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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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