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    <p>Dear KK,</p>
    <p>Thanks for your advice. I am afraid that the "initialize"
      function would make the initial parameters for our machine
      learning using an improved ABC method.</p>
    <p>After this learning, we got a thousand of selected parameter sets
      which would mimic the updated parameter distributions, those are
      described in var.mat.all in this case. Then, this time we use this
      like simulate_R(var.mat.all, fobs="observed data", interval=6).</p>
    <p>Thus, I am afraid that we do not need the initialize function for
      simulation when we use the updated parameter sets. In fact, I
      confirmed the simulation using simulate_R() works in R but did not
      give me the "out" list as a result.</p>
    <p>In this term, I am thinking the "out" list was not generated, due
      to "the initialization of the array". But I have no idea how to
      generate "out" list.</p>
    <p>Best,</p>
    <p>Takeshi<br>
    </p>
    <br>
    <div class="moz-cite-prefix">On 2017/07/10 14:04, Qiang Kou wrote:<br>
    </div>
    <blockquote
cite="mid:CAJ_LAMBF6jsLTSuAbLwV2wp2Nm6WAmw682o943UFwXRJwCOiaw@mail.gmail.com"
      type="cite">
      <div dir="ltr">I mean line 49 in ge-model.cpp. You have a function
        called "<span style="font-size:12.8px">initialize</span>" there.
        <div><br>
        </div>
        <div>The "<span style="font-size:12.8px">initialize</span>"
          function will initialize the _rand array.</div>
        <div><br>
        </div>
        <div>Best,</div>
        <div><br>
        </div>
        <div>KK</div>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On Sun, Jul 9, 2017 at 9:55 PM, 井澤 毅 <span
            dir="ltr"><<a moz-do-not-send="true"
              href="mailto:a-izawa@mail.ecc.u-tokyo.ac.jp"
              target="_blank">a-izawa@mail.ecc.u-tokyo.ac.jp</a>></span>
          wrote:<br>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div bgcolor="#FFFFFF" text="#000000">
              <p>Dear KK,</p>
              <p>Sorry for bothering you again, I still have some
                problems.<br>
              </p>
              <p>According to your advice, in order to initialize the
                array in ge-r.cpp,</p>
              <p>I put <br>
              </p>
              <p><br>
                                Model.out_y=cube(Model.n_acc,
                Model._obs._n_group, Model._obs._n_out_date,fill::<wbr>zeros);<br>
                                Model.out_res_1=cube(Model.n_<wbr>acc,Model._obs._n_group,
                Model._obs._n_out_date,fill::<wbr>zeros);<br>
                                Model.out_res_2=cube(Model.n_<wbr>acc,Model._obs._n_group,
                Model._obs._n_out_date,fill::<wbr>zeros);<br>
                                Model.out_res_clock=cube(<wbr>Model.n_acc,Model._obs._n_<wbr>group,
                Model._obs._n_out_date,fill::<wbr>zeros);<br>
                                Model.out_res_dev=cube(Model.<wbr>n_acc,Model._obs._n_group,
                Model._obs._n_out_date,fill::<wbr>zeros);<br>
              </p>
              instead of the old ones,<span class=""><br>
                <br>
                                Model.out_y=cube(Model.n_acc,
                Model._obs._n_group, Model._obs._n_out_date);<br>
                                Model.out_res_1=cube(Model.n_<wbr>acc,Model._obs._n_group,
                Model._obs._n_out_date);<br>
                                Model.out_res_2=cube(Model.n_<wbr>acc,Model._obs._n_group,
                Model._obs._n_out_date);<br>
                                Model.out_res_clock=cube(<wbr>Model.n_acc,Model._obs._n_<wbr>group,
                Model._obs._n_out_date);<br>
                                Model.out_res_dev=cube(Model.<wbr>n_acc,Model._obs._n_group,
                Model._obs._n_out_date);<br>
                <br>
              </span>
              <div class="m_2137384927404188588moz-cite-prefix">However,
                I got the same error in R.<br>
                <br>
                What should I do next ?<br>
                <br>
                I am afraid that I do not know how rand generated in
                ge-model.cpp (line 37) is linked to the array in
                ge-r.cpp (line 49) yet. Should I use fill:: randu
                instead of fill:: zeros?<br>
                <br>
                Best,<br>
                <br>
                Takeshi
                <div>
                  <div class="h5"><br>
                     <br>
                    <br>
                    <br>
                    On 2017/07/10 13:03, 井澤 毅 wrote:<br>
                  </div>
                </div>
              </div>
              <div>
                <div class="h5">
                  <blockquote type="cite">
                    <p>Dear KK,</p>
                    <p>Thanks for this explanation. Now I got it.</p>
                    <p>I did not think that ge-model.cpp is involved in
                      this problem since it works well as a C++ script
                      even in our current system.</p>
                    <p>I still wonder why this ge-r.cpp works in the old
                      system, but I will ask this to the maintainer of
                      our system.<br>
                    </p>
                    I have learned a lot from your suggestion.<br>
                    <br>
                    Thanks again!<br>
                    <br>
                    Best,<br>
                    <br>
                    Takeshi<br>
                    <br>
                    <br>
                    <div class="m_2137384927404188588moz-cite-prefix">On
                      2017/07/10 10:34, Qiang Kou wrote:<br>
                    </div>
                    <blockquote type="cite">
                      <div dir="ltr">
                        <div>In line 37 of ge-model.cpp, you try to free
                          _rand. However, if you don't call initialize
                          in line 49 first, the array won't be
                          initialized.</div>
                        <div><br>
                        </div>
                        <div>Best,</div>
                        <div><br>
                        </div>
                        <div>KK</div>
                      </div>
                      <div class="gmail_extra"><br>
                        <div class="gmail_quote">On Sun, Jul 9, 2017 at
                          4:45 PM, 井澤 毅 <span dir="ltr"><<a
                              moz-do-not-send="true"
                              href="mailto:a-izawa@mail.ecc.u-tokyo.ac.jp"
                              target="_blank">a-izawa@mail.ecc.u-tokyo.ac.<wbr>jp</a>></span>
                          wrote:<br>
                          <blockquote class="gmail_quote"
                            style="margin:0 0 0 .8ex;border-left:1px
                            #ccc solid;padding-left:1ex">
                            <div bgcolor="#FFFFFF" text="#000000">
