Fix reporting scripts + reset W to identity at each OptimParams()

diff --git a/pkg/R/optimParams.R b/pkg/R/optimParams.R
index 894aebd..5a88ed9 100644 (file)
--- a/pkg/R/optimParams.R
+++ b/pkg/R/optimParams.R
@@ -102,7 +102,7 @@ setRefClass(
 
       n <<- nrow(X)
       d <<- ncol(X)
 
       n <<- nrow(X)
       d <<- ncol(X)

-      W <<- diag(d+d^2+d^3) #initialize at W = Identity
+      # W will be initialized when calling run()

     },
 
     expArgs = function(v)
     },
 
     expArgs = function(v)


@@ -264,6 +264,10 @@ setRefClass(
         θ0$b = rep(0, K)
       else if (!is.numeric(θ0$b) || length(θ0$b) != K || any(is.na(θ0$b)))
         stop("θ0$b: length K, no NA")
         θ0$b = rep(0, K)
       else if (!is.numeric(θ0$b) || length(θ0$b) != K || any(is.na(θ0$b)))
         stop("θ0$b: length K, no NA")

+
+      # (Re)Set W to identity, to allow several run from the same object
+      W <<- diag(d+d^2+d^3)
+

       # TODO: stopping condition? N iterations? Delta <= epsilon ?
       loopMax <- 2
       for (loop in 1:loopMax)
       # TODO: stopping condition? N iterations? Delta <= epsilon ?
       loopMax <- 2
       for (loop in 1:loopMax)

diff --git a/reports/accuracy.R b/reports/accuracy.R
index fd22a31..d628436 100644 (file)
--- a/reports/accuracy.R
+++ b/reports/accuracy.R
@@ -1,13 +1,13 @@
-optimBeta <- function(N, n, K, p, beta, b, link, ncores)
+optimBeta <- function(N, n, p, beta, b, link, ncores)

 {
   library(morpheus)
   res <- multiRun(
 {
   library(morpheus)
   res <- multiRun(

-    list(n=n, p=p, beta=beta, b=b, K=K, link=link),
+    list(n=n, p=p, beta=beta, b=b, link=link),

     list(
       # morpheus
       function(fargs) {
         library(morpheus)
     list(
       # morpheus
       function(fargs) {
         library(morpheus)

-        K <- fargs$K
+        K <- ncol(fargs$beta)

         M <- computeMoments(fargs$X, fargs$Y)
         mu <- computeMu(fargs$X, fargs$Y, list(K=K, M=M))
         op <- optimParams(fargs$X, fargs$Y, K, fargs$link, M)
         M <- computeMoments(fargs$X, fargs$Y)
         mu <- computeMu(fargs$X, fargs$Y, list(K=K, M=M))
         op <- optimParams(fargs$X, fargs$Y, K, fargs$link, M)


@@ -23,7 +23,7 @@ optimBeta <- function(N, n, K, p, beta, b, link, ncores)
 #      function(fargs) {
 #        library(flexmix)
 #        source("../patch_Bettina/FLXMRglm.R")
 #      function(fargs) {
 #        library(flexmix)
 #        source("../patch_Bettina/FLXMRglm.R")

-#        K <- fargs$K
+#        K <- ncol(fargs$beta)

 #        dat <- as.data.frame( cbind(fargs$Y,fargs$X) )
 #        res2 <- NULL
 #        tryCatch({
 #        dat <- as.data.frame( cbind(fargs$Y,fargs$X) )
 #        res2 <- NULL
 #        tryCatch({


@@ -60,7 +60,7 @@ optimBeta <- function(N, n, K, p, beta, b, link, ncores)
   res
 }
 
   res
 }
 

-#model = binomial; default values:
+# Default values:

 link = "logit"
 N <- 10
 d <- 2
 link = "logit"
 N <- 10
 d <- 2


@@ -87,28 +87,20 @@ for (arg in cmd_args)
 }
 
 if (d == 2) {
 }
 
 if (d == 2) {

-  K <- 2

   p <- .5
   b <- c(-.2, .5)
   p <- .5
   b <- c(-.2, .5)

-  beta <- matrix( c(1,-2, 3,1), ncol=K )
+  beta <- matrix( c(1,-2, 3,1), ncol=2 )

