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

Roman Luštrik roman.lustrik at gmail.com
Thu Sep 11 18:12:52 CEST 2014 

On Wed, Sep 10, 2014 at 5:40 PM, Rajendra Mohan panda <rmp.iit.kgp at gmail.com
> wrote:

> Dear Roman
>
> In species_sample predictions.csv in the output result and in the
> train/test column I donot find any test data related information what I
> usually get in taking separate test and training datasets in direct maxent
> run. And also in ROC and Omission curve there is no test related
> information. This makes me surprise that I am right or not?
>

Unfortunately I'm not following about which tests you want. Perhaps someone
more knowledgeable can chip in?


>
> At the same time I would request you to advise on taking background value
> in following command.
> bg <- randomPoints(predictors, 500)
> What is the basis of selecting this number?
>

`randomPoints` samples 500 cells from predictors variable (RasterStack?).


> A lots of appreciation to those who have guided me to this level especially
> Roman
>
>
> With best Regards
> Rajendra M Panda
> School of Water Resources
> Indian Institute of Technology Kharagpur
>

HTH,
Roman



>
> On Wed, Sep 10, 2014 at 7:46 PM, Roman Luštrik <roman.lustrik at gmail.com>
> wrote:
>
> > What you get is a warning, not an error.
> > I'm afraid I don't understand your second part of the question.
> >
> > Cheers,
> > Roman
> >
> >
> > On Wed, Sep 10, 2014 at 3:50 PM, Rajendra Mohan panda <
> > rmp.iit.kgp at gmail.com> wrote:
> >
> >>  Dear Lustrik
> >>
> >> It is possible to run maxent in 64 bit operrating system with 64 bit R
> >> only
> >> after downloading Java from the link you provided.
> >> However I get following error (same for both the operating systems)
> >>
> >> me <- maxent(predictors, occtrain)
> >> Warning message:
> >> In .local(x, p, ...) :
> >>   1 (0.16%) of the presence points have NA predictor values
> >>
> >> I get output here by using predict function but no information on test
> >> gain
> >> is there. The column showing zero values.
> >> Am I wrong anywhere or this happens in "dismo" package.
> >> Kindly advise.
> >>
> >>
> >> With best Regards
> >> Rajendra M Panda
> >> IIT Kharagpur
> >>
> >> On Tue, Sep 9, 2014 at 10:53 PM, Rajendra Mohan panda <
> >> rmp.iit.kgp at gmail.com
> >> > wrote:
> >>
> >> > Dear All
> >> >
> >> > I am very much thankful to all who have responded to my queries and
> also
> >> > to the forum. My special thanks to Li and Lustrik for the patience to
> >> guide
> >> > me.
> >> > I am at the same time happy to inform you all that I could
> successfully
> >> > run maxent in 32 bit R and 32bit operating system with proper Java
> >> > installation.
> >> >
> >> >
> >> >
> >> > With best Regards
> >> > Rajendra M Panda
> >> > School of Water Resources
> >> > IIT Kharagpur
> >> >
> >> > On Tue, Sep 9, 2014 at 11:48 AM, Roman Luštrik <
> roman.lustrik at gmail.com
> >> >
> >> > wrote:
> >> >
> >> >> I solved my problem by installing Java JRE/JDK (link
> >> >> <
> >>
> http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html
> >> >),
> >> >> not "just" Java <https://java.com/en/download/index.jsp>.
> >>
> >> >>
> >> >>
> >> >> On Tue, Sep 9, 2014 at 6:12 AM, Rajendra Mohan panda <
> >> >> rmp.iit.kgp at gmail.com> wrote:
> >> >>
> >> >>> Dear All
> >> >>>
> >> >>> I am grateful to you for your response to my queries related to
