Romain, Thanks for your quick response. I've already received that suggestion, but, besides of haven't ever used C++, I wanted to understand first what am I doing wrong. Still, would you give me a small example, in R C++, of:
- Creating a generic vector "L1" of size N - Creating a data.frame "D" and increasing its the number of rows of it - Storing the data.frame "D" in the first element of "L1" I would be very gratefull if you can do that. Thanks again! George Vega Yon +56 9 7 647 2552 http://ggvega.cl 2013/11/7 Romain Francois <rom...@r-enthusiasts.com>: > Hello, > > Any particular reason you're not using Rcpp? You would have access to nice > abstraction instead of these MACROS all over the place. > > The cost of these abstractions is close to 0. > > Looping around and SET_LENGTH is going to be quite expensive. I would urge > you to accumulate data in data structures that know how to grow efficiently, > i.e. a std::vector and then convert that to an R vector when you're done > with them. > > Romain > > Le 07/11/2013 14:03, George Vega Yon a écrit : > >> Hi! >> >> I didn't wanted to do this but I think that this is the easiest way >> for you to understand my problem (thanks again for all the comments >> that you have made). Here is a copy of the function that I'm working >> on. This may be tedious to analyze, so I understand if you don't feel >> keen to give it a time. Having dedicated many hours to this (as a new >> user of both C and R C API), I would be very pleased to know what am I >> doing wrong here. >> >> G0 is a Nx2 matrix. The first column is a group id (can be shared with >> several observations) and the second tells how many individuals are in >> that group. This matrix can look something like this: >> >> id_group nreps >> 1 3 >> 1 3 >> 1 3 >> 2 1 >> 3 1 >> 4 2 >> 5 1 >> 6 1 >> 4 2 >> ... >> >> L0 is list of two column data.frames with different sizes. The first >> column (id) are row indexes (with values 1 to N) and the second column >> are real numbers. L0 can look something like this >> [[1]] >> id lambda >> 3 0.5 >> 15 0.3 >> 25 0.2 >> [[2]] >> id lambda >> 15 0.8 >> 40 0.2 >> ... >> [[N]] >> id lambda >> 80 1 >> >> TE0 is a int scalar in {0,1,2} >> >> T0 is a dichotomous vector of length N that can look something like this >> [1] 0 1 0 1 1 1 0 ... >> [N] 1 >> >> L1 (the expected output) is a modified version of L0, that, for >> instance can look something like this (note the rows marked with "*") >> >> [[1]] >> id lambda >> 3 0.5 >> *15 0.15 (15 was in the same group of 50, so I added this new row and >> divided the value of lambda by two) >> 25 0.2 >> *50 0.15 >> [[2]] >> id lambda >> 15 0.8 >> 40 0.2 >> ... >> [[N]] >> id lambda >> *80 0.333 (80 shared group id with 30 and 100, so lambda is divided by 3) >> *30 0.333 >> *100 0.333 >> >> That said, the function is as follows >> >> SEXP distribute_lambdas( >> SEXP G0, // Groups ids (matrix of Nx2). First column = Group Id, >> second column: Elements in the group >> SEXP L0, // List of N two-column dataframes with different number of >> rows >> SEXP TE0, // Treatment effect (int scalar): ATE(0) ATT(1) ATC(2) >> SEXP T0 // Treat var (bool vector, 0/1, of size N) >> ) >> { >> >> int i, j, l, m; >> const int *G = INTEGER_POINTER(PROTECT(G0 = AS_INTEGER(G0 ))); >> const int *T = INTEGER_POINTER(PROTECT(T0 = AS_INTEGER(T0 ))); >> const int *TE= INTEGER_POINTER(PROTECT(TE0= AS_INTEGER(TE0))); >> double *L, val; >> int *I, nlambdas, nreps; >> >> const int n = length(T0); >> >> PROTECT_INDEX pin0, pin1; >> SEXP L1; >> PROTECT(L1 = allocVector(VECSXP,n)); >> SEXP