major folder reorganisation, R pkg is now epclust/ at first level. Experimental usage...

[epclust.git] / code / stage1 / wrapper.R

diff --git a/code/stage1/wrapper.R b/code/stage1/wrapper.R
deleted file mode 100644 (file)
index 0a957d8..0000000
--- a/code/stage1/wrapper.R
+++ /dev/null
@@ -1,35 +0,0 @@
-ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL,
-       args="DontLetMeEmptyPlease!")
-{
-       command_line = paste("mpirun -np ",np," ",path,"/ppam.exe cluster",sep="")
-
-       #if data provided (as data.frame or matrix...): binarize it, and add it as first argument
-       if (!is.null(data))
-       {
-               if (!is.character(data))
-               {
-                       #assuming matrix or data.frame, WITH row names
-                       #( identifiers; could be line number... e.g. data <- cbind(1:nrow(data),data) )
-                       write.table(data, "/tmp/data_csv", sep=",", row.names=FALSE, col.names=FALSE)
-                       system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
-               } else
-               {
-                       system(paste(path,"/ppam.exe serialize ",data," /tmp/data_bin 0 0",sep=""))
-               }
-               command_line = paste(command_line," /tmp/data_bin",sep="")
-       }
-
-       command_line = paste(command_line," ",args,sep="")
-       system(command_line)
-}
-
-#NOTE: identifiers in first column
-getMedoids = function(path=".", xmlResult = "ppamResult.xml",
-       finalSeries = "ppamFinalSeries.bin")
-{
-       system(paste(path,"/ppam.exe deserialize ",finalSeries," ppamFinalSeries.csv -1",sep=""))
-       curves = read.table("ppamFinalSeries.csv", sep=",")
-       library(XML)
-       ranks = as.integer( xmlToList( xmlParse(xmlResult) )$ranks )
-       return ( curves[ranks,] ) # == medoids
-}