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AI-GEOSTATS: geoR and memory

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  • Marcelo Alexandre Bruno
    Dear list-members I try to run geoR for generate interpolation maps. My data is: x(longitud, decimal degree),y(latitud, decimal degree),z(Sa, acoustic
    Message 1 of 11 , Oct 22, 2003
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      Dear list-members

      I try to run geoR for generate interpolation maps.
      My data is: x(longitud, decimal degree),y(latitud,
      decimal degree),z(Sa, acoustic parameter, limits range
      is 0 to 1000000, extremely skewed, represent
      backscatering echoes signals of fish schools). The
      dataset is 3007 nautic miles of sampling!

      The analysis is run according to steps of Dr. Paulo
      Justiano's homepage
      http://www.est.ufpr.br/~paulojus/geoR/geoRdoc/geoRintro.html#starting
      .
      When kriging run, consume all memory of system,
      (R.bin with only geoR consumes 86.8mb!! in Athlon
      xp1.6GHz, Linux redhat 9.0, 250mb + swapp 541mb).
      Is there something wrong (possible newbie question)
      or its possible vectorizing computations to
      reduce memory consume?


      "The necessary reliance on a n by n matrix, where n
      represents the number of observations, greatly impedes
      traditional spatial statistics from handling larger
      sample sizes." published from:
      Pace, R. Kelley, and Ronald Barry, "Fast CARs,"
      Journal of Statistical Computation and Simulation,
      Volume 59, Number 2, 1997, p. 123-147.

      This is the case??
      (Apologies for my long msg.)
      Thanks for all.

      =====
      ## ~~~~~~~ Oceanólogo ~~~~~~~ ##
      # Marcelo Alexandre Bruno
      # Linux User: 124592
      # Pós-graduação Oceanografia Biológica
      # FUNDACAO UNIV. FEDERAL do RIO GRANDE
      # Departamento de Oceanografia
      # Lab. de Tecnologia Pesqueira e Hidroacústica
      # AV. ITÁLIA km 8 s/n - CARREIROS
      # 96201-900 (0xx53) 2336528
      # Rio Grande - RS - BRAZIL
      ## ---------------------------------------- ##

      Yahoo! Mail - o melhor webmail do Brasil
      http://mail.yahoo.com.br

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    • Edzer J. Pebesma
      Marcelo, although I would like to wait for Paulo s comments, here are my two brief remarks: 1. if your data set is large, say over 3000 observations, and you
      Message 2 of 11 , Oct 22, 2003
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        Marcelo,

        although I would like to wait for Paulo's comments, here are
        my two brief remarks:

        1. if your data set is large, say over 3000 observations, and you
        want to use kriging, you'd better use kriging in a local
        neighbourhood. I think geoR does not provide this, another
        R package that does so is package gstat. The quote you
        mention ignores this common practice.
        2. if your data are in lat/lon, you may want to project them
        first -- to my knowledge all geostats software assumes data
        in a plane (or 3D data, but not on a sphere): one unit in x direction
        should equal one unit in y direction. In lat/lon, it generally doesn't.

        Best regards,
        --
        Edzer

        Marcelo Alexandre Bruno wrote:

