covariance matrix input option

[kingfish777]

please add option to add covariance or correlation matrix into rcausal
Thanks!

[scottporter]

Has this been addressed? It might just be a documentation issue. I can't tell for sure that this isn't supported, but there aren't any examples listed, and I haven't been able to figure out how to get the function rCovMatrix2TetradCovMatrix to work.

[scottporter]

In case it's useful... I did hack through this and figured out all the necessary pieces are there, it just hasn't been exposed.

As a rough test, I overwrote the tetradrunner with the below and was able to call it with a covariance matrix. It wouldn't be too hard to do a pull request, but I'm not even sure the repo is active at the moment.

tetradrunner <- function(algoId, dataType, df = NULL, dfs = NULL, testId = NULL, scoreId = NULL, 
	priorKnowledge = NULL, numCategoriesToDiscretize = 4,java.parameters = NULL, cov_names = NULL, cov_sample_size = NULL, ...) {

	arguments <- list(...)
	
	params <- list()
	# result
	tetradrunner <- list()

	if(!is.null(java.parameters)){
		options(java.parameters = java.parameters)
		params <- c(java.parameters = java.parameters)
	}

	algoAnno_instance <- .jcall("edu/cmu/tetrad/annotation/AlgorithmAnnotations",
							"Ledu/cmu/tetrad/annotation/AlgorithmAnnotations;",
							"getInstance")
	algoClasses <- algoAnno_instance$getAnnotatedClasses()

	algoClass <- .jnull("java/lang/Class")
		algoAnno <- NULL

	algoClasses <- algoClasses$toArray()
	for(i in 1:algoClasses$length){
		algo <- algoClasses[[i]]		
		cmd <- algo$getAnnotation()$command()

		if(cmd == algoId){
			algoClass <- algo$getClazz()
			algoAnno <- algo$getAnnotation()
			break
		}
	}

	if(is.null(algoAnno)){
		cat(algoId,' is not found!\n')
		return
	}

	tetradProperties <- .jcall("edu/cmu/tetrad/util/TetradProperties",
							"Ledu/cmu/tetrad/util/TetradProperties;",
							"getInstance")

	# testId
	testClass <- .jnull("java/lang/Class")
	if(!is.null(testId) || algoAnno_instance$requireIndependenceTest(algoClass)){
		testAnno_instance <- .jcall("edu/cmu/tetrad/annotation/TestOfIndependenceAnnotations",
								"Ledu/cmu/tetrad/annotation/TestOfIndependenceAnnotations;",
								"getInstance")
		testClasses <- testAnno_instance$getAnnotatedClasses()
		testClasses <- testClasses$toArray()

		defaultTestClassName <- NULL

		# Default dataType
		continuous <- 'datatype.continuous.test.default'
		discrete <- 'datatype.discrete.test.default'
		mixed <- 'datatype.mixed.test.default'

		if(dataType == 'continuous' | dataType == 'covariance'){
			defaultTestClassName <- tetradProperties$getValue(continuous)
		}else if(dataType == 'discrete'){
			defaultTestClassName <- tetradProperties$getValue(discrete)
		}else{
			defaultTestClassName <- tetradProperties$getValue(mixed)
		}	
		
		for(i in 1:testClasses$length){
			test <- testClasses[[i]]
			cmd <- test$getAnnotation()$command()
			tClass <- test$getClazz()
			name <- tClass$getName()

			if(name == defaultTestClassName){
				testClass <- tClass
			}
			
			if(!is.null(testId) && cmd == testId){
				testClass <- tClass
				break
			}
		}	
	}	

	# scoreId
	scoreClass <- .jnull("java/lang/Class")
	if(!is.null(scoreId) || algoAnno_instance$requireScore(algoClass)){
		scoreAnno_instance <- .jcall("edu/cmu/tetrad/annotation/ScoreAnnotations",
								"Ledu/cmu/tetrad/annotation/ScoreAnnotations;",
								"getInstance")
		scoreClasses <- scoreAnno_instance$getAnnotatedClasses()
		scoreClasses <- scoreClasses$toArray()

		defaultScoreClassName <- NULL

		# Default dataType
		continuous <- 'datatype.continuous.score.default'
		discrete <- 'datatype.discrete.score.default'
		mixed <- 'datatype.mixed.score.default'

		if(dataType == 'continuous' | dataType == 'covariance'){
			defaultScoreClassName <- tetradProperties$getValue(continuous)
		}else if(dataType == 'discrete'){
			defaultScoreClassName <- tetradProperties$getValue(discrete)
		}else{
			defaultScoreClassName <- tetradProperties$getValue(mixed)
		}	

		for(i in 1:scoreClasses$length){
			score <- scoreClasses[[i]]
			cmd <- score$getAnnotation()$command()
			sClass <- score$getClazz()
			name <- sClass$getName()

			if(name == defaultScoreClassName){
				scoreClass <- sClass
			}

			if(!is.null(scoreId) && cmd == scoreId){
				scoreClass <- sClass
				break
			}
		}	
	}

