Dear KK,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.
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).
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.
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.
Best, Takeshi On 2017/07/10 14:04, Qiang Kou wrote:
I mean line 49 in ge-model.cpp. You have a function called "initialize" there.The "initialize" function will initialize the _rand array. Best, KKOn Sun, Jul 9, 2017 at 9:55 PM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp <mailto:a-iz...@mail.ecc.u-tokyo.ac.jp>> wrote:Dear KK, Sorry for bothering you again, I still have some problems. According to your advice, in order to initialize the array in ge-r.cpp, I put Model.out_y=cube(Model.n_acc, Model._obs._n_group, Model._obs._n_out_date,fill::zeros);Model.out_res_1=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date,fill::zeros);Model.out_res_2=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date,fill::zeros);Model.out_res_clock=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date,fill::zeros);Model.out_res_dev=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date,fill::zeros); instead of the old ones, Model.out_y=cube(Model.n_acc, Model._obs._n_group, Model._obs._n_out_date);Model.out_res_1=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date);Model.out_res_2=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date);Model.out_res_clock=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date);Model.out_res_dev=cube(Model.n_acc,Model._obs._n_group,Model._obs._n_out_date); However, I got the same error in R. What should I do next ? 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? Best, Takeshi On 2017/07/10 13:03, 井澤 毅 wrote:Dear KK, Thanks for this explanation. Now I got it. 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. I still wonder why this ge-r.cpp works in the old system, but I will ask this to the maintainer of our system. I have learned a lot from your suggestion. Thanks again! Best, Takeshi On 2017/07/10 10:34, Qiang Kou wrote: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. Best, KK On Sun, Jul 9, 2017 at 4:45 PM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp <mailto:a-iz...@mail.ecc.u-tokyo.ac.jp>> wrote: Dear KK, I owe you a lot! I will check it as soon as possible. Since I am not familiar with this much, I would be very happy to tell me some urls describing "initialize". Best, Takeshi On 2017/07/10 7:38, Qiang Kou wrote:Hi, professor, I think the problem is in ge-r. cpp, you forgot to call *initialize*. The error has nothing to do with Rcpp. Best, KK On Tue, Jul 4, 2017 at 2:45 AM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp <mailto:a-iz...@mail.ecc.u-tokyo.ac.jp>> wrote: Sorry, I forgot the attached file. On 2017/07/04 18:43, 井澤 毅 wrote:Dear KK, Thanks for your kind reply. I am afraid that one of the input file is very heavy, this time but I am sending a ZIP file including all. Please make v30 package using install.simulate_R_1.r and then install.simulate_R_2.r. Then, try ge-r_test.r, please. 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. As the input file, we need var.mat.all matrix data in R and obs.Os01g0182600_g1.nc <http://obs.Os01g0182600_g1.nc> file in the directry. Then, you will see the error I have been suffering from for a month. The obs.Os01g0182600_g1.nc <http://obs.Os01g0182600_g1.nc> file is a file containing environmental fluctuation data. Best, Takeshi On 2017/07/04 5:40, Qiang Kou wrote:Hi, I am afraid the example you provided is not a reproducible example. First, we don't know the content of ge-model.h. Second, we don't know which input will trigger the fault. Please provide a reproducible example if you really want to get help. Best, KK On Sat, Jul 1, 2017 at 11:06 AM, 井澤 毅 <a-iz...@mail.ecc.u-tokyo.ac.jp <mailto:a-iz...@mail.ecc.u-tokyo.ac.jp>> wrote: Dear rcpp-devel@lists.r-forge.r-project.org <mailto:rcpp-devel@lists.r-forge.r-project.org>, Sorry for bothering you much, but do me a favor please. Please help me some. I am just a molecular biologist working on plants. Thus, I am still a newcomer in this field. 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. 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. 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. 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. Please give me an advice, please. Of course, I can give you more information on the C++ script in details if you need. Best regards, Takeshi ge-r.cpp #ifndef __R__ #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)]] // [[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_procs(); 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_rows; 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_acc,Model._obs._n_group, Model._obs._n_out_date); Model.out_res_2=cube(Model.n_acc,Model._obs._n_group, Model._obs._n_out_date); Model.out_res_clock=cube(Model.n_acc,Model._obs._n_group, Model._obs._n_out_date); Model.out_res_dev=cube(Model.n_acc,Model._obs._n_group, Model._obs._n_out_date); cout << "output matrix initialized.\n"; //necessary for simulate_obs Model._distance=vec(Model.n_acc); Model.simulate(0,Model.n_acc-1,true); cout << "simulation complete.\n"; fflush(stdout); cout << size(Model.out_y)<<".\n"<< Model.out_y[0]<<".\n"<<Model.out_y[1]<<".\n"<<Model.out_y[2]<<".\n"; Rcpp::List out = Rcpp::List::create( Rcpp::Named("out_y")=Model.out_y, Rcpp::Named("out_res_1")=Model.out_res_1, Rcpp::Named("out_res_2")=Model.out_res_2, Rcpp::Named("out_res_clock")=Model.out_res_clock, Rcpp::Named("out_res_dev")=Model.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); } } _______________________________________________ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org <mailto:Rcpp-devel@lists.r-forge.r-project.org> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel <https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel>-- Qiang Kouq...@umail.iu.edu <mailto:q...@umail.iu.edu> School of Informatics and Computing, Indiana University-- Qiang Kouq...@umail.iu.edu <mailto:q...@umail.iu.edu> School of Informatics and Computing, Indiana University-- Qiang Kouq...@umail.iu.edu <mailto:q...@umail.iu.edu> School of Informatics and Computing, Indiana University-- Qiang Kou q...@umail.iu.edu <mailto:q...@umail.iu.edu> School of Informatics and Computing, Indiana University
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