                              <p>Dear KK,</p>
                              <p>I owe you a lot! I will check it as
                                soon as possible.</p>
                              <p>Since I am not familiar with this much,
                                I would be very happy to tell me some
                                urls describing "initialize".</p>
                              <p>Best,</p>
                              <p>Takeshi<br>
                              </p>
                              <div>
                                <div class="m_2137384927404188588h5"> <br>
                                  <div
                                    class="m_2137384927404188588m_-5732849694471883078moz-cite-prefix">On
                                    2017/07/10 7:38, Qiang Kou wrote:<br>
                                  </div>
                                  <blockquote type="cite">
                                    <div dir="ltr">Hi, professor,
                                      <div><br>
                                      </div>
                                      <div>I think the problem is in
                                        ge-r. cpp, you forgot to call <b>initialize</b>.</div>
                                      <div><br>
                                      </div>
                                      <div>The error has nothing to do
                                        with Rcpp.</div>
                                      <div><br>
                                      </div>
                                      <div>Best,</div>
                                      <div><br>
                                      </div>
                                      <div>KK</div>
                                    </div>
                                    <div class="gmail_extra"><br>
                                      <div class="gmail_quote">On Tue,
                                        Jul 4, 2017 at 2:45 AM, 井澤 毅 <span
                                          dir="ltr"><<a
                                            moz-do-not-send="true"
                                            href="mailto:a-izawa@mail.ecc.u-tokyo.ac.jp"
                                            target="_blank">a-izawa@mail.ecc.u-tokyo.ac.j<wbr>p</a>></span>
                                        wrote:<br>
                                        <blockquote class="gmail_quote"
                                          style="margin:0 0 0
                                          .8ex;border-left:1px #ccc
                                          solid;padding-left:1ex">
                                          <div bgcolor="#FFFFFF"
                                            text="#000000">
                                            <p>Sorry, I forgot the
                                              attached file.<br>
                                            </p>
                                            <div
class="m_2137384927404188588m_-5732849694471883078m_3086009423684693569moz-cite-prefix">On
                                              2017/07/04 18:43, 井澤 毅
                                              wrote:<br>
                                            </div>
                                            <blockquote type="cite">
                                              <p>Dear KK,</p>
                                              <p>Thanks for your kind
                                                reply.</p>
                                              <p>I am afraid that one of
                                                the input file is very
                                                heavy, this time but I
                                                am sending a ZIP file
                                                including all.</p>
                                              <p>Please make v30 package
                                                using
                                                install.simulate_R_1.r
                                                and then
                                                install.simulate_R_2.r.
                                                Then, try ge-r_test.r,
                                                please.</p>
                                              <p>To make the v30
                                                package, we need
                                                ge-r.cpp, ge-model.cpp,
                                                ge-model.h, ge-obs.cpp,
                                                ge-obs.h, ge-range.h.</p>
                                              <p>As the input file, we
                                                need var.mat.all matrix
                                                data in R and <a
                                                  moz-do-not-send="true"
href="http://obs.Os01g0182600_g1.nc" target="_blank">obs.Os01g0182600_g1.nc</a>
                                                file in the directry. <br>
                                              </p>
                                              <p>Then, you will see the
                                                error I have been
                                                suffering from for a
                                                month.</p>
                                              <p>The <a
                                                  moz-do-not-send="true"
href="http://obs.Os01g0182600_g1.nc" target="_blank">obs.Os01g0182600_g1.nc</a> file
                                                is a file containing
                                                environmental
                                                fluctuation data.</p>
                                              <p>Best,</p>
                                              <p>Takeshi<br>
                                              </p>
                                              <div>
                                                <div
                                                  class="m_2137384927404188588m_-5732849694471883078h5">
                                                  <br>
                                                  <div
class="m_2137384927404188588m_-5732849694471883078m_3086009423684693569moz-cite-prefix">On
                                                    2017/07/04 5:40,
                                                    Qiang Kou wrote:<br>
                                                  </div>
                                                  <blockquote
                                                    type="cite">
                                                    <div dir="ltr">Hi, I
                                                      am afraid the
                                                      example you
                                                      provided is not a