> >> maxent. I
> >> >>> succeeded to install rJava in 32bit R (not able to install in 64bit
> >> R).
> >> >>> Still maxent jar file is not executing.
> >> >>> My operating system is 64 bit.
> >> >>> Kindly advise what necessary corrections I should take keeping my 64
> >> bit
> >> >>> operating system intact.
> >> >>> Shall I install 32 bit Java for 32bit R with operating system 64bit.
> >> >>> I would try but what are technical problems I do not know.
> >> >>> I have various options available to me by using 32bit computers of
> my
> >> lab
> >> >>> also. Each time I fail to execute maxent jar file.
> >> >>> I would appreciate your kind response.
> >> >>>
> >> >>> Thanking you
> >> >>>
> >> >>> With best Regards
> >> >>> Rajendra M Panda
> >> >>> School of Water Resources
> >> >>> Indian Institute of Technology Kharagpur
> >> >>>
> >> >>> On Mon, Sep 8, 2014 at 7:50 PM, Francisco Rodriguez Sanchez <
> >> >>> f.rodriguez.sanc at gmail.com> wrote:
> >> >>>
> >> >>> > Dear Rajendra,
> >> >>> >
> >> >>> > Are you running the 64-bit version of R? In that case I think you
> >> will
> >> >>> > need to install the 64-bit version of Java as well, or
> alternatively
> >> >>> switch
> >> >>> > to the 32-bit version of R to run these analyses (that is what I
> did
> >> >>> when I
> >> >>> > had this same problem).
> >> >>> >
> >> >>> > Try loading rJava (and dismo) with the 32-bit R version - does it
> >> work?
> >> >>> >
> >> >>> > Hope it helps,
> >> >>> >
> >> >>> > Paco
> >> >>> >
> >> >>> >
> >> >>> > El 05/09/2014 18:00, Rajendra Mohan panda escribió:
> >> >>> >
> >> >>> >  Dear All
> >> >>> >>
> >> >>> >> As you know from my trail mail, my maxent is not executing in r
> >> >>> (working
> >> >>> >> well directly).
> >> >>> >> I think there is some java configuration problem what I see from
> >> the
> >> >>> >> following errors after using some online available codes in
> >> >>> StackOverflow
> >> >>> >> site. Your kind advise is highly appreciated for how can I solve
> >> these
> >> >>> >> errors?
> >> >>> >> I have 64 bit PC operating system and rJava successfully
> installed.
> >> >>> >> utils:::menuInstallLocal()
> >> >>> >> package ‘rJava’ successfully unpacked and MD5 sums checked
> >> >>> >>
> >> >>> >>  library(rJava)
> >> >>> >>>
> >> >>> >> Error : .onLoad failed in loadNamespace() for 'rJava', details:
> >> >>> >>    call: fun(libname, pkgname)
> >> >>> >>    error: No CurrentVersion entry in Software/JavaSoft registry!
> >> Try
> >> >>> >> re-installing Java and make sure R and Java have matching
> >> >>> architectures.
> >> >>> >> Error: package or namespace load failed for ‘rJava’
> >> >>> >>
> >> >>> >>  Sys.getenv("JAVA_HOME")
> >> >>> >>>
> >> >>> >> [1] ""
> >> >>> >>
> >> >>> >>> if (Sys.getenv("JAVA_HOME")!="")
> >> >>> >>>
> >> >>> >> +   Sys.setenv(JAVA_HOME="")
> >> >>> >>
> >> >>> >>> library(rJava)
> >> >>> >>>
> >> >>> >> Error : .onLoad failed in loadNamespace() for 'rJava', details:
> >> >>> >>    call: fun(libname, pkgname)
> >> >>> >>    error: No CurrentVersion entry in Software/JavaSoft registry!
> >> Try
> >> >>> >> re-installing Java and make sure R and Java have matching
> >> >>> architectures.
> >> >>> >> Error: package or namespace load failed for ‘rJava’
> >> >>> >>
> >> >>> >>> Sys.setenv(JAVA_HOME="C:\\Program Files\\Java\\jre7\\")