id, lambda; >> >> // Fixing size >> for(i=0;i<n;i++) >> { >> SET_VECTOR_ELT(L1, i, allocVector(VECSXP, 2)); >> // SET_VECTOR_ELT(VECTOR_ELT(L1,i), 0, NEW_INTEGER(100)); >> // SET_VECTOR_ELT(VECTOR_ELT(L1,i), 1, NEW_NUMERIC(100)); >> } >> >> // For over the list, i.e observations >> for(i=0;i<n;i++) >> { >> >> R_CheckUserInterrupt(); >> >> // Checking if has to be analyzed. >> if ( >> ((TE[0] == 1 & !T[i]) | (TE[0] == 2 & T[i])) | >> (length(VECTOR_ELT(L0,i)) != 2) >> ) >> { >> SET_VECTOR_ELT(L1,i,R_NilValue); >> continue; >> } >> >> // Checking how many rows does the i-th data.frame has >> nlambdas = length(VECTOR_ELT(VECTOR_ELT(L0,i),0)); >> >> // Pointing to the data.frame's origianl values >> I = >> INTEGER_POINTER(AS_INTEGER(PROTECT(VECTOR_ELT(VECTOR_ELT(L0,i),0)))); >> L = >> NUMERIC_POINTER(AS_NUMERIC(PROTECT(VECTOR_ELT(VECTOR_ELT(L0,i),1)))); >> >> // Creating a copy of the pointed values >> PROTECT_WITH_INDEX(id = duplicate(VECTOR_ELT(VECTOR_ELT(L0,i),0)), >> &pin0); >> PROTECT_WITH_INDEX(lambda=duplicate(VECTOR_ELT(VECTOR_ELT(L0,i),1)), >> &pin1); >> >> // Over the rows of the i-th data.frame >> nreps=0; >> for(l=0;l<nlambdas;l++) >> { >> // If the current lambda id is repeated, ie ther are more >> individuals >> // with the same covariates, then enter. >> if (G[n+I[l]-1] > 1) >> { >> /* Changing the length of the object */ >> REPROTECT(SET_LENGTH(id, length(lambda) + G[n+I[l]-1] -1), >> pin0); >> REPROTECT(SET_LENGTH(lambda,length(lambda) + G[n+I[l]-1] -1), >> pin1); >> >> // Getting the new value >> val = L[l]/G[n+I[l] - 1]; >> REAL(lambda)[l] = val; >> >> // Looping over the full set of groups >> m = -1,j = -1; >> while(m < (G[n+I[l]-1] - 1)) >> { >> // Looking for individuals in the same group >> if (G[++j] != G[I[l]-1]) continue; >> >> // If it is the current lambda, then do not asign it >> if (j == (I[l] - 1)) continue; >> >> INTEGER(id)[length(id) - (G[n+I[l]-1] - 1) + ++m] = j+1; >> REAL(lambda)[length(id) - (G[n+I[l]-1] - 1) + m] = val; >> } >> >> nreps+=1; >> } >> } >> >> if (nreps) >> { >> // Replacing elements from of the list (modified) >> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 0, duplicate(id)); >> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 1, duplicate(lambda)); >> } >> else { >> // Setting the list with the old elements >> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 0, >> duplicate(VECTOR_ELT(VECTOR_ELT(L0,i),0))); >> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 1, >> duplicate(VECTOR_ELT(VECTOR_ELT(L0,i),1))); >> } >> >> // Unprotecting elements >> UNPROTECT(4); >> } >> >> Rprintf("Exito\n") ; >> UNPROTECT(4); >> >> return L1; >> } >> >> Thanks again in advanced. >> >> George Vega Yon >> +56 9 7 647 2552 >> http://ggvega.cl >> >> 2013/11/5 George Vega Yon <g.vega...@gmail.com>: >>> >>> Either way, understanding that it may not be the best way of do it, is >>> there anything wrong in what I'm doing?? >>> George Vega Yon >>> +56 9 7 647 2552 >>> http://ggvega.cl >>> >>> >>> 2013/11/5 Gabriel Becker <gmbec...@ucdavis.edu>: >>>> >>>> George, >>>> >>>> My point is you don't need to create them and then grow them.... >>>> >>>> >>>> for(i=0;i<n;i++) >>>> { >>>> // Creating the "id" and "lambda" vectors. I do this in every >>>> repetition >>>> of >>>> // the loop. >>>> >>>> // ... Some other instructions where I set the value of an integer >>>> // z, which tells how much do the vectors have to grow ... >>>> >>>> PROTECT(id=allocVector(INTSXP, 4 +z)); >>>> PROTECT(lambda=allocVector(REALSXP, 4 +z)); >>>> >>>> >>>> // ... some lines where I fill the vectors ... >>>> >>>> // Storing the new vectors at the i-th element of the list >>>> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 0, duplicate(id)); >>>> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 1, duplicate(lambda)); >>>> >>>> // Unprotecting the "id" and "lambda" vectors >>>> UNPROTECT(2); >>>> } >>>> >>>> ~G >>>> >>>> >>>> On Tue, Nov 5, 2013 at 1:56 PM, George Vega Yon <g.vega...