	# dataset
	tetradData <- NULL
	if(!is.null(df)){


		if(dataType == 'covariance'){
				tetradData <- rcausal:::rCovMatrix2TetradCovMatrix(df,cov_names,cov_sample_size) 
		}else if(dataType == 'continuous'){
				tetradData <- loadContinuousData(df)
		}else if(dataType == 'discrete'){
				tetradData <- loadDiscreteData(df)
		}else{
				tetradData <- loadMixedData(df, numCategoriesToDiscretize)
		}
		
		tetradData <- .jcast(tetradData, 'edu/cmu/tetrad/data/DataModel')

	}else if(!is.null(dfs)){
		
		tetradData <- .jnew("java/util/ArrayList")
		for(i in 1:length(dfs)){
			df <- dfs[[i]]

			if(dataType == 'continuous'){
					df <- loadContinuousData(df)
			}else if(dataType == 'discrete'){
					df <- loadDiscreteData(df)
			}else{
					df <- loadMixedData(df, numCategoriesToDiscretize)
			}

			df <- .jcast(df, 'edu/cmu/tetrad/data/DataModel')

			tetradData$add(df)
		}

		tetradData <- .jcast(tetradData, "java/util/List")
	}else{
		cat("Dataset is required!")
		return
	}

	algo_instance <- .jcall("edu/cmu/tetrad/algcomparison/algorithm/AlgorithmFactory",
							"Ledu/cmu/tetrad/algcomparison/algorithm/Algorithm;",
							"create",algoClass, testClass, scoreClass)

	if(!is.null(priorKnowledge)){
		algo_instance$setKnowledge(priorKnowledge)
	}

	# Parameters
	paramDescs_instance <- .jcall("edu/cmu/tetrad/util/ParamDescriptions",
								"Ledu/cmu/tetrad/util/ParamDescriptions;",
								"getInstance")

	parameters_instance <- .jnew("edu/cmu/tetrad/util/Parameters")
	for(arg in names(arguments)){
		if(!is.null(paramDescs_instance$get(arg))){

			value <- arguments[[arg]]
			parameter_instance <- NULL
			obj_value <- NULL

			if(!is.character(value)){
				if(is.logical(value)){
						obj_value <- .jnew("java/lang/Boolean", value)
				}else if(value%%1 == 0){
						obj_value <- .jnew("java/lang/Integer", as.integer(value))
				}else{
						obj_value <- .jnew("java/lang/Double", value)
				}

				parameter_instance <- .jcast(obj_value, "java/lang/Object")
				parameters_instance$set(arg, parameter_instance)
			}

		}
	# print(arg) # argument's name
	# print(arguments[arg]) # argument's value
	}

	# Search
	tetrad_graph <- .jcall(algo_instance, "Ledu/cmu/tetrad/graph/Graph;", 
		"search", tetradData, parameters_instance, check=FALSE)

	if(!is.null(e <- .jgetEx())){
		.jclear()
		tetradrunner$nodes <- colnames(df)
		tetradrunner$edges <- NULL
		# print("Java exception was raised")
		# print(e)
	}else{
		tetradrunner$graph <- tetrad_graph

		V <- rcausal:::extractTetradNodes(tetrad_graph)

		tetradrunner$nodes <- V

		# extract edges
		tetradrunner_edges <- rcausal:::extractTetradEdges(tetrad_graph)

		tetradrunner$edges <- tetradrunner_edges        
	}

	return(tetradrunner)
}

tetradrunner.tetradGraphToDot <- function(tetrad_graph){
	graph_dot <- .jcall("edu/cmu/tetrad/graph/GraphUtils",
							"S","graphToDot",tetrad_graph)
	return(graph_dot)
}

tetradrunner.listAlgorithms <- function(){
	algoAnno_instance <- .jcall("edu/cmu/tetrad/annotation/AlgorithmAnnotations",
							"Ledu/cmu/tetrad/annotation/AlgorithmAnnotations;",
							"getInstance")
	algoClasses <- algoAnno_instance$getAnnotatedClasses()

	algoClasses <- algoClasses$toArray()
	for(i in 1:algoClasses$length){
		algo <- algoClasses[[i]]		
		algoType <- algo$getAnnotation()$algoType()$toString()
		if(algoType != 'orient_pairwise'){
			cmd <- algo$getAnnotation()$command()
			cat(cmd,"\n")
		}
	}
}

tetradrunner.listIndTests <- function(){
	testAnno_instance <- .jcall("edu/cmu/tetrad/annotation/TestOfIndependenceAnnotations",
							"Ledu/cmu/tetrad/annotation/TestOfIndependenceAnnotations;",
							"getInstance")
	testClasses <- testAnno_instance$getAnnotatedClasses()
	testClasses <- testClasses$toArray()
		
	for(i in 1:testClasses$length){
		test <- testClasses[[i]]
		cmd <- test$getAnnotation()$command()
		cat(cmd,"\n")
	}
}