        >Dear list-members
        >
        >I try to run geoR for generate interpolation maps.
        >My data is: x(longitud, decimal degree),y(latitud,
        >decimal degree),z(Sa, acoustic parameter, limits range
        >is 0 to 1000000, extremely skewed, represent
        >backscatering echoes signals of fish schools). The
        >dataset is 3007 nautic miles of sampling!
        >
        >The analysis is run according to steps of Dr. Paulo
        >Justiano's homepage
        >http://www.est.ufpr.br/~paulojus/geoR/geoRdoc/geoRintro.html#starting
        >.
        >When kriging run, consume all memory of system,
        >(R.bin with only geoR consumes 86.8mb!! in Athlon
        >xp1.6GHz, Linux redhat 9.0, 250mb + swapp 541mb).
        >Is there something wrong (possible newbie question)
        >or its possible vectorizing computations to
        >reduce memory consume?
        >
        >
        >"The necessary reliance on a n by n matrix, where n
        >represents the number of observations, greatly impedes
        >traditional spatial statistics from handling larger
        >sample sizes." published from:
        >Pace, R. Kelley, and Ronald Barry, "Fast CARs,"
        >Journal of Statistical Computation and Simulation,
        >Volume 59, Number 2, 1997, p. 123-147.
        >
        >This is the case??
        >(Apologies for my long msg.)
        >Thanks for all.
        >
        >=====
        >## ~~~~~~~ Oceanólogo ~~~~~~~ ##
        ># Marcelo Alexandre Bruno
        ># Linux User: 124592
        ># Pós-graduação Oceanografia Biológica
        ># FUNDACAO UNIV. FEDERAL do RIO GRANDE
        ># Departamento de Oceanografia
        ># Lab. de Tecnologia Pesqueira e Hidroacústica
        ># AV. ITÁLIA km 8 s/n - CARREIROS
        ># 96201-900 (0xx53) 2336528
        ># Rio Grande - RS - BRAZIL
        >## ---------------------------------------- ##
        >
        >Yahoo! Mail - o melhor webmail do Brasil
        >http://mail.yahoo.com.br
        >
        >--
        >* To post a message to the list, send it to ai-geostats@...
        >* As a general service to the users, please remember to post a summary of any useful responses to your questions.
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        >
        >


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      • Ernesto Jardim
        ... Hi Marcelo, It s commom to run out of memory with R, in particular if you are using a version older than 1.4 (see man pages in that case). Also in versions
        Message 3 of 11 , Oct 22, 2003
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          On Wed, 2003-10-22 at 12:03, Marcelo Alexandre Bruno wrote:
          > Dear list-members
          >
          > I try to run geoR for generate interpolation maps.
          > My data is: x(longitud, decimal degree),y(latitud,
          > decimal degree),z(Sa, acoustic parameter, limits range
          > is 0 to 1000000, extremely skewed, represent
          > backscatering echoes signals of fish schools). The
          > dataset is 3007 nautic miles of sampling!
          >
          > The analysis is run according to steps of Dr. Paulo
          > Justiano's homepage
          > http://www.est.ufpr.br/~paulojus/geoR/geoRdoc/geoRintro.html#starting
          > .
          > When kriging run, consume all memory of system,
          > (R.bin with only geoR consumes 86.8mb!! in Athlon
          > xp1.6GHz, Linux redhat 9.0, 250mb + swapp 541mb).
          > Is there something wrong (possible newbie question)
          > or its possible vectorizing computations to
          > reduce memory consume?
          >
          >
          > "The necessary reliance on a n by n matrix, where n
          > represents the number of observations, greatly impedes
          > traditional spatial statistics from handling larger
          > sample sizes." published from:
          > Pace, R. Kelley, and Ronald Barry, "Fast CARs,"
          > Journal of Statistical Computation and Simulation,
          > Volume 59, Number 2, 1997, p. 123-147.
          >
          > This is the case??
          > (Apologies for my long msg.)
          > Thanks for all.
          >
          > =====
          > ## ~~~~~~~ Oceanólogo ~~~~~~~ ##
          > # Marcelo Alexandre Bruno
          > # Linux User: 124592
          > # Pós-graduação Oceanografia Biológica
          > # FUNDACAO UNIV. FEDERAL do RIO GRANDE
          > # Departamento de Oceanografia
          > # Lab. de Tecnologia Pesqueira e Hidroacústica
          > # AV. ITÁLIA km 8 s/n - CARREIROS
          > # 96201-900 (0xx53) 2336528
          > # Rio Grande - RS - BRAZIL
          > ## ---------------------------------------- ##
          >
          > Yahoo! Mail - o melhor webmail do Brasil
          > http://mail.yahoo.com.br
          >
          > --
          > * To post a message to the list, send it to ai-geostats@...
          > * As a general service to the users, please remember to post a summary of any useful responses to your questions.
          > * To unsubscribe, send an email to majordomo@... with no subject and "unsubscribe ai-geostats" followed by "end" on the next line in the message body. DO NOT SEND Subscribe/Unsubscribe requests to the list
          > * Support to the list is provided at http://www.ai-geostats.org

          Hi Marcelo,

          It's commom to run out of memory with R, in particular if you are using
          a version older than 1.4 (see man pages in that case). Also in versions
          newer than 1.7 R loads a lot of libraries that may not be needed. You
          can detach those libraries to get more memory.

