pmetrics.rscript

#!/usr/bin/env Rscript
#sabryr 2020-02-14
# This script is not supposed to be used directly,
# and should be invoked from pmetrics.sh

args <- commandArgs(trailingOnly = TRUE)
r <- getOption("repos")
r["CRAN"] <- "http://cran.r-project.org" 
options(repos=r)
Sys.setenv(R_INSTALL_STAGED = FALSE)

valmap <- list()
valmap$auto <- TRUE
valmap$include <- FALSE
valmap$exclude <- FALSE
valmap$indpts <- FALSE
valmap$salt <- FALSE
valmap$intern <- FALSE
valmap$silent <- FALSE
valmap$overwrite <- FALSE
valmap$nocheck <- FALSE
valmap$alq <- FALSE
valmap$remote <- FALSE
valmap$run <- FALSE
valmap$aucint <- FALSE
valmap$prior <- FALSE
valmap$cycles <- 100
valmap$ode <- -4
valmap$tol <- 0.01
valmap$idelta <- 12
valmap$parallel <- NA
valmap$model <- "model.txt"
valmap$data <- "data.csv"
valmap$icen <- "median"
valmap$server_address <- NULL


if (length(args)>=8) {
  loc = args[1]
  dataset_file = args[2]
  model_file = args[3] 
  mycycles = args[4]
  myindpts = args[5]
  parallel = args[6]
  data_file_new_name =  args[7]#"data.csv"
  model_file_new_name =  args[8] #"model.txt"
  
  if (length(args)>=10) {
    valmap$ode <- args[9]
    valmap$tol <- args[10]

  }
   
  if (!suppressWarnings(require("Pmetrics"))){
    devtools::install_github("Sabryr/Pmetrics", ref = "debug",  upgrade = FALSE)
    library(Pmetrics)
    PMbuild()
  }
  print("Paths")
  print(.libPaths())
  library(Pmetrics)
  fortranloc  <- paste(trimws(Sys.getenv("HOME")),".config/Pmetrics/compiledFortran", sep = "/")
  #print(fortranloc)
  #if(!file.exists(fortranloc)){
  # PMbuild()
  #}
  setwd(loc)
  print(paste("Current working directory", getwd(), sep = " : "))
  #file.copy(from=c(model_file, dataset_file), to=getwd(), overwrite=T)
  file.copy(from=model_file, to=getwd(), overwrite=T)
  file.copy(from=dataset_file, to=getwd(), overwrite=T)
  
  print(paste("model_file was ", model_file, " now "))
  print(list.files(pattern="*txt"))

  print(paste("dataset_file ",dataset_file, " now "))
  print(list.files(pattern="*csv"))

  #if(!file.exists(model_file_new_name)){
  #	print("Safe, No model.txt found , renaming ")
  file.rename(basename(model_file), model_file_new_name)
  print(paste(basename(model_file),  "  renamed to ", model_file_new_name))

  #}

  #if(!file.exists(data_file_new_name)){
  #print("No model.txt")
  file.rename(basename(dataset_file), data_file_new_name )
  print(paste(basename(dataset_file),  "  renamed to ", data_file_new_name))
  #}
  #print(paste(" model_file_new_name ", model_file_new_name, sep = " : "))
  #print(paste(" data_file_new_name ", data_file_new_name, sep = " : "))
  #print(paste("Files in  ", getwd(), list.files(), sep = " : "))
  print(paste("ode =", valmap$ode, "  tol = ",valmap$tol))
  NPrun(model = model_file_new_name, data = data_file_new_name, cycles = mycycles, indpts = myindpts , overwrite = T,  parallel = TRUE , ode = valmap$ode, tol = valmap$tol ) 
}else{
  stop("Needs 8 arguments", call.=FALSE)
}