Revert sample.R back to working code

diff --git a/pkg/R/sampleIO.R b/pkg/R/sampleIO.R
index 753e00d..6fa38ae 100644 (file)
--- a/pkg/R/sampleIO.R
+++ b/pkg/R/sampleIO.R
@@ -51,7 +51,7 @@ generateSampleIO = function(n, p, β, b, link)
        {
                index = c(index, rep(i, classes[i]))
                newXblock = cbind( MASS::mvrnorm(classes[i], zero_mean, id_sigma), 1 )
        {
                index = c(index, rep(i, classes[i]))
                newXblock = cbind( MASS::mvrnorm(classes[i], zero_mean, id_sigma), 1 )

-               arg_link = newXblock %*% β
+               arg_link = newXblock %*% β[,i] #β

                probas =
                        if (link == "logit")
                        {
                probas =
                        if (link == "logit")
                        {


@@ -61,10 +61,10 @@ generateSampleIO = function(n, p, β, b, link)
                        else #"probit"
                                pnorm(arg_link)
                probas[is.nan(probas)] = 1 #overflow of exp(x)
                        else #"probit"
                                pnorm(arg_link)
                probas[is.nan(probas)] = 1 #overflow of exp(x)

-               probas = rowSums(p * probas)
+               #probas = rowSums(p * probas)

                X = rbind(X, newXblock)
                X = rbind(X, newXblock)

-               Y = c( Y, vapply(probas, function(p) (ifelse(p >= .5, 1, 0)), 1) )
-               #Y = c( Y, vapply(probas, function(p) (rbinom(1,1,p)), 1) )
+               #Y = c( Y, vapply(probas, function(p) (ifelse(p >= .5, 1, 0)), 1) )
+               Y = c( Y, vapply(probas, function(p) (rbinom(1,1,p)), 1) )

        }
        shuffle = sample(n)
        # Returned X should not contain an intercept column (it's an argument of estimation
        }
        shuffle = sample(n)
        # Returned X should not contain an intercept column (it's an argument of estimation

diff --git a/reports/multistart.R b/reports/multistart.R
index c5d9f51..252de91 100644 (file)
--- a/reports/multistart.R
+++ b/reports/multistart.R
@@ -2,7 +2,7 @@ library(morpheus)
 
 testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
 {
 
 testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
 {

-  ms <- multiRun(
+  res <- multiRun(

     list(n=n,p=p,beta=beta,b=b,optargs=list(K=K,d=d,link=link,nstart=nstart)),
     list(
       function(fargs) {
     list(n=n,p=p,beta=beta,b=b,optargs=list(K=K,d=d,link=link,nstart=nstart)),
     list(
       function(fargs) {


@@ -11,11 +11,11 @@ testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
         K <- fargs$optargs$K
         op <- optimParams(K, fargs$optargs$link, fargs$optargs)
         x_init <- list(p=rep(1/K,K-1), beta=fargs$mu, b=rep(0,K))
         K <- fargs$optargs$K
         op <- optimParams(K, fargs$optargs$link, fargs$optargs)
         x_init <- list(p=rep(1/K,K-1), beta=fargs$mu, b=rep(0,K))

-                               res <- NULL
+                               res2 <- NULL

                                tryCatch({
                                tryCatch({

-          res <- do.call(rbind, op$run(x_init))
+          res2 <- do.call(rbind, op$run(x_init))

                                }, error = function(e) {})
                                }, error = function(e) {})

-                               res
+                               res2

       },
       function(fargs) {
         # B starts
       },
       function(fargs) {
         # B starts


@@ -58,8 +58,8 @@ testMultistart <- function(N, n, d, K, p, beta, b, link, nstart, ncores)
                        fargs
     }, N=N, ncores=ncores, verbose=TRUE)
   for (i in 1:2)
                        fargs
     }, N=N, ncores=ncores, verbose=TRUE)
   for (i in 1:2)

-    ms[[i]] <- alignMatrices(ms[[i]], ref=rbind(p,beta,b), ls_mode="exact")
-  ms
+    res[[i]] <- alignMatrices(ms[[i]], ref=rbind(p,beta,b), ls_mode="exact")
+  res

 }
 
 #model = binomial
 }
 
 #model = binomial


@@ -101,8 +101,8 @@ betas <- list(
        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) ) ]]
 
        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) ) ]]
 

-ms <- testMultistart(N, n, d, K, p, beta, b, link, nstart, ncores)
-ms_params <- list("N"=N, "nc"=ncores, "n"=n, "K"=K, "d"=d, "link"=link,
+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,

        "p"=c(p,1-sum(p)), "beta"=beta, "b"=b, "nstart"=nstart)
 
        "p"=c(p,1-sum(p)), "beta"=beta, "b"=b, "nstart"=nstart)
 

-save("ms", "ms_params", file=paste("res_",n,"_",d,"_",link,"_",nstart,".RData",sep=""))
+save("mr", "mr_params", file=paste("res_",n,"_",d,"_",link,"_",nstart,".RData",sep=""))