          My R.bin with geoR uses 16252k, the values you're getting includes the
          memory occupied by your data.

          When I have that kind of problems I try to reduce the data to the
          minimum necessary and run R directly on the terminal, without X running.

          Maybe Paulo Ribeiro can give you some hints about the way geoR processes
          the data and try to optimize your computer resources.

          Best regards

          EJ

          --
          Ernesto Jardim <ernesto@...>
          Biólogo Marinho/Marine Biologist
          IPIMAR - Instituto Nacional de Investigação Agrária e das Pescas
          IPIMAR - National Research Institute for Agriculture and Fisheries
          Av. Brasilia, 1400-006
          Lisboa, Portugal
          Tel: +351 213 027 000
          Fax: +351 213 015 948
          http://ernesto.freezope.org


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        • Martin Roseveare
          Just to reinforce what Edzer said about projections - convert your longitude and latitude data into a planar projection first - UTM should be OK though check
          Message 4 of 11 , Oct 24, 2003
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            Just to reinforce what Edzer said about projections - convert your longitude
            and latitude data into a planar projection first - UTM should be OK though
            check your data doesn't cross zones. If you don't do this the stats will not
            produce meaningful results as degrees are not a correct spatial measure.
            Even for very small areas the shape and hence the interrelationship between
            data is very different for long lat and metres.

            Martin Roseveare
            ______________________________________

            ArchaeoPhysica Ltd.
            Reconnaissance & Geophysics for Archaeology

            Telephone: +44 (0) 7050 369789
            E-mail: mail@...
            Website: http://www.archaeophysica.co.uk
            ______________________________________

            This e-mail is intended only for the addressee
            named above and may contain confidential or
            privileged information. If you receive this e-mail
            by mistake please advise the sender and destroy
            it without further disclosure of its content.

            Unless otherwise stated no opinions expressed in
            this e-mail should be regarded as representative of
            any policy of ArchaeoPhysica Ltd.
            ----- Original Message -----
            From: "Marcelo Alexandre Bruno" <marcelo2lei@...>
            To: <Paulo.Ribeiro@...>
            Cc: <ai-geostats@...>
            Sent: Wednesday, October 22, 2003 12:03 PM
            Subject: AI-GEOSTATS: geoR and memory


            > Dear list-members
            >
            > I try to run geoR for generate interpolation maps.
            > My data is: x(longitud, decimal degree),y(latitud,
            > decimal degree),z(Sa, acoustic parameter, limits range
            > is 0 to 1000000, extremely skewed, represent
            > backscatering echoes signals of fish schools). The
            > dataset is 3007 nautic miles of sampling!
            >
            > The analysis is run according to steps of Dr. Paulo
            > Justiano's homepage
            > http://www.est.ufpr.br/~paulojus/geoR/geoRdoc/geoRintro.html#starting
            > .
            > When kriging run, consume all memory of system,
            > (R.bin with only geoR consumes 86.8mb!! in Athlon
            > xp1.6GHz, Linux redhat 9.0, 250mb + swapp 541mb).
            > Is there something wrong (possible newbie question)
            > or its possible vectorizing computations to
            > reduce memory consume?
            >
            >
            > "The necessary reliance on a n by n matrix, where n
            > represents the number of observations, greatly impedes
            > traditional spatial statistics from handling larger
            > sample sizes." published from:
            > Pace, R. Kelley, and Ronald Barry, "Fast CARs,"
            > Journal of Statistical Computation and Simulation,
            > Volume 59, Number 2, 1997, p. 123-147.
            >
            > This is the case??
            > (Apologies for my long msg.)
            > Thanks for all.
            >
            > =====
            > ## ~~~~~~~ Oceanslogo ~~~~~~~ ##
            > # Marcelo Alexandre Bruno
            > # Linux User: 124592
            > # Pss-graduagco Oceanografia Biolsgica
            > # FUNDACAO UNIV. FEDERAL do RIO GRANDE
            > # Departamento de Oceanografia
            > # Lab. de Tecnologia Pesqueira e Hidroaczstica
            > # AV. ITALIA km 8 s/n - CARREIROS
            > # 96201-900 (0xx53) 2336528
            > # Rio Grande - RS - BRAZIL
            > ## ---------------------------------------- ##
            >
            > Yahoo! Mail - o melhor webmail do Brasil
            > http://mail.yahoo.com.br
            >
            > --
            > * To post a message to the list, send it to ai-geostats@...
            > * As a general service to the users, please remember to post a summary of
            any useful responses to your questions.
            > * To unsubscribe, send an email to majordomo@... with no subject and
            "unsubscribe ai-geostats" followed by "end" on the next line in the message
            body. DO NOT SEND Subscribe/Unsubscribe requests to the list
            > * Support to the list is provided at http://www.ai-geostats.org
            >