@gmail.com> >>>> wrote: >>>>> >>>>> >>>>> Gabriel, >>>>> >>>>> While the length (in terms of number of SEXP elements it stores) of L1 >>>>> doesn't changes, the vectors within L1 do (sorry if I didn't explained >>>>> it well before). >>>>> >>>>> The post was about a SEXP object that grows, in my case, every pair of >>>>> vectors in L1 (id and lambda) can change lengths, this is why I need >>>>> to reprotect them. I populate the i-th element of L1 by creating the >>>>> vectors "id" and "lambda", setting the length of these according to >>>>> some rule (that's the part where lengths change)... here is a reduced >>>>> form of my code: >>>>> >>>>> //////////////////////////////////////// C >>>>> //////////////////////////////////////// >>>>> const int = length(L0); >>>>> SEXP L1; >>>>> PROTECT(L1 = allocVector(VECSXP,n)); >>>>> SEXP id, lambda; >>>>> >>>>> // Fixing size >>>>> for(i=0;i<n;i++) >>>>> SET_VECTOR_ELT(L1, i, allocVector(VECSXP, 2)); >>>>> >>>>> for(i=0;i<n;i++) >>>>> { >>>>> // Creating the "id" and "lambda" vectors. I do this in every >>>>> repetition >>>>> of >>>>> // the loop. >>>>> PROTECT_WITH_INDEX(id=allocVector(INTSXP, 4), &ipx0); >>>>> PROTECT_WITH_INDEX(lambda=allocVector(REALSXP, 4), &ipx1); >>>>> >>>>> // ... Some other instructions where I set the value of an integer >>>>> // z, which tells how much do the vectors have to grow ... >>>>> >>>>> REPROTECT(SET_LENGTH(id, length(lambda) + z), ipx0); >>>>> REPROTECT(SET_LENGTH(lambda,length(lambda) + z), ipx1); >>>>> >>>>> // ... some lines where I fill the vectors ... >>>>> >>>>> // Storing the new vectors at the i-th element of the list >>>>> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 0, duplicate(id)); >>>>> SET_VECTOR_ELT(VECTOR_ELT(L1, i), 1, duplicate(lambda)); >>>>> >>>>> // Unprotecting the "id" and "lambda" vectors >>>>> UNPROTECT(2); >>>>> } >>>>> >>>>> UNPROTECT(1); >>>>> >>>>> return L1; >>>>> //////////////////////////////////////// C >>>>> //////////////////////////////////////// >>>>> >>>>> I can't set the length from the start because every pair of vectors in >>>>> L1 have different lengths, lengths that I cannot tell before starting >>>>> the loop. >>>>> >>>>> Thanks for your help, >>>>> >>>>> Regards, >>>>> >>>>> George Vega Yon >>>>> +56 9 7 647 2552 >>>>> http://ggvega.cl >>>>> >>>>> >>>>> 2013/11/5 Gabriel Becker <gmbec...@ucdavis.edu>: >>>>>> >>>>>> George, >>>>>> >>>>>> I don't see the relevance of the stackoverflow post you linked. In the >>>>>> post, >>>>>> the author wanted to change the length of an existing "mother list" >>>>>> (matrix, >>>>>> etc), while you specifically state that the length of L1 will not >>>>>> change. >>>>>> >>>>>> You say that the child lists (vectors if they are INTSXP/REALSXP) are >>>>>> variable, but that is not what the linked post was about unless I am >>>>>> completely missing something. >>>>>> >>>>>> I can't really say more without knowing the details of how the vectors >>>>>> are >>>>>> being created and why they cannot just have the right length from the >>>>>> start. >>>>>> >>>>>> As for the error, that is a weird one. I imagine it means that a SEXP >>>>>> thinks >>>>>> that it has a type other than ones defined in Rinternals. I can't >>>>>> speak >>>>>> to >>>>>> how that could have happened from what you posted though. >>>>>> >>>>>> Sorry I can't be of more help, >>>>>> ~G >>>>>> >>>>>> >>>>>> >>>>>> On Mon, Nov 4, 2013 at 8:00 PM, George Vega Yon <g.vega...