---
title: "Modules and outputs"
output: html_vignette
vignette: >
   %\VignetteIndexEntry{Modules and outputs}
   %\VignetteEngine{knitr::rmarkdown}
---

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#-------------------------------------------------------------------------------
# Copyright (c) 2012 University of Illinois, NCSA.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the 
# University of Illinois/NCSA Open Source License
# which accompanies this distribution, and is available at
# http://opensource.ncsa.illinois.edu/license.html
#-------------------------------------------------------------------------------
-->

To get a better understanding on what files are created where, Rob created a workflow as an SVG diagram. You can find the diagram at

http://isda.ncsa.illinois.edu/~kooper/EBI/workflow.svg

In this graph the square boxes represent processes running, the rhomboids
are inputs and outputs.

To create this I used the trace functionality in R to capture the files
saved/loaded

```{r, eval = FALSE}
library("ncdf4")
trace(nc_open, quote(cat(c("LOAD : ", filename, "\n"), file="files.txt", append=TRUE)))
trace(nc_create, quote(cat(c("SAVE : ", filename, "\n"), file="files.txt", append=TRUE)))
trace(save, quote(cat(c("SAVE : ", file, "\n"), file="files.txt", append=TRUE)))
trace(load, quote(cat(c("LOAD : ", file, "\n"), file="files.txt", append=TRUE)))
trace(cat, quote(if ((raster::trim(file) != "") && (file != "files.txt") && (file != stdout()) && (file != stderr())) { 
  cat(c("CAT  : ", file, "\n"), file="files.txt", append=TRUE)}))
trace(writeLines, quote(if ((con != stdout()) && (con != stderr()))
  {cat(c("WRIT : ", con, "\n"), file="files.txt", append=TRUE)}))
```

Once these traces are set, you can run a PEcAn workflow.R and get a list of the files output at each stage


```{r}

```