[R-sig-eco] Query related to maxent file in dismo package

[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:

> 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:
>
> > 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.skoien at 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]]
> >>>
> >>> _______________________________________________
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> >>>
> >>>
> >>>
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> >>
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> >
>
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