X-Git-Url: https://git.auder.net/?a=blobdiff_plain;f=reports%2Ftimings.R;fp=reports%2Ftimings.R;h=0000000000000000000000000000000000000000;hb=cc87714e5ad552260857c3abd508155355f10796;hp=704fd82bd6c17695509b8f7f02ebef86a469e149;hpb=476a79d4b332d378716e320fdfd95fa3e1d7be9f;p=morpheus.git

diff --git a/reports/timings.R b/reports/timings.R
deleted file mode 100644
index 704fd82..0000000
--- a/reports/timings.R
+++ /dev/null
@@ -1,84 +0,0 @@
-# flexmix optimization to get beta
-fmOptim <- function(X, Y, K, link)
-{
-	dat <- as.data.frame( cbind(Y,X) )
-	fm <- flexmix( cbind(Y, 1-Y) ~ .-Y, data=dat, k=K,
-		model = FLXMRglm(family = binomial(link = link)) )
-	p <- mean(fm@posterior[["scaled"]][,1])
-	out <- refit(fm)
-	beta_b <- sapply( seq_len(K), function(i) as.double( out@components[[1]][[i]][,1] ) )
-	list("p"=p, "beta"=beta_b[2:nrow(beta_b),], "b"=beta_b[1,])
-	NULL
-}
-
-# Our package optimization for beta (using mu as a starting point)
-ourOptim <- function(X, Y, K, link)
-{
-	M <- computeMoments(X, Y)
-	mu <- computeMu(X, Y, list(K=K,M=M))
-	x_init = c(1/2, as.double(mu), c(0,0))
-	optimParams(K, link, list(M=M))$run(x_init)
-	NULL
-}
-
-# Get timings for both methods with the same beta matrix
-getTimings <- function(link)
-{
-	timings <- list('fm'=matrix(0,nrow=10,ncol=7),'our'=matrix(0,nrow=10,ncol=7))
-	K <- 2
-	for (d in c(2,5,10))
-	{
-		beta <- matrix(runif(d*K,min=-5,max=5),ncol=K)
-		for (logn in 4:6)
-		{
-			n <- 10^logn
-			io <- generateSampleIO(n, rep(1/K,K-1), beta, runif(K), link)
-			timings[['fm']][d,logn] <- system.time(fmOptim(io$X,io$Y,K,link))[3]
-			timings[['our']][d,logn] <- system.time(ourOptim(io$X,io$Y,K,link))[3]
-		}
-	}
-	timings
-}
-
-#model = binomial
-link <- "logit"
-ncores <- 1
-N <- 100
-
-cmd_args <- commandArgs()
-for (arg in cmd_args)
-{
-	if (substr(arg,1,1)!='-')
-	{
-		spl <- strsplit(arg,'=')[[1]]
-		if (spl[1] == "link") {
-			link <- spl[2]
-		} else if (spl[1] == "nc") {
-			ncores <- as.integer(spl[2])
-		} else if (spl[1] == "N") {
-			N <- as.integer(spl[2])
-		}
-	}
-}
-
-library(morpheus)
-library(flexmix)
-source("../patch_Bettina/FLXMRglm.R")
-
-tm <-
-	if (ncores == 1) {
-		lapply(1:N, function(i) {
-			print(paste("Run",i))
-			getTimings(link)
-		})
-	} else {
-		library(parallel)
-		mclapply(1:N, function(i) {
-			print(paste("Run",i))
-			getTimings(link)
-		},
-		mc.preschedule=FALSE, mc.cores=ncores)
-	}
-tm_params <- list("link"=link, "N"=N, "nc"=ncores)
-
-save("tm", "tm_params", file="timings.RData")