atlantisdrive

library(atlantisdrive)

The idea behind atlantisdrive is to allow a user to select groups of files produced by Atlantis, add a naming convention, and push them to google drive in a systematic way. All the user requires, is the id of the root folder on google drive and authentication credentials to access the folder. Google drive then becomes an organized repository for Atlantis output. Others can then use atlantisdrive to pull output, after which they can use atlantisom and/or atlantisdiagnostics to explore the model run output.

Example

We first run Atlantis (on Linux) using:

atlantisMerged -i neus_init.nc 0 -o neus_output.nc -r at_run.prm -f at_force_LINUX.prm 
-p at_physics.prm -b at_biology.prm -h at_harvest.prm -e at_economics.prm -s neus_groups.csv
-q neus_fisheries.csv -t . -d outputDir

The neus_itit.nc file, the .prm and csv files are input files to the model. The neus_output.nc is the name of the main output file and the text string neus_output is used as a prefix to many of the output files. outputDir is the name or path to the directory where all output will be saved.

A typical run will output core files with the extensions:

  1. txt
  2. ts
  3. xml
  4. nc

All of the “txt” and “nc” files are prefixed with neus_output (in general the prefix string is the name of the output file)

We now want to push all of these core files to google drive for archiving and/or sharing with others. We can achieve this in a couple of steps.

  1. Define the path to the output on the local machine

For example:

localPath <- here::here("outputFolder")
  1. Get the names of the core files to push to google drive
coreFiles <- atlantisdrive::list_core_files(localPath)
  1. Obtain the root id of google drive and authenticate ones self
# this is a ficticious number
rootid <- "23kcfkn3vjk56ivknk44nkcn4985c"
  1. Push files to google drive

For example, push to myWork folder (you will be prompted to create the folder if it doesn’t exist)

atlantisdrive::push_to_drive(rootid=rootid,localPath = localPath,googledriveFolder = "myWork")