From: emilie <emilie@devijver.org>
Date: Thu, 23 Mar 2017 15:42:44 +0000 (+0100)
Subject: update generateBlabla
X-Git-Url: https://git.auder.net/variants/img/current/assets/css/doc/common.css?a=commitdiff_plain;h=c1eca3d7a9affe8703c4ce8a098f9637ed71fd21;p=valse.git

update generateBlabla
---

diff --git a/data/LLF b/data/LLF
new file mode 100644
index 0000000..bfbcab7
--- /dev/null
+++ b/data/LLF
@@ -0,0 +1,10 @@
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diff --git a/data/S b/data/S
new file mode 100644
index 0000000..48bdc35
--- /dev/null
+++ b/data/S
@@ -0,0 +1,450 @@
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diff --git a/data/X b/data/X
new file mode 100644
index 0000000..eb6acba
--- /dev/null
+++ b/data/X
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new file mode 100644
index 0000000..3156c2b
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index 0000000..81d3460
--- /dev/null
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diff --git a/data/gamInit b/data/gamInit
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diff --git a/data/rhoInit b/data/rhoInit
new file mode 100644
index 0000000..3f748b1
--- /dev/null
+++ b/data/rhoInit
@@ -0,0 +1,300 @@
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diff --git a/data/tau b/data/tau
new file mode 100644
index 0000000..f6b3d0b
--- /dev/null
+++ b/data/tau
@@ -0,0 +1 @@
+1e-06
diff --git a/pkg/R/generateSampleInputs.R b/pkg/R/generateSampleInputs.R
index 7ec361f..4da1ea5 100644
--- a/pkg/R/generateSampleInputs.R
+++ b/pkg/R/generateSampleInputs.R
@@ -1,32 +1,34 @@
 #' Generate a sample of (X,Y) of size n
-#' @param meanX matrix of group means for covariates (p x K)
-#' @param covX covariance for covariates (p x p x K)
-#' @param covY covariance for the response vector (m x m x K)
-#' @param pi proportion for each cluster
+#' @param meanX matrix of group means for covariates (of size p)
+#' @param covX covariance for covariates (of size p*p)
+#' @param covY covariance for the response vector (of size m*m*K)
+#' @param pi	 proportion for each cluster
 #' @param beta regression matrix, of size p*m*k
-#' @param n sample size
+#' @param n		sample size
 #'
 #' @return list with X and Y
 #' @export
 generateXY = function(meanX, covX, covY, pi, beta, n)
 {
-	p = dim(covX)[1]
-	m = dim(covY)[1]
-	k = dim(covY)[3]
-
-	X = matrix(nrow=n,ncol=p)
-	Y = matrix(nrow=n,ncol=m)
-	class = matrix(nrow = n)
-
-	require(MASS) #simulate from a multivariate normal distribution
-	for (i in 1:n)
-	{
-		class[i] = sample(1:k, 1, prob=pi)
-		X[i,] = mvrnorm(1, meanX[,class[i]], covX[,,class[i]])
-		Y[i,] = mvrnorm(1, X[i,] %*% beta[,,class[i]], covY[,,class[i]])
-	}
-
-	return (list(X=X,Y=Y, class = class))
+  p = dim(covX)[1]
+  m = dim(covY)[1]
+  k = dim(covY)[3]
+  
+  X = matrix(nrow=n,ncol=p)
+  Y = matrix(nrow=n,ncol=m)
+  class = matrix(nrow = n)
+  
+  require(MASS) #simulate from a multivariate normal distribution
+  for (i in 1:n)
+  {
+    class[i] = sample(1:k, 1, prob=pi)
+    X[i,] = mvrnorm(1, meanX, covX)
+    print(X[i,])
+    print(beta[,,class[i]])
+    Y[i,] = mvrnorm(1, X[i,] %*% beta[,,class[i]], covY[,,class[i]])
+  }
+  
+  return (list(X=X,Y=Y, class = class))
 }
 
 #' Generate a sample of (X,Y) of size n with default values
@@ -38,26 +40,24 @@ generateXY = function(meanX, covX, covY, pi, beta, n)
 #' @export
 generateXYdefault = function(n, p, m, k)
 {
-	rangeX = 100
-	meanX = rangeX * matrix(1 - 2*runif(p*k), ncol=k)
-	covX = array(dim=c(p,p,k))
-	covY = array(dim=c(m,m,k))
-	for(r in 1:k)
-	{
-		covX[,,r] = diag(p)
-		covY[,,r] = diag(m)
-	}
-	pi = rep(1./k,k)
-	#initialize beta to a random number of non-zero random value
-	beta = array(0, dim=c(p,m,k))
-	for (j in 1:p)
-	{
-		nonZeroCount = sample(1:m, 1)
-		beta[j,1:nonZeroCount,] = matrix(runif(nonZeroCount*k), ncol=k)
-	}
-
-	sample_IO = generateXY(meanX, covX, covY, pi, beta, n)
-	return (list(X=sample_IO$X,Y=sample_IO$Y))
+  meanX = rep(0, p)
+  covX = diag(p)
+  covY = array(dim=c(m,m,k))
+  for(r in 1:k)
+  {
+    covY[,,r] = diag(m)
+  }
+  pi = rep(1./k,k)
+  #initialize beta to a random number of non-zero random value
+  beta = array(0, dim=c(p,m,k))
+  for (j in 1:p)
+  {
+    nonZeroCount = sample(1:m, 1)
+    beta[j,1:nonZeroCount,] = matrix(runif(nonZeroCount*k), ncol=k)
+  }
+  
+  sample_IO = generateXY(meanX, covX, covY, pi, beta, n)
+  return (list(X=sample_IO$X,Y=sample_IO$Y))
 }
 
 #' Initialize the parameters in a basic way (zero for the conditional mean, uniform for weights,
@@ -70,19 +70,19 @@ generateXYdefault = function(n, p, m, k)
 #' @export
 basicInitParameters = function(n,p,m,k)
 {
-	phiInit = array(0, dim=c(p,m,k))
-
-	piInit = (1./k)*rep(1,k)
-
-	rhoInit = array(dim=c(m,m,k))
-	for (i in 1:k)
-		rhoInit[,,i] = diag(m)
-
-	gamInit = 0.1 * matrix(1, nrow=n, ncol=k)
-	R = sample(1:k, n, replace=TRUE)
-	for (i in 1:n)
-		gamInit[i,R[i]] = 0.9
-	gamInit = gamInit/sum(gamInit[1,])
-
-	return (list("phiInit" = phiInit, "rhoInit" = rhoInit, "piInit" = piInit, "gamInit" = gamInit))
+  phiInit = array(0, dim=c(p,m,k))
+  
+  piInit = (1./k)*rep(1,k)
+  
+  rhoInit = array(dim=c(m,m,k))
+  for (i in 1:k)
+    rhoInit[,,i] = diag(m)
+  
+  gamInit = 0.1 * matrix(1, nrow=n, ncol=k)
+  R = sample(1:k, n, replace=TRUE)
+  for (i in 1:n)
+    gamInit[i,R[i]] = 0.9
+  gamInit = gamInit/sum(gamInit[1,])
+  
+  return (list("phiInit" = phiInit, "rhoInit" = rhoInit, "piInit" = piInit, "gamInit" = gamInit))
 }