@gmail.com> >>>>>> wrote: >>>>>>> >>>>>>> >>>>>>> Dear R-devel, >>>>>>> >>>>>>> A couple of weeks ago I started to use the R C API for package >>>>>>> development. Without knowing much about C, I've been able to write >>>>>>> some routines sucessfully... until now. >>>>>>> >>>>>>> My problem consists in dynamically creating a list ("L1") of lists >>>>>>> using .Call, the tricky part is that each element of the "mother >>>>>>> list" >>>>>>> contains two vectors (INTSXP and REALEXP types) with varying sizes; >>>>>>> sizes that I set while I'm looping over another list's ("L1") >>>>>>> elements >>>>>>> (input list). The steps I've follow are: >>>>>>> >>>>>>> FIRST: Create the "mother list" of size "n=length(L0)" (doesn't >>>>>>> change) and protect it as >>>>>>> PROTECT(L1=allocVector(VECEXP, length(L0))) >>>>>>> and filling it with vectors of length two: >>>>>>> for(i=0;i<n;i++) SET_VECTOR_ELT(L1,i, allocVector(VECSXP, 2)); >>>>>>> >>>>>>> then, for each element of the mother list: >>>>>>> >>>>>>> for(i=0;i<n;i++) { >>>>>>> >>>>>>> SECOND: By reading this post in Stackoverflow >>>>>>> >>>>>>> >>>>>>> >>>>>>> http://stackoverflow.com/questions/7458364/growing-an-r-matrix-inside-a-c-loop/7458516#7458516 >>>>>>> I understood that it was necesary to (1) create the "child lists" and >>>>>>> protecting them with PROTECT_WITH_INDEX, and (2) changing its size >>>>>>> using SETLENGTH (Rf_lengthgets) and REPROTECT ing the lists in order >>>>>>> to tell the GC that the vectors had change. >>>>>>> >>>>>>> THIRD: Once my two vectors are done ("id" and "lambda"), assign them >>>>>>> to the i-th element of the "mother list" L1 using >>>>>>> SET_VECTOR_ELT(VECTOR_ELT(L1,i), 0, duplicate(id)); >>>>>>> SET_VECTOR_ELT(VECTOR_ELT(L1,i), 1, duplicate(lambda)); >>>>>>> >>>>>>> and unprotecting the elements protected with index: UNPROTECT(2); >>>>>>> >>>>>>> } >>>>>>> >>>>>>> FOURTH: Unprotecting the "mother list" (L1) and return it to R >>>>>>> >>>>>>> With small datasets this works fine, but after trying with bigger >>>>>>> ones >>>>>>> R (my code) keeps failing and returning a strange error that I >>>>>>> haven't >>>>>>> been able to identify (or find in the web) >>>>>>> >>>>>>> "unimplemented type (29) in 'duplicate'" >>>>>>> >>>>>>> This happens right after I try to use the returned list from my >>>>>>> routine (trying to print it or building a data-frame). >>>>>>> >>>>>>> Does anyone have an idea of what am I doing wrong? >>>>>>> >>>>>>> Best regards, >>>>>>> >>>>>>> PS: I didn't wanted to copy the entire function... but if you need it >>>>>>> I can do it. >>>>>>> >>>>>>> George Vega Yon >>>>>>> +56 9 7 647 2552 >>>>>>> http://ggvega.cl >>>>>>> >>>>>>> ______________________________________________ >>>>>>> R-devel@r-project.org mailing list >>>>>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Gabriel Becker >>>>>> Graduate Student >>>>>> Statistics Department >>>>>> University of California, Davis >>>> >>>> >>>> >>>> >>>> >>>> -- >>>> Gabriel Becker >>>> Graduate Student >>>> Statistics Department >>>> University of California, Davis >> >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > -- > Romain Francois > Professional R Enthusiast > +33(0) 6 28 91 30 30 > > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
