2012.06.07 Range Maps

Owned by narro
Last updated: Jul 02, 2012Version comment

12-06-07 Range Maps

 Participants

John Donoghue, Edwin Skidmore, Nirav Merchant, Martha Narro, Jim Regetz, Mark Schildhauer

Agenda

Discussion topics document from John

  1. Current range modeling status
  2. Proposed range mapping deliverables
  3. Range modeling decision tree
  4. Script changes and need for retesting new scripts in the cluster
  5. Raster to vector conversion issues
  6. Scheduling a model run in the cluster
  7. Need to archive maxent results that are stored in temp path
  8. Scheduling subsequent analysis runs in the cluster
  9. Range mapping API 
Notes

John's meeting notes

Mark and Nirav:

  • NM: Parametric launcher (used to compute range models at TACC) is now in Python
    • Previously was in shell.
    • Ideal when have lots of independent tasks.
  • MS: interested in connecting Kepler workflow system to iPlant big iron.
  • Nirav discussed this with Matt Jones about 2 weeks ago.
    • Wants to integrate the Kepler wfs into DE.
    • Also talked to Regan about making iPlant data store visible in Kepler, which has hooks for it.

John:

1-3. Overview by John

4. Script changes and need for retesting new scripts in the cluster

  • New models in the work flow, so those need to be added.
  • Edwin will connect with Matt to see how to get the necessary R packages on TACC.

7. Need to archive maxent results that are stored in temp path

  • Some of the files written in the tmp directories need to be captured.
  • John will need to write a script to mine those tmp files to pull out the ones that are needed.
  • Parameterize to rename based on each species.
  • John will determine size of maxent output files.

5. Raster to vector conversion issues

  • John will send Jim examples of raster files (er mapper format, binary so all 0 and 1’s) that do and don’t run when converting to vector.
  • (goodle or grass)

6. Scheduling a model run in the cluster

  • The run is a ways out, so can table this.
  • Get the set up work done first.

8. Scheduling subsequent analysis runs in the cluster

  • Once have range maps, will want to do some science on them – looking at how environmental variables impact them. In R.
  • Dismo package is in R for modeling.
  • Open modler (gbif uses it to provide range models). Is on source forge.
  • The idea was to be able to plug different model algorithms into it.
  • JR: Robert on raster packages. He’s good about making changes to fix bugs and optimizing.

9. API

  • Out a ways. Discussion tabled for now.

Misc.

  • Wiki page to document the project and instructions for how to execute the range model computations. 
To Do List
  • Jim will set up a wiki page on NCEAS Redmine under the BIEN project, then Martha will set up an iPlant wiki page to point to it.
  • Jim will set up a git repository for the range map project (at NCEAS).
  • John send Edwin a list of updates to R packages and preferred versions.
  • John will write a script to mine the tmp files to extract files others in BIEN need. Includes parameterizing to rename based on each species.
  • John will finalize the scripts for the next round of modeling.
  • John will determine size of maxent output files and let Edwin know.
  • John will send Jim examples of raster files that do and don’t run when converting to vector. (may not be a problem any more)
  • Martha will set up a regular meeting every 2 weeks for Thursdays 1:15.
  • Martha and John work out an organizational framework for the wiki.
  • Martha – Question how should the license be structured?
    • iPlant license on the R source code for map modeling. NCEAS license too?
    • Then, decisions about where source code lives.