL)

Arguments

`cma`	CMA-ES Java object, as created by `cmaNew`
`seed`	[NULL] if not NULL, set the seed to the given value
`dimension`	[NULL] if not NULL, overwrite the dimension setting from `propFile` (`cmaNew`)
`initialX`	[NULL] if not NULL, overwrite the initialX setting from `propFile` (`cmaNew`). initialX can be a double or a double vector of length `dimension`.
`initialStandardDeviations`	[NULL] if not NULL, overwrite the initialStandardDeviations setting from `propFile` `cmaNew`. initialStandardDeviations can be a double or a double vector of length `dimension`.

Value

fitness, a vector of 0's with the length of the intended population.

Note

As a side effect, the CMA-ES Java object cma of class CMAEvolutionStrategy is transferred into an augmented state. As a second side effect, the population size is set to

$\lambda = 4 + 3 floor(ln(n))$

where $n=$ dimension.

Author(s)

Wolfgang Konen, FHK, 2013

Examples

cma <- cmaNew();
   cmaInit(cma,seed=42,dimension=2,initialX=1.5);
cma <- cmaNew();
   cmaInit(cma,seed=42,dimension=2,initialX=1.5);

Create a new CMA-ES Java object.

Description

Create a new CMA-ES Java object.

Usage

cmaNew(propFile = NULL)
cmaNew(propFile = NULL)

Arguments

propFile

[NULL] filename of a file with property settings. If NULL, read file
CMAEvolutionStrategy.properties from the package directory (find.package("rCMA"))

Value

the new CMA-ES Java object of class CMAEvolutionStrategy, which has as additional attribute props, the Java Properties object as read from propFile.

Note

The default properties file can be found in CMAEvolutionStrategy.properties. A read-only copy can be inspected by browsing to "Index" (of package rCMA), then "Overview of user guides ...".
It allows to set more parameter, especially more stop conditions.

Author(s)

Wolfgang Konen, FHK, 2013

Examples

## show how element initialX can be inferred from attribute props:
   ## (see  cmaEvalMeanX-documentation for further details on .jcall and its argument "S")
   cma <- cmaNew();
   props <- attr(cma,"props");
   initialX = rJava::.jcall(props,"S","getProperty","initialX");
   print(initialX);
## show how element initialX can be inferred from attribute props:
   ## (see  cmaEvalMeanX-documentation for further details on .jcall and its argument "S")
   cma <- cmaNew();
   props <- attr(cma,"props");
   initialX = rJava::.jcall(props,"S","getProperty","initialX");
   print(initialX);

Perform a CMA-ES optimization with constraints (DP).

Description

The optimization uses DP (death penalty) for handling constraint violations: Each time an infeasible individual is encountered, it is thrown away and a new individual is resampled from the CMA distribution.

Usage

cmaOptimDP(cma, fitFunc, isFeasible = function(x) {     TRUE },
  maxDimPrint = 5, iterPrint = 10, verbose = 2)
cmaOptimDP(cma, fitFunc, isFeasible = function(x) {     TRUE },
  maxDimPrint = 5, iterPrint = 10, verbose = 2)

Arguments

`cma`	CMA-ES Java object, already initialized with `cmaInit`
`fitFunc`	a function to be minimized. Signature: accepts a vector `x`, returns a `double`.
`isFeasible`	[`function(x){TRUE}`] a Boolean function checking the feasibility of the vector `x`. The default is to return always `TRUE`.
`maxDimPrint`	[5] how many dimensions of vector `x` to print in diagnostic output
`iterPrint`	[10] after how many iterations should diagnostic output be printed?
`verbose`	[2] possible values are 0 (no output), 1, 2 (much output)

Details

This functions loops through iterations (generations) until a stop condition is met: In each iteration, a population is sampled (infeasible individuals are replaced via Java function resampleSingle), its fitness vector is evaluated and the CMA distribution is updated according to this fitness vector.

Every iterPrint generations a one-line diagnostic output of the form

     iter  fitness | x1 x2 ... xp

is printed where fitness is the current best value of the fitness function to be minimized and x1 x2 ... xp are the first maxDimPrint dimensions of the corresponding best point in input space.

Value

res, a list with diagnostic output from the optimization run:

`sMsg`	a string vector with all console output from the optimization run. To print it, use: `cat(sMsg)` or `for (x in sMsg) cat(x)`
`bestX`	vector of length `dimension` with the best-ever solution X
`bestFitness`	the corresponding best-ever fitness
`bestEvalNum`	the fitness function evaluation number which gave this best-ever result
`nIter`	number of iterations
`fitnessVec`	vector of length `nIter`: the best fitness after each iteration
`xMat`	(`nIter x dimension`)-matrix: `xMat[i,]` is the best solution X after iteration `i`
`cfe`	number of constraint function evaluations (`isFeasible`)
`ffe`	number of fitness function evaluations (`fitFunc`)

Note

If your fitness function depends on other parameters besides x, then encapsulate it in a new function fitFunc at a place where the other parameters are accessible and rely on R's mechanism to locate the other parameters in the environment surrounding fitFunc:

     par1 <- someObject;

     fitFunc <- function(x) {  myFuncWithOtherPars(x,par1); }

Author(s)

