Modules and outputs

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

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

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