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          • Isobel Clark
            Martin ... Do you have an algorithm that works everywhere in the world? Isobel http://geoecosse.bizland.com/whatsnew.htm
            Message 5 of 11 , Oct 24, 2003
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              Martin

              > - convert your longitude
              > and latitude data into a planar projection first
              Do you have an algorithm that works everywhere in the
              world?

              Isobel
              http://geoecosse.bizland.com/whatsnew.htm

              ________________________________________________________________________
              Want to chat instantly with your online friends? Get the FREE Yahoo!
              Messenger http://mail.messenger.yahoo.co.uk

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            • Susan King
              I would like to have algorithms for converting lat/long into different projections (albers, utm). Susan L. King Operations Research Analyst USDA Forest
              Message 6 of 11 , Oct 24, 2003
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                I would like to have algorithms for converting lat/long into different
                projections (albers, utm).




                Susan L. King
                Operations Research Analyst
                USDA Forest Service
                11 Campus Blvd., Suite 200
                Newtown Square, PA 19073
                Phone: (610) 557-4048
                Email: sking01@...
                FAX: (610) 557-4250



                Isobel Clark
                <drisobelclark@y To: Martin Roseveare <martin_roseveare@...>
                ahoo.co.uk> cc: ai-geostats@...
                Sent by: Subject: Re: AI-GEOSTATS: geoR and memory
                ai-geostats-list
                @...


                10/24/2003 11:06
                AM
                Please respond
                to Isobel Clark






                Martin

                > - convert your longitude
                > and latitude data into a planar projection first
                Do you have an algorithm that works everywhere in the
                world?

                Isobel
                http://geoecosse.bizland.com/whatsnew.htm

                ________________________________________________________________________
                Want to chat instantly with your online friends? Get the FREE Yahoo!
                Messenger http://mail.messenger.yahoo.co.uk

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              • Martin Roseveare
                Isobel, There are published algorithms that will do this - one of the advantages of the UTM projection is that it can be generated anywhere, with the zoning of
                Message 7 of 11 , Oct 24, 2003
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                  Isobel,

                  There are published algorithms that will do this - one of the advantages of
                  the UTM projection is that it can be generated anywhere, with the zoning of
                  the projection accounting for the necessary differences around the globe.
                  Good software should be able to deal with UTM zones and hence work anywhere.
                  The disadvantage of UTM is that other commerical mapping (including State)
                  is more likely to use a local grid for the area concerned.

                  It may be possible to find free or shareware that will do the projection -
                  one issue that needs to be addressed though is precision as a lot of the
                  free code is limited in this respect and of course the desired spatial
                  accuracy of subsequent statistical processes needs to be incorporated within
                  this. Otherwise there is often software tailor made for specific countries,
                  e.g., for the UK and Ireland that usually offers a higher precision. It
                  depends on the source data and what you want to do with it - we work to
                  sub-metre precision and this can be a problem.

                  If any of the list need to pursue this further I have a contact who is
                  renowned for his work on co-ordinate transformations in the aerial
                  photography world and who would probably be able to advise.