Wolfgang Konen, FHK, 2013-2015

Examples

## demo/demoCMA2.R: demo usage of package rCMA.
##
## After doing the unconstrained sphere (as in demoCMA1.r, for later reference in plot), 
## the constrained sphere problem TR2 is solved. 
## The problem TR2 has in addition to the fitness function 'sphere' the constraint function
## 'above the hyperplane sum_i(x_i) = n', where n is the input space dimension.
## The constrained optimum is at (1,...,1) and it has the value fTarget2=n.
##
## Note that in this second case, the optimimum lies exactly at the boundary 
## of the feasible region: res2$bestX=c(1,...,1).
##
## This script does exactly the same as class CMAExampleConstr in cma_jAll.jar,
## but it allows to define the functions fitFunc and isFeasible on the R side. 
## They can be replaced by arbitrary other R functions, which may depend on other 
## R variables as well. 
##
## The constraint handling approach is a very simple one: death penalty, i.e. if we get an 
## infeasible individual, it is immediately discarded and a new one is drawn from the distribution. 
## (This approach will run into trouble if the current distribution does not allow to reach any  
## feasible solutions.)
## 
library(rCMA)
fitFunc <- function(x) {  sum(x*x); }
isFeasible <- function(x) {  (sum(x) - length(x)) >= 0;  }
n = 2;

cma <- cmaNew(propFile="CMAEvolutionStrategy.properties");
cmaInit(cma,seed=42,dimension=n,initialX=1.5, initialStandardDeviations=0.2);
res1 = cmaOptimDP(cma,fitFunc,iterPrint=30);

cma <- cmaNew(propFile="CMAEvolutionStrategy.properties");
cmaInit(cma,seed=42,dimension=n,initialX=1.5, initialStandardDeviations=0.2);
res2 = cmaOptimDP(cma,fitFunc,isFeasible,iterPrint=30);

fTarget =c(0,n); 
plot(res1$fitnessVec-fTarget[1],type="l",log="y",xlim=c(1,max(res1$nIter,res2$nIter))
    ,xlab="Iteration",ylab="Distance to target fitness");
lines(res2$fitnessVec-fTarget[2],col="red");
legend("topright",legend=c("TR2","sphere"),lwd=rep(1,2),col=c("red","black"))
str(res2);

bestSolution=rCMA::cmaEvalMeanX(cma,fitFunc,isFeasible);
str(bestSolution);

## demo/demoCMA2.R: demo usage of package rCMA.
##
## After doing the unconstrained sphere (as in demoCMA1.r, for later reference in plot), 
## the constrained sphere problem TR2 is solved. 
## The problem TR2 has in addition to the fitness function 'sphere' the constraint function
## 'above the hyperplane sum_i(x_i) = n', where n is the input space dimension.
## The constrained optimum is at (1,...,1) and it has the value fTarget2=n.
##
## Note that in this second case, the optimimum lies exactly at the boundary 
## of the feasible region: res2$bestX=c(1,...,1).
##
## This script does exactly the same as class CMAExampleConstr in cma_jAll.jar,
## but it allows to define the functions fitFunc and isFeasible on the R side. 
## They can be replaced by arbitrary other R functions, which may depend on other 
## R variables as well. 
##
## The constraint handling approach is a very simple one: death penalty, i.e. if we get an 
## infeasible individual, it is immediately discarded and a new one is drawn from the distribution. 
## (This approach will run into trouble if the current distribution does not allow to reach any  
## feasible solutions.)
## 
library(rCMA)
fitFunc <- function(x) {  sum(x*x); }
isFeasible <- function(x) {  (sum(x) - length(x)) >= 0;  }
n = 2;

cma <- cmaNew(propFile="CMAEvolutionStrategy.properties");
cmaInit(cma,seed=42,dimension=n,initialX=1.5, initialStandardDeviations=0.2);
res1 = cmaOptimDP(cma,fitFunc,iterPrint=30);

cma <- cmaNew(propFile="CMAEvolutionStrategy.properties");
cmaInit(cma,seed=42,dimension=n,initialX=1.5, initialStandardDeviations=0.2);
res2 = cmaOptimDP(cma,fitFunc,isFeasible,iterPrint=30);

fTarget =c(0,n); 
plot(res1$fitnessVec-fTarget[1],type="l",log="y",xlim=c(1,max(res1$nIter,res2$nIter))
    ,xlab="Iteration",ylab="Distance to target fitness");
lines(res2$fitnessVec-fTarget[2],col="red");
legend("topright",legend=c("TR2","sphere"),lwd=rep(1,2),col=c("red","black"))
str(res2);

bestSolution=rCMA::cmaEvalMeanX(cma,fitFunc,isFeasible);
str(bestSolution);

Sample a population from the current CMA-ES distribution.

Description

The population size is given by cmaGetPopulationSize(cma). It can be either set manually with cmaSetPopulationSize(cma,p), prior to cmaInit(cma), or CMA-ES will use the default population size
popSize = 4 + 3*log(dimension).