 } else if (d == 5) {
 } else if (d == 5) {

-  K <- 2

   p <- .5
   b <- c(-.2, .5)
   p <- .5
   b <- c(-.2, .5)

-  beta <- matrix( c(1,2,-1,0,3, 2,-3,0,1,0), ncol=K )
+  beta <- matrix( c(1,2,-1,0,3, 2,-3,0,1,0), ncol=2 )

 } else if (d == 10) {
 } else if (d == 10) {

-  K <- 3

   p <- c(.3, .3)
   b <- c(-.2, 0, .5)
   p <- c(.3, .3)
   b <- c(-.2, 0, .5)

-  beta <- matrix( c(1,2,-1,0,3,4,-1,-3,0,2, 2,-3,0,1,0,-1,-4,3,2,0, -1,1,3,-1,0,0,2,0,1,-2), ncol=K )
-} else if (d == 20) {
-  K <- 3
-  p <- c(.3, .3)
-  b <- c(-.2, 0, .5)
-  beta <- matrix( c(1,2,-1,0,3,4,-1,-3,0,2,2,-3,0,1,0,-1,-4,3,2,0, -1,1,3,-1,0,0,2,0,1,-2,1,2,-1,0,3,4,-1,-3,0,2, 2,-3,0,1,0,-1,-4,3,2,0,1,1,2,2,-2,-2,3,1,0,0), ncol=K )
+  beta <- matrix( c(1,2,-1,0,3,4,-1,-3,0,2, 2,-3,0,1,0,-1,-4,3,2,0, -1,1,3,-1,0,0,2,0,1,-2), ncol=3 )

 }
 
 }
 

-mr <- optimBeta(N, n, K, p, beta, b, link, ncores)
+mr <- optimBeta(N, n, p, beta, b, link, ncores)

 mr_params <- list("N"=N, "nc"=ncores, "n"=n, "K"=K, "d"=d, "link"=link,
   "p"=c(p,1-sum(p)), "beta"=beta, "b"=b)
 
 mr_params <- list("N"=N, "nc"=ncores, "n"=n, "K"=K, "d"=d, "link"=link,
   "p"=c(p,1-sum(p)), "beta"=beta, "b"=b)
 

diff --git a/reports/multistart.R b/reports/multistart.R
index 6804b6b..7cc0a5e 100644 (file)
--- a/reports/multistart.R
+++ b/reports/multistart.R
@@ -1,15 +1,15 @@
 library(morpheus)
 
 library(morpheus)
 

-testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
+testMultistart <- function(N, n, p, beta, b, link, nstart, ncores)

 {
   res <- multiRun(
 {
   res <- multiRun(

-    list(n=n,p=p,beta=beta,b=b,optargs=list(K=K,d=d,link=link,nstart=nstart)),
+    list(n=n, p=p, beta=beta, b=b, link=link, nstart=nstart),

     list(
       function(fargs) {
         # 1 start
         library(morpheus)
     list(
       function(fargs) {
         # 1 start
         library(morpheus)

-        K <- fargs$optargs$K
-        op <- optimParams(K, fargs$optargs$link, fargs$optargs)
+        K <- ncol(fargs$beta)
+        op <- optimParams(fargs$X, fargs$Y, K, fargs$link, fargs$M)

         x_init <- list(p=rep(1/K,K-1), beta=fargs$mu, b=rep(0,K))
                                res2 <- NULL
                                tryCatch({
         x_init <- list(p=rep(1/K,K-1), beta=fargs$mu, b=rep(0,K))
                                res2 <- NULL
                                tryCatch({


@@ -20,12 +20,12 @@ testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
       function(fargs) {
         # B starts
         library(morpheus)
       function(fargs) {
         # B starts
         library(morpheus)

-        K <- fargs$optargs$K
-                               d <- fargs$optargs$d
-        op <- optimParams(K, fargs$optargs$link, fargs$optargs)
+        K <- ncol(fargs$beta)
+                               d <- nrow(fargs$beta)
+        op <- optimParams(fargs$X, fargs$Y, K, fargs$link, fargs$M)

         best_val <- Inf
         best_par <- list()
         best_val <- Inf
         best_par <- list()

