-ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL, args="DontLetMeEmpty")
+ppam_exe = function(path=".", np=parallel::detectCores(), data=NULL,
+ args="DontLetMeEmptyPlease!")
{
- command_line = paste("mpirun -np ",np," ",path,"/ppam.exe",sep="")
+ 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))
{
- write.csv(data, "/tmp/data_csv")
- system(paste(path,"/ppam.exe serialize /tmp/data_csv /tmp/data_bin 0 0",sep=""))
- command_line = paste(command_line," ","/tmp/data_bin",sep="")
+ 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
+}