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Query related to maxent file in dismo package

8 messages · Li Wen, Rajendra Mohan panda, Jon Olav Skoien

Original
Rajendra Mohan panda
# 
Dear All
What is the procedure to fix maxent jar file in "dismo" java file? I am
doing it after extracting "dismo" zip file.However, the file is not
executing. I think some silly mistake is there on my part. I would
highly appreciate
if anyone of advise in this regard.

With best Regards
 Rajendra M Panda
 SWR, Indian Institute of Technology Kharagpur
Li Wen
# 
Hi, Raj

After installing the dismo package from R (menu -> packages->install package(s) from local zip files), paste the file 'maxent.jar'  in R -> library -> dicmo ->java.

Cheers
Li
 

-----Original Message-----
From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Rajendra Mohan panda
Sent: Monday, 18 August 2014 2:43 PM
To: R-sig-ecology at r-project.org
Subject: [R-sig-eco] Query related to maxent file in dismo package

Dear All
What is the procedure to fix maxent jar file in "dismo" java file? I am doing it after extracting "dismo" zip file.However, the file is not executing. I think some silly mistake is there on my part. I would highly appreciate if anyone of advise in this regard.

With best Regards
 Rajendra M Panda
 SWR, Indian Institute of Technology Kharagpur


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Jon Olav Skoien
# 
Did you download the maxent.jar file from
http://www.cs.princeton.edu/~schapire/maxent/
and put it in the folder with the name returned by:
as described in the man-page of maxent?

If you have already tried this, you have to describe your problem better 
for anyone to be able to help.

Best wishes,
Jon
On 8/18/2014 6:42 AM, Rajendra Mohan panda wrote:

  
  


  


      

    

    

      
      

        


  

        

      Rajendra Mohan panda
    

    

      
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Thank you Won and Jon

I am now able to put my maxent jar file in appropriate folder.
However I have little more confusion on extraction of environmental
variables to R.
Can we use Climond data for extract values for use in maxent model in R?


With best Regards
Rajendra M Panda
SWR, IIT Kharagpur


On Tue, Aug 19, 2014 at 12:33 PM, Jon Skoien <jon.skoien at jrc.ec.europa.eu>
wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Jon Olav Skoien
    

    

      
      #
    

  


  

      
It depends what you mean by using Climond data for extracting values, I 
do not know the data set particularly well.
But I assume you can use Climond data if you download a format which can 
be opened by raster. If you want a more specific answer, you need to 
describe more specific what you want to do. It is generally a good 
advice to follow the mail-recommendations from the r-help list:

PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Best wishes,
Jon

        
On 8/19/2014 11:09 AM, Rajendra Mohan panda wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Rajendra Mohan panda
    

    

      
      #
    

  


  

      
Thanks a lot Jon

I have more than 1100 sample points. I want to extract values for 19
variables in Bioclim data for maxent model.
I do not understand if the following code automatically loads bioclim
variables grd file or not?

logo <- stack(system.file("external/rlogo.grd", package="raster"))

If I have to go for my downloaded grd files then how shall I do? path to
defined (system or any drive etc)

I also face problem to define the point matrix for huge datasets as given
in example in dismo package. Is there any easy way out?

#presence data
pts <- matrix(c(48.243420, 48.243420, 47.985820, 52.880230, 49.531423,
46.182616, 54.168232,
69.839163, 73.233228, 63.239594, 45.892154, 43.252326, 28.356155) , ncol=2)

I also request you all to know the way I can use ArcGIS extracted grd/ascii
file for my sample points to run maxent in R?

I hope it may help me huge datasets I have. Not sure.

Your kind advise is highly appreciated.



With best Regards
Rajendra M Panda
SWR, IIT Kharagpur


On Tue, Aug 19, 2014 at 5:25 PM, Jon Skoien <jon.skoien at jrc.ec.europa.eu>
wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Li Wen
    

    

      
      #
    

  


  

      
HI, Raj

1100 points is not huge. Anyway, there are a number of ways to extract values from raster layers.
1. Suppose you sample points are an excel datasheet of X (longitude) and Y (latitude). Saving it as .csv file, then read it into R as spatial data:
	Samples<-SpatialPoints(read.csv("yourfilename.csv"))
	Extracteddataset<- extract(yourrasterstack, Samples)
2. If you have a shape file (from ArcGIS) of the sample points:
	require(rgdal)	
	Samples<-  readOGR(".", layer="yourshapefilename")  ## without ".shp" and the shp file in your working folder

HTH
Li



-----Original Message-----
From: r-sig-ecology-bounces at r-project.org [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Rajendra Mohan panda
Sent: Wednesday, 20 August 2014 2:19 AM
To: r-sig-ecology at r-project.org
Subject: Re: [R-sig-eco] Query related to maxent file in dismo package

Thanks a lot Jon

I have more than 1100 sample points. I want to extract values for 19 variables in Bioclim data for maxent model.
I do not understand if the following code automatically loads bioclim variables grd file or not?

logo <- stack(system.file("external/rlogo.grd", package="raster"))

If I have to go for my downloaded grd files then how shall I do? path to defined (system or any drive etc)

I also face problem to define the point matrix for huge datasets as given in example in dismo package. Is there any easy way out?

#presence data
pts <- matrix(c(48.243420, 48.243420, 47.985820, 52.880230, 49.531423, 46.182616, 54.168232, 69.839163, 73.233228, 63.239594, 45.892154, 43.252326, 28.356155) , ncol=2)

I also request you all to know the way I can use ArcGIS extracted grd/ascii file for my sample points to run maxent in R?

I hope it may help me huge datasets I have. Not sure.

Your kind advise is highly appreciated.



With best Regards
Rajendra M Panda
SWR, IIT Kharagpur


On Tue, Aug 19, 2014 at 5:25 PM, Jon Skoien <jon.skoien at jrc.ec.europa.eu>
wrote:

            

      
      
      
    

        

      
      
    

        
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
----------------------------------------------------------------------------------------------------------------------------------------------------------------------
This email is intended for the addressee(s) named and may contain confidential and/or privileged information. 
If you are not the intended recipient, please notify the sender and then delete it immediately.
Any views expressed in this email are those of the individual sender except where the sender expressly and with authority states them to be the views of the NSW Office of Environment and Heritage.

PLEASE CONSIDER THE ENVIRONMENT BEFORE PRINTING THIS EMAIL

  
  


  


      

    

    

      
      

        


  

        

      Rajendra Mohan panda
    

    

      
      #
    

  


  

      
My sincere thanks to Li for his simplified answer to my queries.


With best Regards
Rajendra M Panda
SWR, IIT Kharagpur


On Wed, Aug 20, 2014 at 5:50 AM, Li Wen <Li.Wen at environment.nsw.gov.au>
wrote: