'update'

[morpheus.git] / reports / timings.R

diff --git a/reports/timings.R b/reports/timings.R
deleted file mode 100644 (file)
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")