Skip to Content.

mget-help - Re: [mget-help] Problem running Diversity Index

Please Wait...

Subject: Marine Geospatial Ecology Tools (MGET) help

Text archives


Re: [mget-help] Problem running Diversity Index


Chronological Thread 
    < Chronological >      < Thread >
  • From: "BERRY, Robert" <>
  • To: Jason Roberts <>, "" <>
  • Subject: Re: [mget-help] Problem running Diversity Index
  • Date: Wed, 24 Aug 2016 08:15:26 +0000
  • Accept-language: en-GB, en-US
  • Authentication-results: spf=none (sender IP is ) ;
  • Spamdiagnosticmetadata: NSPM
  • Spamdiagnosticoutput: 1:99

Hi Jason


Many thanks for your prompt and helpful reply. I now have MGET 0.8a64 running perfectly with an install of R 3.3.0. This will be extremely useful for my research in allowing me to calculate landscape diversity (shannon) for different land areas. Thanks for making the software freely available.  


Best wishes


Rob



From: Jason Roberts <>
Sent: 23 August 2016 19:43
To: BERRY, Robert;
Subject: RE: Problem running Diversity Index
 

Hi Robert,

 

Sorry for your trouble here. The problem is that MGET is not compatible with R 3.2.4. I am away from my main computer now so cannot easily refer back to my notes, but my memory is that there was some confusion or problem on the R team’s side with building 3.2.4, and whatever happened made it difficult to build compatibility for MGET with 3.2.4.

 

You can solve this problem by upgrading to a newer version of R (uninstall your old one, then install a newer one). At present, the version of MGET available on the website, 0.8a64, is compatible with versions of R up to and including 3.3.0. MGET 0.8a65 is compatible with R 3.3.1. I have built it but not posted to the website yet (I am on vacation until 29 August),. If you need that version of MGET because you desire compatibility with R 3.3.1, you can download it from here. (This assumes you have ArcGIS 10.1 or later, which I see you do.)

 

You can ignore the bit about setting RHOME. Once a compatible version if R is installed, MGET can handle the necessary steps of locating it for use from Python by the rpy module.

 

Best,

Jason

 

From: [mailto:] On Behalf Of BERRY, Robert
Sent: Tuesday, August 23, 2016 12:11 PM
To:
Subject: [mget-help] Problem running Diversity Index

 

Hi All

 

I think I have all the tools in place to run MGET (it has installed properly) but I'm receiving the following error message when I attempt to run a diversity index. It is related to RPy:

 

Messages
Executing: SpeciesDiversityCalculateDiversityIndexForArcGISPolygons C:\Users\Rob\Dropbox\Data\1_RESEARCH\Resilience\Landscape_Diversity\Boundaries\Counties_NOHOLES.shp "Shannon index" HECTARES C:\Users\Rob\Dropbox\Data\1_RESEARCH\Resilience\Landscape_Diversity\LCM\2007_1k_point_clipBNG.shp Land_Type Land_Type # #
Start Time: Tue Aug 23 16:54:37 2016
Running script SpeciesDiversityCalculateDiversityIndexForArcGISPolygons...

Traceback (most recent call last):
  File "C:\Program Files\GeoEco\ArcGISToolbox\Scripts\SpeciesDiversityCalculateDiversityIndexForArcGISPolygons.py", line 5, in <module>
    ExecuteMethodFromCommandLineAsArcGISTool('GeoEco.SpatialAnalysis.Diversity', 'SpeciesDiversity', 'CalculateDiversityIndexForArcGISPolygons')
  File "C:\Python27\ArcGIS10.2\lib\site-packages\GeoEco\ArcGISScripts.py", line 210, in ExecuteMethodFromCommandLineAsArcGISTool
    exec sourceCode in globals(), locals()
  File "<string>", line 1, in <module>
  File "C:\Python27\ArcGIS10.2\lib\site-packages\GeoEco\SpatialAnalysis\Diversity.py", line 31, in CalculateDiversityIndexForArcGISPolygons
    cls.__doc__.Obj.ValidateMethodInvocation()
  File "C:\Python27\ArcGIS10.2\lib\site-packages\GeoEco\Metadata.py", line 462, in ValidateMethodInvocation
    self.InitializeDependency(d)
  File "C:\Python27\ArcGIS10.2\lib\site-packages\GeoEco\Metadata.py", line 512, in InitializeDependency
    d.Initialize()
  File "C:\Python27\ArcGIS10.2\lib\site-packages\GeoEco\R.py", line 386, in Initialize
    from GeoEco.AssimilatedModules.rpy import rpy
  File "C:\Python27\ArcGIS10.2\lib\site-packages\GeoEco\AssimilatedModules\rpy\rpy.py", line 150, in <module>
    """ % RVERSION)
RuntimeError: No module named _rpy3024

      RPy module can not be imported. Please check if your rpy
      installation supports R 3.2.4. If you have multiple R versions
      installed, you may need to set RHOME before importing rpy. For
      example:
 
      >>> from rpy_options import set_options
      >>> set_options(RHOME='c:/progra~1/r/rw2011/')
      >>> from rpy import *
      
     
Failed to execute (SpeciesDiversityCalculateDiversityIndexForArcGISPolygons).
Failed at Tue Aug 23 16:54:37 2016 (Elapsed Time: 0.11 seconds)



I'm not sure what I have to do in terms of setting RHOME

Any help much appreciated

Cheers

Rob


 

Dr Robert Berry
Research Fellow
Countryside and Community Research Institute (CCRI)
University of Gloucestershire
Oxstalls Campus
Gloucester, UK
GL2 9HW

T: 01242 714120
M: 07970 433587
Skype: robert_berry_uk
@rural_gis

Staff Web page

CCRI Website
CCRI Year in Review
CCRI on Twitter
CCRI on Facebook
CCRI on Slideshare

 


Archive powered by MHonArc 2.6.19.

Top of Page