From: Benjamin Auder <benjamin.auder@somewhere>
Date: Tue, 11 Apr 2017 12:41:31 +0000 (+0200)
Subject: Add 'fast' argument to select C code or R code
X-Git-Url: https://git.auder.net/?p=valse.git;a=commitdiff_plain;h=a3105972158da4773b33d41e1ead65a942c15f80

Add 'fast' argument to select C code or R code
---

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 0a1c30e..32ed6a8 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -37,7 +37,5 @@ Collate:
     'initSmallEM.R'
     'EMGrank.R'
     'EMGLLF.R'
-    'EMGrank_R.R'
-    'EMGLLF_R.R'
     'generateXY.R'
     'A_NAMESPACE.R'
diff --git a/pkg/R/A_NAMESPACE.R b/pkg/R/A_NAMESPACE.R
index 359cf88..81e91ec 100644
--- a/pkg/R/A_NAMESPACE.R
+++ b/pkg/R/A_NAMESPACE.R
@@ -1,6 +1,4 @@
 #' @include generateXY.R
-#' @include EMGLLF_R.R
-#' @include EMGrank_R.R
 #' @include EMGLLF.R
 #' @include EMGrank.R
 #' @include initSmallEM.R
diff --git a/pkg/R/EMGLLF.R b/pkg/R/EMGLLF.R
index 0158914..1739204 100644
--- a/pkg/R/EMGLLF.R
+++ b/pkg/R/EMGLLF.R
@@ -28,7 +28,7 @@ EMGLLF <- function(phiInit, rhoInit, piInit, gamInit,
 	if (!fast)
 	{
 		# Function in R
-		return (EMGLLF_R(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,tau))
+		return (.EMGLLF_R(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,tau))
 	}
 
 	# Function in C
@@ -45,7 +45,7 @@ EMGLLF <- function(phiInit, rhoInit, piInit, gamInit,
 }
 
 # R version - slow but easy to read
-EMGLLF_R = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,tau)
+.EMGLLF_R = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,tau)
 {
 	# Matrix dimensions
 	n = dim(X)[1]
diff --git a/pkg/R/EMGrank.R b/pkg/R/EMGrank.R
index e30b605..0e68cb4 100644
--- a/pkg/R/EMGrank.R
+++ b/pkg/R/EMGrank.R
@@ -22,7 +22,7 @@ EMGrank <- function(Pi, Rho, mini, maxi, X, Y, tau, rank, fast=TRUE)
 	if (!fast)
 	{
 		# Function in R
-		return (EMGrank_R(Pi, Rho, mini, maxi, X, Y, tau, rank))
+		return (.EMGrank_R(Pi, Rho, mini, maxi, X, Y, tau, rank))
 	}
 
 	# Function in C
@@ -47,7 +47,7 @@ matricize <- function(X)
 }
 
 # R version - slow but easy to read
-EMGrank_R = function(Pi, Rho, mini, maxi, X, Y, tau, rank)
+.EMGrank_R = function(Pi, Rho, mini, maxi, X, Y, tau, rank)
 {
   #matrix dimensions
   n = dim(X)[1]
diff --git a/test/generateRunSaveTest_EMGLLF.R b/test/generateRunSaveTest_EMGLLF.R
index 8a61c1b..bf37b5f 100644
--- a/test/generateRunSaveTest_EMGLLF.R
+++ b/test/generateRunSaveTest_EMGLLF.R
@@ -1,4 +1,5 @@
 source("helper.R")
+library(valse)
 
 generateRunSaveTest_EMGLLF = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
 	gamma=1., lambda=0.5, tau=1e-6)
@@ -6,7 +7,6 @@ generateRunSaveTest_EMGLLF = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
 	testFolder = "../data/"
 	dir.create(testFolder, showWarnings=FALSE, mode="0755")
 
-	require(valse)
 	params = basicInitParameters(n, p, m, k)
 	xy = generateXYdefault(n, p, m, k)
 
@@ -36,14 +36,14 @@ generateRunSaveTest_EMGLLF = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
 	write.table(as.integer(c(n,p,m,k)), paste(testFolder,"dimensions",sep=""),
 		row.names=F, col.names=F)
 
-	res = EMGLLF_R(params$phiInit,params$rhoInit,params$piInit,params$gamInit,mini,maxi,
-		gamma,lambda,xy$X,xy$Y,tau)
+	res = valse::EMGLLF(params$phiInit,params$rhoInit,params$piInit,params$gamInit,mini,
+		maxi,gamma,lambda,xy$X,xy$Y,tau,fast=FALSE)
 
 	#save outputs
-	write.table(as.double(res$phi), paste(testFolder,"phi",sep=""), row.names=F, col.names=F)
-	write.table(as.double(res$rho), paste(testFolder,"rho",sep=""), row.names=F, col.names=F)
-	write.table(as.double(res$pi), paste(testFolder,"pi",sep=""), row.names=F, col.names=F)
-	write.table(as.double(res$llh), paste(testFolder,"llh",sep=""), row.names=F, col.names=F)
-	write.table(as.double(res$S), paste(testFolder,"S",sep=""), row.names=F, col.names=F)
-	write.table(as.integer(res$affec), paste(testFolder,"affec",sep=""), row.names=F, col.names=F)
+	write.table(as.double(res$phi),paste(testFolder,"phi",sep=""),row.names=F,col.names=F)
+	write.table(as.double(res$rho),paste(testFolder,"rho",sep=""),row.names=F,col.names=F)
+	write.table(as.double(res$pi),paste(testFolder,"pi",sep=""),row.names=F,col.names=F)
+	write.table(as.double(res$llh),paste(testFolder,"llh",sep=""),row.names=F,col.names=F)
+	write.table(as.double(res$S),paste(testFolder,"S",sep=""),row.names=F,col.names=F)
+	write.table(as.integer(res$affec),paste(testFolder,"affec",sep=""),row.names=F,col.names=F)
 }
diff --git a/test/generateRunSaveTest_EMGrank.R b/test/generateRunSaveTest_EMGrank.R
index becf62a..935eada 100644
--- a/test/generateRunSaveTest_EMGrank.R
+++ b/test/generateRunSaveTest_EMGrank.R
@@ -1,4 +1,5 @@
 source("helper.R")
+library(valse)
 
 generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10, gamma=1.0,
 	rank = c(1,2,4))
@@ -8,7 +9,6 @@ generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
   rho = array(dim=c(m,m,k))
   for(i in 1:k)
     rho[,,i] = diag(1,m)
-	require(valse)
   xy = generateXYdefault(n, p, m, k)
 
   testFolder = "../data/"
@@ -33,9 +33,9 @@ generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
   write.table(as.integer(c(n,p,m,k)), paste(testFolder,"dimensions",sep=""),
 		row.names=F, col.names=F)
 
-  res = EMGrank_R(pi,rho,mini,maxi,xy$X,xy$Y,tau,rank)
+  res = valse::EMGrank(pi,rho,mini,maxi,xy$X,xy$Y,tau,rank,fast=FALSE)
 
   #save output
-  write.table(as.double(res$phi), paste(testFolder,"phi",sep=""), row.names=F,col.names=F)
-  write.table(as.double(res$LLF), paste(testFolder,"LLF",sep=""), row.names=F,col.names=F)
+  write.table(as.double(res$phi),paste(testFolder,"phi",sep=""),row.names=F,col.names=F)
+  write.table(as.double(res$LLF),paste(testFolder,"LLF",sep=""),row.names=F,col.names=F)
 }