                                                      reproducible
                                                      example.
                                                      <div><br>
                                                      </div>
                                                      <div>First, we
                                                        don't know the
                                                        content of
                                                        ge-model.h.
                                                        Second, we don't
                                                        know which input
                                                        will trigger the
                                                        fault.</div>
                                                      <div><br>
                                                      </div>
                                                      <div>Please
                                                        provide a
                                                        reproducible
                                                        example if you
                                                        really want to
                                                        get help.</div>
                                                      <div><br>
                                                      </div>
                                                      <div>Best,</div>
                                                      <div><br>
                                                      </div>
                                                      <div>KK</div>
                                                    </div>
                                                    <div
                                                      class="gmail_extra"><br>
                                                      <div
                                                        class="gmail_quote">On
                                                        Sat, Jul 1, 2017
                                                        at 11:06 AM,
                                                        井澤 毅 <span
                                                          dir="ltr"><<a
moz-do-not-send="true" href="mailto:a-izawa@mail.ecc.u-tokyo.ac.jp"
                                                          target="_blank">a-izawa@mail.ecc.u-tokyo.ac.j<wbr>p</a>></span>
                                                        wrote:<br>
                                                        <blockquote
                                                          class="gmail_quote"
style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
                                                          <div
                                                          bgcolor="#FFFFFF"
                                                          text="#000000">
                                                          <div
class="m_2137384927404188588m_-5732849694471883078m_3086009423684693569m_8471227266221235016moz-text-flowed"
style="font-family:-moz-fixed;font-size:14px" lang="x-unicode">Dear <a
moz-do-not-send="true"
class="m_2137384927404188588m_-5732849694471883078m_3086009423684693569m_8471227266221235016moz-txt-link-abbreviated"
href="mailto:rcpp-devel@lists.r-forge.r-project.org" target="_blank">rcpp-devel@lists.r-forge.r-pro<wbr>ject.org</a>,
                                                          <br>
                                                          <br>
                                                          Sorry for
                                                          bothering you
                                                          much, but do
                                                          me a favor
                                                          please. Please
                                                          help me some.
                                                          <br>
                                                          <br>
                                                          I am just a
                                                          molecular
                                                          biologist
                                                          working on
                                                          plants. Thus,
                                                          I am still a
                                                          newcomer in
                                                          this field. <br>
                                                          <br>
                                                          Recently, I
                                                          have been
                                                          working with a
                                                          script using
                                                          RcppArmadillo,
                                                          This has
                                                          helped me a
                                                          lot. However,
                                                          after updating
                                                          the system in
                                                          our institute,
                                                          the script
                                                          gives me an
                                                          error
                                                          repeatedly. My
                                                          former Postdoc
                                                          wrote this
                                                          script. Thus,
                                                          I did not know
                                                          this inside
                                                          much. <br>
                                                          <br>
                                                          I have tried
                                                          to fix it for
                                                          more than a
                                                          month, but now
                                                          I have no idea
                                                          how to fix it.
                                                          I would
                                                          appreciate it
                                                          very much if