Usage

cmaSamplePopulation(cma)
cmaSamplePopulation(cma)

Arguments

cma

CMA-ES Java object, already initialized with cmaInit

Value

popR, a (dimension x popSize) matrix with popR[,1] being the first individuum in the population.
dimension = cmaGetDimension(cma)
popSize = cmaGetPopulationSize(cma)

Author(s)

Wolfgang Konen, FHK, 2013

Examples

cma <- cmaNew();
   cmaInit(cma,dimension=2,initialX=1.5);
   popR <- cmaSamplePopulation(cma);
cma <- cmaNew();
   cmaInit(cma,dimension=2,initialX=1.5);
   popR <- cmaSamplePopulation(cma);

rCMA Getters and Setters.

Description

Get or set various elements of CMA-ES Java object cma.

cmaSetDimension sets the problem dimension (only prior to cmaInit)
cmaGetDimension returns the problem dimension
cmaSetPopulationSize sets the population size (only prior to cmaInit)
cmaGetPopulationSize returns the population size
cmaSetInitialX set the mean vector for the initial population (only prior to cmaInit)
cmaGetInitialX returns the mean vector for the initial population
cmaSetCountEval sets the counter for fitness function evaluations (only prior to cmaInit)
cmaGetCountEval returns the counter for fitness function evaluations

Usage

cmaSetDimension(cma, i)

cmaGetDimension(cma)

cmaSetPopulationSize(cma, i)

cmaGetPopulationSize(cma)

cmaSetInitialX(cma, initialX)

cmaGetInitialX(cma)

cmaSetCountEval(cma, p)

cmaGetCountEval(cma)
cmaSetDimension(cma, i)

cmaGetDimension(cma)

cmaSetPopulationSize(cma, i)

cmaGetPopulationSize(cma)

cmaSetInitialX(cma, initialX)

cmaGetInitialX(cma)

cmaSetCountEval(cma, p)

cmaGetCountEval(cma)

Arguments

`cma`	CMA-ES Java object, created with `cmaNew`
`i`	a parameter of type integer
`initialX`	either a double or a double vector of length `cmaGetDimension`
`p`	a parameter of type long

Value

none for the setters, the requested element(s) for the getters

rCMA Stop Conditions.

Description

Set various stop conditions of CMA-ES Java object cma (only prior to cmaInit).

cmaSetStopFitness sets the stop condition: fitness function below d (default: DOUBLE.MinValue)
cmaSetStopMaxFunEvals sets the stop condition: max number of fitness function evaluations
cmaSetStopTolFun sets the stop condition: delta of fitness function below d (default: 1e-12)

Usage

cmaSetStopFitness(cma, d)

cmaSetStopMaxFunEvals(cma, p)

cmaSetStopTolFun(cma, d)
cmaSetStopFitness(cma, d)

cmaSetStopMaxFunEvals(cma, p)

cmaSetStopTolFun(cma, d)

Arguments

`cma`	CMA-ES Java object, created with `cmaNew`
`d`	a parameter of type double
`p`	a parameter of type long

Note

If your fitness can become negative, you need to set cmaSetStopFitness to a value different from the default to prevent premature stopping.

The properties file (read by cmaNew) can be used to set further stop conditions. If they are not set, the following defaults are active:

name	default setting	meaning
stopTolFunHist	1e-13	similar to stopTolFun, see CMA-ES Javadoc for details
stopTolX	0.0	stop if seacrh steps become smaller than stopTolX
stopTolXfactor	0.0	stop if search steps become smaller than stopTolXFactor * initial step size
stopMaxIter	+Inf	stop if number of iterations (generations) are greater

Update CMA-ES distribution with the fitness vector of the last population.

Description

Update CMA-ES distribution with the fitness vector of the last population.

Usage

cmaUpdateDistribution(cma, fitness)
cmaUpdateDistribution(cma, fitness)

Arguments

`cma`	CMA-ES Java object, already initialized with `cmaInit`
`fitness`	vector of length `cmaGetPopulationSize(cma)` with the fitness of each individuum

Note

As a side effect, the CMA-ES Java object cma of class CMAEvolutionStrategy is augmented.

Author(s)

Wolfgang Konen, FHK, 2013

Package 'rCMA'

Help Index

R interface to the Java CMA-ES of Niko Hansen

Description

Details

Author(s)

References

Calculate the fitness of a population.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Evaluate the meanX of the current population.

Description

Usage

Arguments

Details

Value

Author(s)

References

See Also

Examples

Initialize a CMA-ES Java object.

Description

Usage

Arguments

Value

Note

Author(s)

See Also

Examples

Create a new CMA-ES Java object.

Description

Usage

Arguments

Value

Note

Author(s)

See Also

Examples

Perform a CMA-ES optimization with constraints (DP).

Description

Usage

Arguments

Details

Value

Note

Author(s)

See Also

Examples

Sample a population from the current CMA-ES distribution.

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

rCMA Getters and Setters.

Description

Usage

Arguments

Value

See Also

rCMA Stop Conditions.

Description

Usage

Arguments

Note

See Also

Update CMA-ES distribution with the fitness vector of the last population.

Description

Usage

Arguments

Note

Author(s)

See Also