> >> >>> >>> options(java.home="C:\\Program Files\\Java\\jre7\\")
> >> >>> >>> library(rJava)
> >> >>> >>>
> >> >>> >> Error : .onLoad failed in loadNamespace() for 'rJava', details:
> >> >>> >>    call: inDL(x, as.logical(local), as.logical(now), ...)
> >> >>> >>    error: unable to load shared object 'C:/Program
> >> >>> >> Files/R/R-3.1.1/library/rJava/libs/x64/rJava.dll':
> >> >>> >>    LoadLibrary failure:  The specified module could not be found.
> >> >>> >>
> >> >>> >> Error: package or namespace load failed for ‘rJava’
> >> >>> >>
> >> >>> >>
> >> >>> >>
> >> >>> >> With best Regards
> >> >>> >> Rajendra M Panda
> >> >>> >> SWR, IIT KGP
> >> >>> >>
> >> >>> >>
> >> >>> >> On Fri, Sep 5, 2014 at 8:23 PM, Roman Luštrik <
> >> >>> roman.lustrik at gmail.com>
> >> >>> >> wrote:
> >> >>> >>
> >> >>> >>  Well there you go. Follow the instruction in `?maxent` and put
> the
> >> >>> >>> appropriate .jar file into the /java folder.
> >> >>> >>>
> >> >>> >>> Cheers,
> >> >>> >>> Roman
> >> >>> >>>
> >> >>> >>>
> >> >>> >>> On Fri, Sep 5, 2014 at 4:48 PM, Rajendra Mohan panda <
> >> >>> >>> rmp.iit.kgp at gmail.com> wrote:
> >> >>> >>>
> >> >>> >>>  Dear Lustrik
> >> >>> >>>>
> >> >>> >>>> Thanks for your quick response. For your kind information
> maxent
> >> >>> runs
> >> >>> >>>> well
> >> >>> >>>> in my PC without any trouble directly but shows following error
> >> in R
> >> >>> >>>> me <- maxent(predictors, occtrain)
> >> >>> >>>> Error in .getMeVersion() : file missing:
> >> >>> >>>> C:/Program Files/R/R-3.1.1/library/dismo/java/maxent.jar.
> >> >>> >>>> Please download it here:
> >> >>> http://www.cs.princeton.edu/~schapire/maxent/
> >> >>> >>>> In addition: Warning message:
> >> >>> >>>> In .local(x, p, ...) :
> >> >>> >>>>    2 (0.31%) of the presence points have NA predictor values
> >> >>> >>>>
> >> >>> >>>>
> >> >>> >>>> With best Regards
> >> >>> >>>> Rajendra M Panda
> >> >>> >>>> SWR, IIT KGP
> >> >>> >>>>
> >> >>> >>>>
> >> >>> >>>> On Fri, Sep 5, 2014 at 8:13 PM, Rajendra Mohan panda <
> >> >>> >>>> rmp.iit.kgp at gmail.com>
> >> >>> >>>> wrote:
> >> >>> >>>>
> >> >>> >>>>  Dear All
> >> >>> >>>>>
> >> >>> >>>>> I have my java installed to my PC. Maxent downloaded from
> >> official
> >> >>> >>>>> site.
> >> >>> >>>>> maxent.jar file in java folder of "dismo". Still if I check
> for
> >> >>> maxent
> >> >>> >>>>>
> >> >>> >>>> run,
> >> >>> >>>>
> >> >>> >>>>> it shows nonavailability to run the model. Kindly advise.
> >> >>> >>>>>
> >> >>> >>>>> Your kind response is highly appreciated.
> >> >>> >>>>>
> >> >>> >>>>> With best Regards
> >> >>> >>>>> Rajendra M Panda
> >> >>> >>>>> SWR, IIT Kharagpur, India
> >> >>> >>>>>
> >> >>> >>>>>
> >> >>> >>>>> ---------- Forwarded message ----------
> >> >>> >>>>> From: Rajendra Mohan panda <rmp.iit.kgp at gmail.com>
> >> >>> >>>>> Date: Fri, Sep 5, 2014 at 8:03 PM
> >> >>> >>>>> Subject: Re: [R-sig-eco] Query related to maxent file in dismo
> >> >>> package
> >> >>> >>>>> To: Roman Luštrik <roman.lustrik at gmail.com>
> >> >>> >>>>>
> >> >>> >>>>>
> >> >>> >>>>> Dear Lustrik
> >> >>> >>>>>
> >> >>> >>>>> I didn't get it. Kindly clarify which java you mean?
> >> >>> >>>>>
> >> >>> >>>>> Cheers
> >> >>> >>>>> RMP
> >> >>> >>>>>
> >> >>> >>>>>
> >> >>> >>>>>
> >> >>> >>>>>
> >> >>> >>>>>
> >> >>> >>>>>
> >> >>> >>>>> On Fri, Sep 5, 2014 at 7:45 PM, Roman Luštrik <