                                                          you could help
                                                          and give me
                                                          your advice. <br>
                                                          <br>
                                                          Please see an
                                                          attached cpp
                                                          file, termed
                                                          ge-r.cpp. With
                                                          this cpp file
                                                          and other
                                                          ones, I have
                                                          succeeded to
                                                          install a
                                                          skeleton R
                                                          package into R
                                                          using your
                                                          function
                                                          Rcpp.package.skeleton.
                                                          <br>
                                                          <br>
                                                          In this
                                                          ge-r.cpp,
                                                          there is one R
                                                          function
                                                          called
                                                          simulate_R()
                                                          written. In
                                                          this R
                                                          fucntion,
                                                          there are two
                                                          C++ functions,
                                                          load() and
                                                          simulate(),
                                                          both are
                                                          described in
                                                          other cpp
                                                          files, called
                                                          from C++ into
                                                          R. With cout
                                                          function
                                                          described in
                                                          simulate_R(),
                                                          I confirmed
                                                          these two
                                                          function work
                                                          in R thanks to
                                                          RcppArmadillo,
                                                          however, it
                                                          suddenly stops
                                                          with an
                                                          error, 
                                                          address(nil)
                                                          cause
                                                          'unknown' in
                                                          R. It has
                                                          seemed to stop
                                                          when it return
                                                          (out) at the
                                                          last in
                                                          ge-r.cpp. I do
                                                          not know why
                                                          it happens.
                                                          Note that the
                                                          C++ script
                                                          works normally
                                                          after the
                                                          update of the
                                                          system. Only
                                                          this
                                                          RcppArmadillo
                                                          conversion
                                                          from C++
                                                          function into
                                                          a R function
                                                          is deformed. <br>
                                                          <br>
                                                          Please give me
                                                          an advice,
                                                          please. Of
                                                          course, I can
                                                          give you more
                                                          information on
                                                          the C++ script
                                                          in details if
                                                          you need. <br>
                                                          <br>
                                                          Best regards,
                                                          <br>
                                                          <br>
                                                          Takeshi <br>
                                                          <br>
                                                          <br>
                                                          <br>
                                                          </div>
                                                          ge-r.cpp<br>
                                                          <br>
                                                          #ifndef __R__
                                                          <div
class="m_2137384927404188588m_-5732849694471883078m_3086009423684693569m_8471227266221235016moz-text-plain"
style="font-family:-moz-fixed;font-size:14px" lang="x-unicode">
                                                          <pre>#define __R__
#endif

