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

Rajendra Mohan panda rmp.iit.kgp at gmail.com
Wed Sep 10 17:40:33 CEST 2014 

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?

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?

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

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]]
>> >>> >>>>>>>
>> >>> >>>>>>> _______________________________________________
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>> >>> >>>>>>>
>> >>> >>>>>>>
>> >>> >>>>>>
>> >>> >>>>>> --
>> >>> >>>>>> In God we trust, all others bring data.
>> >>> >>>>>>
>> >>> >>>>>>
>> >>> >>>>>
>> >>> >>>>>           [[alternative HTML version deleted]]
>> >>> >>>>
>> >>> >>>> _______________________________________________
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>> >>> >>>>
>> >>> >>>>
>> >>> >>>
>> >>> >>> --
>> >>> >>> In God we trust, all others bring data.
>> >>> >>>
>> >>> >>>          [[alternative HTML version deleted]]
>> >>> >>
>> >>> >> _______________________________________________
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>> >>> >>
>> >>> >
>> >>> > --
>> >>> > 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
>> >>> >
>> >>> >
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>> >>>
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>> >>>
>> >>
>> >>
>> >>
>> >> --
>> >> In God we trust, all others bring data.
>> >>
>> >
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
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>
>
>
> --
> In God we trust, all others bring data.
>

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