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

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 0a1c30e..32ed6a8 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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 (file)
--- 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)
 }