#ifndef USE_OMP
#define USE_OMP
#endif


#include <RcppArmadillo.h>


#include "ge-model.h"

using namespace arma;



// input:
//              parameter matrix: row for particle, col for parameter
//              filename of observation
// output:
//              simulation for regular time points: row for particle, col for time, slice for term
//      existing observation to corresponding regular time points

// [[Rcpp::depends(RcppArmadillo)<wbr>]]
// [[Rcpp::export]]
Rcpp::List simulate_R(const arma::mat& param_r, const char* fobs, const int interval) {

        try {
                geModel Model;
                Model.n_thread=omp_get_num_pro<wbr>cs();
                Model._param=param_r;
                cout << "params set.\n";

                cout << "filename of obs: "<< fobs << ".\n";

                 Model._obs.load(fobs);

                 cout << "obs loaded.\n";

                Model.n_acc=Model._param.n_row<wbr>s;
                cout << "n_acc set to be " << Model.n_acc << ".\n";

                Model._obs._out_interval = interval;
                Model._obs._n_out_date = (Model._obs._n_date / Model._obs._out_interval) + 1;

                Model.out_y=cube(Model.n_acc, Model._obs._n_group, Model._obs._n_out_date);
                Model.out_res_1=cube(Model.n_a<wbr>cc,Model._obs._n_group, Model._obs._n_out_date);
                Model.out_res_2=cube(Model.n_a<wbr>cc,Model._obs._n_group, Model._obs._n_out_date);
                Model.out_res_clock=cube(Model<wbr>.n_acc,Model._obs._n_group, Model._obs._n_out_date);
                Model.out_res_dev=cube(Model.n<wbr>_acc,Model._obs._n_group, Model._obs._n_out_date);

                cout << "output matrix initialized.\n";

                //necessary for simulate_obs
                Model._distance=vec(Model.n_ac<wbr>c);

                Model.simulate(0,Model.n_acc-1<wbr>,true);
                cout << "simulation complete.\n";

                fflush(stdout);

                cout << size(Model.out_y)<<".\n"<< Model.out_y[0]<<".\n"<<Model.o<wbr>ut_y[1]<<".\n"<<Model.out_y[2]<wbr><<".\n";

                Rcpp::List out = Rcpp::List::create(
                                Rcpp::Named("out_y")=Model.out<wbr>_y,
                                Rcpp::Named("out_res_1")=Model<wbr>.out_res_1,
                                Rcpp::Named("out_res_2")=Model<wbr>.out_res_2,
                                Rcpp::Named("out_res_clock")=M<wbr>odel.out_res_clock,
                                Rcpp::Named("out_res_dev")=Mod<wbr>el.out_res_dev
                );

                cout << "List constructed.\n";

                 fflush(stdout);

                return (out);
        }

        catch(char* e) {
                cout << e << "\n";
                exit(EXIT_FAILURE);
        }
        catch(...) {
                cout << "Error\n";
                exit(EXIT_FAILURE);
        }
}
</pre>
    </div>
  </div>


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</blockquote></div>

<div>
</div>-- 
<div class="m_2137384927404188588m_-5732849694471883078m_3086009423684693569gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Qiang Kou<div><a moz-do-not-send="true" href="mailto:qkou@umail.iu.edu" target="_blank">qkou@umail.iu.edu</a>
<div>School of Informatics and Computing, Indiana University</div><div>
</div></div></div></div>
</div>



</blockquote>



</div></div></blockquote>
</div></blockquote></div>

<div>
</div>-- 
<div class="m_2137384927404188588m_-5732849694471883078gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Qiang Kou<div><a moz-do-not-send="true" href="mailto:qkou@umail.iu.edu" target="_blank">qkou@umail.iu.edu</a>
<div>School of Informatics and Computing, Indiana University</div><div>
</div></div></div></div>
</div>



</blockquote>
</div></div></div></blockquote></div>

<div>
</div>-- 
<div class="m_2137384927404188588gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Qiang Kou<div><a moz-do-not-send="true" href="mailto:qkou@umail.iu.edu" target="_blank">qkou@umail.iu.edu</a>
<div>School of Informatics and Computing, Indiana University</div><div>
</div></div></div></div>
</div>



</blockquote>



</blockquote>
</div></div></div></blockquote></div>

<div>
</div>-- 
<div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Qiang Kou<div><a moz-do-not-send="true" href="mailto:qkou@umail.iu.edu" target="_blank">qkou@umail.iu.edu</a>
<div>School of Informatics and Computing, Indiana University</div><div>
</div></div></div></div>
</div>



</blockquote>
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