                  Martin
                  ______________________________________

                  ArchaeoPhysica Ltd.
                  Reconnaissance & Geophysics for Archaeology

                  Telephone: +44 (0) 7050 369789
                  E-mail: mail@...
                  Website: http://www.archaeophysica.co.uk
                  ______________________________________

                  This e-mail is intended only for the addressee
                  named above and may contain confidential or
                  privileged information. If you receive this e-mail
                  by mistake please advise the sender and destroy
                  it without further disclosure of its content.

                  Unless otherwise stated no opinions expressed in
                  this e-mail should be regarded as representative of
                  any policy of ArchaeoPhysica Ltd.
                  ----- Original Message -----
                  From: "Isobel Clark" <drisobelclark@...>
                  To: "Martin Roseveare" <martin_roseveare@...>
                  Cc: <ai-geostats@...>
                  Sent: Friday, October 24, 2003 4:06 PM
                  Subject: Re: AI-GEOSTATS: geoR and memory


                  > Martin
                  >
                  > > - convert your longitude
                  > > and latitude data into a planar projection first
                  > Do you have an algorithm that works everywhere in the
                  > world?
                  >
                  > Isobel
                  > http://geoecosse.bizland.com/whatsnew.htm
                  >
                  > ________________________________________________________________________
                  > Want to chat instantly with your online friends? Get the FREE Yahoo!
                  > Messenger http://mail.messenger.yahoo.co.uk


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                • Jim Bash
                  ... There is no single projection that would be appropriate for everywhere in the world at once, just as there is no 2 dimensional (planar) projection that can
                  Message 8 of 11 , Oct 24, 2003
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                    On Fri, 24 Oct 2003, [iso-8859-1] Isobel Clark wrote:
                    > > - convert your longitude
                    > > and latitude data into a planar projection first
                    > Do you have an algorithm that works everywhere in the
                    > world?

                    There is no single projection that would be appropriate for everywhere in
                    the world at once, just as there is no 2 dimensional (planar) projection
                    that can accurately preserve angles, distance, direction and area for an
                    entire map:-) Is that what you are asking for?

                    jim b
                    -----
                    Jim Bash, Associate Director Internet : JBash@...
                    CAGIS (m/c 092) Phone (W): 312/996-6367
                    Program in Geography, Dept of Anthropology Fax : 312/996-6343
                    University of Illinois at Chicago
                    1007 W. Harrison St, Rm 2102 BSB URL : http://www.cagis.uic.edu/
                    Chicago, IL 60607-7138

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                  • Jim Bash
                    ... You might check out http://www.remotesensing.org/proj/ which has source and documentation for PROJ.4, map projection software. I think the source is in C
                    Message 9 of 11 , Oct 24, 2003
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                      On Fri, 24 Oct 2003, Susan King wrote:
                      > I would like to have algorithms for converting lat/long into different
                      > projections (albers, utm).

                      You might check out http://www.remotesensing.org/proj/ which has source
                      and documentation for PROJ.4, map projection software. I think the source
                      is in C and you would probably have to dig for the algorithms, unless they
                      are in the documentation.

                      Sorry but I haven't looked at PROJ.4 in a long time. I normally refer to a
                      book by John Snyder, "Map Projections-- A Working Manual" which was
                      published by USGS as "USGS Professional Paper 1395" in 1987. But that
                      isn't online and I'm not sure it is available anymore.

                      HTH a little,

                      jim b
                      ------
                      Jim Bash, Associate Director Internet : JBash@...
                      CAGIS (m/c 092) Phone (W): 312/996-6367
                      Program in Geography, Dept of Anthropology Fax : 312/996-6343
                      University of Illinois at Chicago
                      1007 W. Harrison St, Rm 2102 BSB URL : http://www.cagis.uic.edu/
                      Chicago, IL 60607-7138

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                    • Julian Burgos
                      Hello everyone, Here is a link to Geotrans, a program developed by the US National Imagery and Mapping Agency to convert locations between different coordinate
                      Message 10 of 11 , Oct 24, 2003
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                        Hello everyone,

                        Here is a link to Geotrans, a program developed by the US National Imagery
                        and Mapping Agency to convert locations between different coordinate
                        systems.
                        http://earth-info.nima.mil/GandG/geotrans/geotrans.html
                        It can work in batch mode.

