[Rcpp-devel] add new components to list without specifying list size initially
Dirk Eddelbuettel
edd at debian.org
Fri Aug 12 23:37:13 CEST 2011
On 12 August 2011 at 16:26, Walrus Foolhill wrote:
| Thanks for your advice, I now understand how to manipulate one-level lists:
|
| fn <- cxxfunction(signature(l_in="list"),
| body='
| using namespace Rcpp;
| List l(l_in);
| IntegerVector lf = l["foo"];
| CharacterVector lb = l["bar"];
| for(int i=0; i<lf.size(); ++i)
| Rprintf("l[%s][%i] %i\\n", "foo", i, lf[i]);
| for(int i=0; i<lb.size(); ++i)
| Rprintf("l[%s][%i] %s\\n", "bar", i, std::string(lb[i]).c_str());
| ', plugin="Rcpp", verbose=TRUE)
| z <- fn(list(foo=c(1,2,3,4),bar=c("bar1","bar2")))
|
| But what about 2-level lists? Why the following code doesn't compile?
|
| fn <- cxxfunction(signature(l_in="list"),
| body='
| using namespace Rcpp;
| List l(l_in);
| List lf(l["foo"]);
| ', plugin="Rcpp", verbose=TRUE)
| z <- fn(list(foo=list(bar=1)))
|
| And what the following message mean? "error: call of overloaded ‘Vector
| (Rcpp::internal::generic_name_proxy<19>)’ is ambiguous"
|
| I had a look at "runit.Vector.R" on r-forge, but couldn't find any test
| involving 2-level (or more) lists, although on SO in June 2010 (http://
| stackoverflow.com/questions/3088650/how-do-i-create-a-list-of-vectors-in-rcpp/
| 3088744#3088744), you said that it should work.
|
| I checked that I can create a 2-level list, but the code below doesn't compile
| if I uncomment the last Rprintf line:
There can be times when the C++ templating gets in the way, so if this
doesn't work in a single statement, decompose it into two (one to assign to a
temp, another to print them temp) and move on.
I have done two-level lists in the past; one key is that a list ... is just
another SEXP, or can be wrap()'ed to a SEXP, and you can hence assign a list
to be a component of another. And then another and so on...
Dirk
|
| fn <- cxxfunction(signature(),
| body='
| using namespace Rcpp;
| IntegerVector vi(2);
| vi[0] = 2;
| vi[1] = 8;
| List ll = List::create(Named("bar")=vi);
| Rprintf("ll.size %i\\n", ll.size());
| List l = List::create(Named("foo")=ll);
| Rprintf("l.size %i\\n", l.size());
| //Rprintf("l.ll.size %i\\n", l["foo"].size());
| return l;
| ', plugin="Rcpp", verbose=TRUE)
| print(fn())
|
| Thus once again I'm stuck, but if I know how to access 2-level lists, I think I
| will be able to go back to my original problem, and stop sending emails on this
| mailing list ;)
|
| On Fri, Aug 12, 2011 at 8:09 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
|
|
| On 12 August 2011 at 01:22, Walrus Foolhill wrote:
| | Ok, I started with smaller examples. I understand more or less how to
| | manipulate IntegerVectors, but not StringVectors (see below), and thus I
| can't
| | even start manipulating a simple list of StringVectors. Even so I looked
| at
| | mailing lists, StackOverflow, package pdf, source code on R-Forge...
| |
| | The following code tells me "warning: cannot pass objects of non-POD type
| | ‘struct Rcpp::internal::string_proxy<16>’ through ‘...’; call will abort
| at
| | runtime": why does it complain about printing the string in vec_s[i]?
|
| Again, simpler helps. That is the standard C / C++ error message of
|
| std:string foo = "bar";
| printf("String is %s \n", foo);
|
| where you need foo.c_str() to pass a char* to printf.
|
| | fn <- cxxfunction(signature(l_in="list"),
| | body='
| | using namespace Rcpp;
| | List l = List(l_in);
| | Rprintf("list size: %d\\n", l.size());
| |
| | IntegerVector vec_i= IntegerVector(2);
| | vec_i[0] = 1;
| | vec_i[1] = 2;
| | List l2 = List::create(_["vec"] = vec_i);
| | Rprintf("vec_i size: %d\\n", vec_i.size());
| | for(int i=0; i<vec_i.size(); ++i)
| | Rprintf("vec_i[%d]=%d\\n", i, vec_i[i]);
| |
| | StringVector vec_s = StringVector::create("toto");
| | vec_s[0] = "toto";
| | Rprintf("vec_s size: %d\\n", vec_s.size());
| | for(int i=0; i<vec_s.size(); ++i)
| | Rprintf("vec_s[%d]=%s\\n", i, vec_s[i]);
|
| Try vec_s[i].c_str() instead.