tetradrunner.listScores <- function(){
	scoreAnno_instance <- .jcall("edu/cmu/tetrad/annotation/ScoreAnnotations",
							"Ledu/cmu/tetrad/annotation/ScoreAnnotations;",
							"getInstance")
	scoreClasses <- scoreAnno_instance$getAnnotatedClasses()
	scoreClasses <- scoreClasses$toArray()
		
	for(i in 1:scoreClasses$length){
		score <- scoreClasses[[i]]
		cmd <- score$getAnnotation()$command()
		cat(cmd,"\n")
	}
}

tetradrunner.getAlgorithmDescription <- function(algoId){
	algoAnno_instance <- .jcall("edu/cmu/tetrad/annotation/AlgorithmAnnotations",
							"Ledu/cmu/tetrad/annotation/AlgorithmAnnotations;",
							"getInstance")
	algoClasses <- algoAnno_instance$getAnnotatedClasses()

	algoClass <- NULL
	algoAnno <- NULL

	algoClasses <- algoClasses$toArray()
	for(i in 1:algoClasses$length){
		algo <- algoClasses[[i]]		
		cmd <- algo$getAnnotation()$command()
		
		
		if(cmd == algoId){
			algoClass <- algo$getClazz()
			algoAnno <- algo$getAnnotation()
			break
		}
	}

	algoDesc_instance <- .jcall("edu/cmu/tetrad/util/AlgorithmDescriptions",
							"Ledu/cmu/tetrad/util/AlgorithmDescriptions;",
							"getInstance")

	cat(algoDesc_instance$get(algoId))
	
	if(algoAnno_instance$requireIndependenceTest(algoClass)){
		cat("\nIt requires the independence test.")
	}
	if(algoAnno_instance$requireScore(algoClass)){
		cat("\nIt requires the score.")
	}
	if(algoAnno_instance$acceptKnowledge(algoClass)){
		cat("\nIt accepts the prior knowledge.")
	}
}

tetradrunner.getAlgorithmParameters <- function(algoId, testId = NULL, scoreId = NULL){
	algoAnno_instance <- .jcall("edu/cmu/tetrad/annotation/AlgorithmAnnotations",
							"Ledu/cmu/tetrad/annotation/AlgorithmAnnotations;",
							"getInstance")
	algoClasses <- algoAnno_instance$getAnnotatedClasses()

	algoClass <- .jnull("java/lang/Class")

	algoClasses <- algoClasses$toArray()
	for(i in 1:algoClasses$length){
		algo <- algoClasses[[i]]		
		cmd <- algo$getAnnotation()$command()

		if(cmd == algoId){
			algoClass <- algo$getClazz()
			break
		}
	}
	
	# testId
	testClass <- .jnull("java/lang/Class")
	
	if(!is.null(testId)){
		testAnno_instance <- .jcall("edu/cmu/tetrad/annotation/TestOfIndependenceAnnotations",
								"Ledu/cmu/tetrad/annotation/TestOfIndependenceAnnotations;",
								"getInstance")
  		testClasses <- testAnno_instance$getAnnotatedClasses()
  		testClasses <- testClasses$toArray()
  		
		for(i in 1:testClasses$length){
			test <- testClasses[[i]]
	  		cmd <- test$getAnnotation()$command()
		  	
		  	if(cmd == testId){
		  		testClass <- test$getClazz()
		  		break
		  	}
		}	
	}

	# scoreId
	scoreClass <- .jnull("java/lang/Class")

	if(!is.null(scoreId)){
		scoreAnno_instance <- .jcall("edu/cmu/tetrad/annotation/ScoreAnnotations",
								"Ledu/cmu/tetrad/annotation/ScoreAnnotations;",
								"getInstance")
		scoreClasses <- scoreAnno_instance$getAnnotatedClasses()
		scoreClasses <- scoreClasses$toArray()

		for(i in 1:scoreClasses$length){
			score <- scoreClasses[[i]]
			cmd <- score$getAnnotation()$command()

			if(cmd == scoreId){
				scoreClass <- score$getClazz()
				break
			}
		}
	}

	algo_instance <- .jcall("edu/cmu/tetrad/algcomparison/algorithm/AlgorithmFactory",
							"Ledu/cmu/tetrad/algcomparison/algorithm/Algorithm;",
							"create",algoClass, testClass, scoreClass)
	
	algoParams <- algo_instance$getParameters()

	paramDescs_instance <- .jcall("edu/cmu/tetrad/util/ParamDescriptions",
								"Ledu/cmu/tetrad/util/ParamDescriptions;",
								"getInstance")
	for(i in 0:(algoParams$size()-1)){
		algoParam <- algoParams$get(i)
		paramDesc <- paramDescs_instance$get(algoParam)
		defaultValue <- paramDesc$getDefaultValue()
		desc <- paramDesc$getDescription()
		
		cat(algoParam,": ",desc," [default:",defaultValue,"]","\n")
	}
	
}