-        for (i in 1:fargs$optargs$nstart)
+        for (i in 1:fargs$nstart)

         {
           #x_init <- list(p=rep(1/K,K-1), beta=i*fargs$mu, b=rep(0,K))
           M <- matrix(rnorm(d*K), nrow=d, ncol=K)
         {
           #x_init <- list(p=rep(1/K,K-1), beta=i*fargs$mu, b=rep(0,K))
           M <- matrix(rnorm(d*K), nrow=d, ncol=K)


@@ -51,10 +51,12 @@ testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
     ),
     prepareArgs = function(fargs, index) {
       library(morpheus)
     ),
     prepareArgs = function(fargs, index) {
       library(morpheus)

-      io = generateSampleIO(fargs$n, fargs$p, fargs$beta, fargs$b, fargs$optargs$link)
-      fargs$optargs$M <- computeMoments(io$X, io$Y)
-      mu <- computeMu(io$X, io$Y, fargs$optargs)
+      io = generateSampleIO(fargs$n, fargs$p, fargs$beta, fargs$b, fargs$link)
+      fargs$M <- computeMoments(io$X, io$Y)
+      mu <- computeMu(io$X, io$Y, list(M=fargs$M))

       fargs$mu <- mu
       fargs$mu <- mu

+      fargs$X <- io$X
+      fargs$Y <- io$Y

                        fargs
     }, N=N, ncores=ncores, verbose=TRUE)
   for (i in 1:2)
                        fargs
     }, N=N, ncores=ncores, verbose=TRUE)
   for (i in 1:2)


@@ -62,14 +64,9 @@ testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
   res
 }
 
   res
 }
 

-#model = binomial
-K <- 2
-p <- .5
-b <- c(-.2, .5)

 # Default values:
 link = "logit"
 N <- 10
 # Default values:
 link = "logit"
 N <- 10

-d <- 2

 n <- 1e4
 ncores <- 1
 nstart <- 3 #nstart-1 random starting points for each MC run
 n <- 1e4
 ncores <- 1
 nstart <- 3 #nstart-1 random starting points for each MC run


@@ -95,14 +92,23 @@ for (arg in cmd_args)
                }
        }
 }
                }
        }
 }

-betas <- list(
-       matrix( c(1,-2, 3,1), ncol=K ), #d=2
-       matrix( c(1,2,-1,0,3, 2,-3,0,1,0), ncol=K ), #d=5
-       matrix( c(1,2,-1,0,3,4,-1,-3,0,2, 2,-3,0,1,0,-1,-4,3,2,0), ncol=K ) ) #d=10
-beta <- betas[[ ifelse( d==2, 1, ifelse(d==5,2,3) ) ]]

 
 

-mr <- testMultistart(N, n, d, K, p, beta, b, link, nstart, ncores)
-mr_params <- list("N"=N, "nc"=ncores, "n"=n, "K"=K, "d"=d, "link"=link,
+if (d == 2) {
+  p <- .5
+  b <- c(-.2, .5)
+  beta <- matrix( c(1,-2, 3,1), ncol=2 )
+} else if (d == 5) {
+  p <- .5
+  b <- c(-.2, .5)
+  beta <- matrix( c(1,2,-1,0,3, 2,-3,0,1,0), ncol=2 )
+} else if (d == 10) {
+  p <- c(.3, .3)
+  b <- c(-.2, 0, .5)
+  beta <- matrix( c(1,2,-1,0,3,4,-1,-3,0,2, 2,-3,0,1,0,-1,-4,3,2,0, -1,1,3,-1,0,0,2,0,1,-2), ncol=3 )
+}
+
+mr <- testMultistart(N, n, p, beta, b, link, nstart, ncores)
+mr_params <- list("N"=N, "nc"=ncores, "n"=n, "link"=link,

        "p"=c(p,1-sum(p)), "beta"=beta, "b"=b, "nstart"=nstart)
 
 save("mr", "mr_params", file=paste("res_",n,"_",d,"_",link,"_",nstart,".RData",sep=""))
        "p"=c(p,1-sum(p)), "beta"=beta, "b"=b, "nstart"=nstart)
 
 save("mr", "mr_params", file=paste("res_",n,"_",d,"_",link,"_",nstart,".RData",sep=""))