                        Julian M. Burgos

                        University of Washington
                        School of Aquatic and Fishery Sciences
                        1122 NE Boat St. (Box 355020)
                        Seattle, WA 98195-5020

                        ----- Original Message -----
                        From: "Susan King" <sking01@...>
                        To: <ai-geostats@...>
                        Sent: Friday, October 24, 2003 12:27 PM
                        Subject: Re: AI-GEOSTATS: geoR and memory


                        >
                        >
                        >
                        >
                        > I would like to have algorithms for converting lat/long into different
                        > projections (albers, utm).
                        >
                        >
                        >
                        >
                        > Susan L. King
                        > Operations Research Analyst
                        > USDA Forest Service
                        > 11 Campus Blvd., Suite 200
                        > Newtown Square, PA 19073
                        > Phone: (610) 557-4048
                        > Email: sking01@...
                        > FAX: (610) 557-4250
                        >
                        >
                        >
                        > Isobel Clark
                        > <drisobelclark@y To: Martin Roseveare
                        <martin_roseveare@...>
                        > ahoo.co.uk> cc:
                        ai-geostats@...
                        > Sent by: Subject: Re: AI-GEOSTATS:
                        geoR and memory
                        > ai-geostats-list
                        > @...
                        >

                        >
                        > 10/24/2003 11:06
                        > AM
                        > Please respond
                        > to Isobel Clark
                        >
                        >
                        >
                        >
                        >
                        >
                        > Martin
                        >
                        > > - convert your longitude
                        > > and latitude data into a planar projection first
                        > Do you have an algorithm that works everywhere in the
                        > world?
                        >
                        > Isobel
                        > http://geoecosse.bizland.com/whatsnew.htm
                        >
                        > ________________________________________________________________________
                        > Want to chat instantly with your online friends? Get the FREE Yahoo!
                        > Messenger http://mail.messenger.yahoo.co.uk
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                      • Martin Roseveare
                        I ve been passed this link regarding co-ordinate conversion - I haven t tried it so can t comment on it s suitability.
                        Message 11 of 11 , Oct 25, 2003
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                          I've been passed this link regarding co-ordinate conversion - I haven't
                          tried it so can't comment on it's suitability.

                          http://www.connect.net/jbanta/Downloads.html#cat01

                          Martin
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                          ----- Original Message -----
                          From: "Jim Bash" <jbash@...>
                          To: "Susan King" <sking01@...>
                          Cc: <ai-geostats@...>; "Cliff Tiedemann" <clifft@...>
                          Sent: Friday, October 24, 2003 10:29 PM
                          Subject: Re: AI-GEOSTATS: geoR and memory


                          >
                          > On Fri, 24 Oct 2003, Susan King wrote:
                          > > I would like to have algorithms for converting lat/long into different
                          > > projections (albers, utm).
                          >
                          > You might check out http://www.remotesensing.org/proj/ which has source
                          > and documentation for PROJ.4, map projection software. I think the source
                          > is in C and you would probably have to dig for the algorithms, unless they
                          > are in the documentation.
                          >
                          > Sorry but I haven't looked at PROJ.4 in a long time. I normally refer to a
                          > book by John Snyder, "Map Projections-- A Working Manual" which was
                          > published by USGS as "USGS Professional Paper 1395" in 1987. But that
                          > isn't online and I'm not sure it is available anymore.
                          >
                          > HTH a little,
                          >
                          > jim b
                          > ------
                          > Jim Bash, Associate Director Internet : JBash@...
                          > CAGIS (m/c 092) Phone (W): 312/996-6367
                          > Program in Geography, Dept of Anthropology Fax : 312/996-6343
                          > University of Illinois at Chicago
                          > 1007 W. Harrison St, Rm 2102 BSB URL :
                          http://www.cagis.uic.edu/
                          > Chicago, IL 60607-7138
                          >
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