> >> >>> roman.lustrik at gmail.com
> >> >>> >>>>> >
> >> >>> >>>>> wrote:
> >> >>> >>>>>
> >> >>> >>>>>  Do you have appropriate Java installed?
> >> >>> >>>>>>
> >> >>> >>>>>> Cheers,
> >> >>> >>>>>> Roman
> >> >>> >>>>>>
> >> >>> >>>>>>
> >> >>> >>>>>>
> >> >>> >>>>>> On Fri, Sep 5, 2014 at 4:12 PM, Rajendra Mohan panda <
> >> >>> >>>>>> rmp.iit.kgp at gmail.com> wrote:
> >> >>> >>>>>>
> >> >>> >>>>>>  Dear All
> >> >>> >>>>>>>
> >> >>> >>>>>>> Inspite of putting maxent.jar file in "dismo" package/ java
> >> >>> folder,
> >> >>> >>>>>>> maxent
> >> >>> >>>>>>> is showing unavailable to run the model. I would highly
> >> >>> appreciate
> >> >>> >>>>>>> for
> >> >>> >>>>>>> your
> >> >>> >>>>>>> kind response.
> >> >>> >>>>>>>
> >> >>> >>>>>>>
> >> >>> >>>>>>>
> >> >>> >>>>>>> With best Regards
> >> >>> >>>>>>> Rajendra M Panda
> >> >>> >>>>>>> School of Water Resources
> >> >>> >>>>>>> Indian Institute of Technology Kharagpur
> >> >>> >>>>>>>
> >> >>> >>>>>>>          [[alternative HTML version deleted]]
> >> >>> >>>>>>>
> >> >>> >>>>>>> _______________________________________________
> >> >>> >>>>>>> R-sig-ecology mailing list
> >> >>> >>>>>>> R-sig-ecology at r-project.org
> >> >>> >>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >> >>> >>>>>>>
> >> >>> >>>>>>>
> >> >>> >>>>>>
> >> >>> >>>>>> --
> >> >>> >>>>>> In God we trust, all others bring data.
> >> >>> >>>>>>
> >> >>> >>>>>>
> >> >>> >>>>>
> >> >>> >>>>>           [[alternative HTML version deleted]]
> >> >>> >>>>
> >> >>> >>>> _______________________________________________
> >> >>> >>>> R-sig-ecology mailing list
> >> >>> >>>> R-sig-ecology at r-project.org
> >> >>> >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >> >>> >>>>
> >> >>> >>>>
> >> >>> >>>
> >> >>> >>> --
> >> >>> >>> In God we trust, all others bring data.
> >> >>> >>>
> >> >>> >>>          [[alternative HTML version deleted]]
> >> >>> >>
> >> >>> >> _______________________________________________
> >> >>> >> R-sig-ecology mailing list
> >> >>> >> R-sig-ecology at r-project.org
> >> >>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >> >>> >>
> >> >>> >
> >> >>> > --
> >> >>> > Dr Francisco Rodriguez-Sanchez
> >> >>> > Integrative Ecology Group
> >> >>> > Estacion Biologica de Doñana - CSIC
> >> >>> > Avda. Americo Vespucio s/n
> >> >>> > 41092 Sevilla (Spain)
> >> >>> > http://sites.google.com/site/rodriguezsanchezf
> >> >>> >
> >> >>> >
> >> >>> > _______________________________________________
> >> >>> > R-sig-ecology mailing list
> >> >>> > R-sig-ecology at r-project.org
> >> >>> > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >> >>> >
> >> >>>
> >> >>>         [[alternative HTML version deleted]]
> >> >>>
> >> >>> _______________________________________________
> >> >>> R-sig-ecology mailing list
> >> >>> R-sig-ecology at r-project.org
> >> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >> >>>
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> In God we trust, all others bring data.
> >> >>
> >> >
> >> >
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> R-sig-ecology mailing list
> >> R-sig-ecology at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
> >>
> >
> >
> >
> > --
> > In God we trust, all others bring data.
> >
>
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>



-- 
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