Merge branch 'master' of auder.net:morpheus

diff --combined reports/accuracy.R
index 57a63db,c33fa0f..05d9e8a
--- 1/reports/accuracy.R
--- 2/reports/accuracy.R
+++ b/reports/accuracy.R
@@@ -1,8 -1,8 +1,8 @@@
- optimBeta <- function(N, n, K, p, beta, b, link, ncores)
+ optimBeta <- function(N, n, K, p, beta, b, link, weights, ncores)
  {
        library(morpheus)
        res <- multiRun(
-               list(n=n, p=p, beta=beta, b=b, optargs=list(K=K, link=link)),
+               list(n=n, p=p, beta=beta, b=b, optargs=list(K=K, link=link, weights=weights)),
                list(
                        # morpheus
                        function(fargs) {
@@@ -13,7 -13,7 +13,7 @@@
                                mu <- computeMu(fargs$X, fargs$Y, fargs$optargs)
                                res2 <- NULL
                                tryCatch({
 -                                      op <- optimParams(K,link,fargs$optargs)
 +                                      op <- optimParams(K,fargs$optargs$link,fargs$optargs)
                                        x_init <- list(p=rep(1/K,K-1), beta=mu, b=rep(0,K))
                                        res2 <- do.call(rbind, op$run(x_init))
                                }, error = function(e) {
@@@ -71,6 -71,7 +71,7 @@@ N <- 1
  d <- 2
  n <- 1e4
  ncores <- 1
+ weights <- c(1,1,1)
  
  cmd_args <- commandArgs()
  for (arg in cmd_args)
@@@ -87,6 -88,8 +88,8 @@@
                        d <- as.integer(spl[2])
                } else if (spl[1] == "link") {
                        link <- spl[2]
+               } else if (spl[1] == "weights") {
+                 weights <- unlist(strsplit(spl[2], ","))
                }
        }
  }
@@@ -113,8 -116,8 +116,8 @@@ if (d == 2) 
        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 )
  }
  
- mr <- optimBeta(N, n, K, p, beta, b, link, ncores)
+ mr <- optimBeta(N, n, K, p, beta, b, link, weights, ncores)
  mr_params <- list("N"=N, "n"=n, "K"=K, "d"=d, "link"=link,
-       "p"=c(p,1-sum(p)), "beta"=beta, "b"=b)
+       "p"=c(p,1-sum(p)), "beta"=beta, "b"=b, "weights"=weights)
  
  save("mr", "mr_params", file=paste("multirun_",n,"_",d,"_",link,".RData",sep=""))