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-boun...@r-project.org
[mailto:r-sig-ecology-boun...@r-project.org] On Behalf Of Rajendra Mohan panda
Sent: Wednesday, 20 August 2014 2:19 AM
To: r-sig-ecology@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.sko...@jrc.ec.europa.eu>
wrote:
> 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:
>
>> 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.sko...@jrc.ec.europa.eu
>> >
>> wrote:
>>
>> 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:
>>>
>>>> system.file("java", package="dismo")
>>>>
>>> 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:
>>>
>>> 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
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> R-sig-ecology mailing listR-sig-ecology@r-project.orghttps://
>>> stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>>
>>>
>>>
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>>
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>
>
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