|
| Dirk
|
| | return l2;
| | ',
| | plugin="Rcpp", verbose=TRUE)
| | print(fn(list(a=c(1,2,3), b=c("a","b","c"))))
| |
| | Moreover, how can I access the component of a list given as input, as
| "l_in"
| | above? Should I use l.begin()? or l[1]? or l["a"]? none of them seems to
| | compile successfully.
| |
| | On Thu, Aug 11, 2011 at 8:54 PM, Dirk Eddelbuettel <edd at debian.org>
| wrote:
| |
| |
| | Howdy,
| |
| | On 11 August 2011 at 20:44, Walrus Foolhill wrote:
| | | Ok, thanks for your answer, but I wasn't clear enough. So here are
| more
| | details
| | | of what I want to do.
| | |
| | | I have one list named "probes":
| | | probes <- list(chr1=data.frame(name=c("p1","p2"),
| | | start=c(81,95),
| | | end=c(85,100),
| | | stringsAsFactors=FALSE))
| | |
| | | I also have one list named "genes":
| | | genes <- list(chr1=data.frame(name=c("g1","g2"), start=c(11,111),
| end=c
| | | (90,190)),
| | | chr2=data.frame(name="g3", start=11, end=90))
| | |
| | | I need to compare those two lists in order to obtain the following
| list
| | which
| | | contains, for each gene, the name of the probes included in it:
| | | links <- list(chr1=list(g1=c("p1")))
| | |
| | | Here is my R function (assuming that the probes are sorted based on
| their
| | start
| | | and end coordinates):
| | |
| | | fun.l <- function(genes, probes){
| | | links <- lapply(names(genes), function(chr.name){
| | | if(! chr.name %in% names(probes))
| | | return(NULL)
| | |
| | | res <- list()
| | |
| | | genes.c <- genes[[chr.name]]
| | | probes.c <- probes[[chr.name]]
| | |
| | | for(gene.name in genes.c$name){
| | | gene <- genes.c[genes.c$name == gene.name,]
| | | res[[gene.name]] <- vector()
| | | for(probe.name in probes.c$name){
| | | probe <- probes.c[probes.c$name == probe.name,]
| | | if(probe$start >= gene$start && probe$end <= gene$end)
| | | res[[gene.name]] <- append(res[[gene.name]], probe.name)
| | | else if(probe$start > gene$end)
| | | break
| | | }
| | | if(length(res[[gene.name]]) == 0)
| | | res[[gene.name]] <- NULL
| | | }
| | |
| | | if(length(res) == 0)
| | | res <- NA
| | | return(res)
| | | })
| | | names(links) <- names(genes)
| | | links <- Filter(function(links.c){!is.null(links.c)}, links)
| | | return(links)
| | | }
| | |
| | | And here is the beginning of my attempt using Rcpp:
| | |
| | | src <- '
| | | using namespace Rcpp;
| | |
| | | List genes = List(genes_in);
| | | int genes_nb_chr = genes.length();
| | | std::vector<std::string> genes_chr = genes.names();
| | |
| | | List probes = List(probes_in);
| | | int probes_nb_chr = probes.length();
| | |
| | | std::vector< std::vector<std::string> > links;
| | |
| | | // the main task is performed in this loop
| | | for(int chrnum=0; chrnum<genes_nb_chr; ++chrnum){
| | | DataFrame genes_c = DataFrame(genes[chrnum]);
| | | // ... add code to map probes on genes, that is fill "links" ...
| | | }
| | |
| | | return wrap(links);
| | | '
| | |
| | | funC <- cxxfunction(signature(genes_in="list",
| | | probes_in="list"),
| | | body=src, plugin="Rcpp")
| | |
| | | The problem starts quite early: when I compile this piece of code,
| I get
| | | "error: call of overloaded ‘DataFrame(Rcpp::internal::generic_proxy
| <19>)’
| | is
| | | ambiguous".
| |
| | Try a simpler mock-up. I don't have it in me to work through this
| now.
| | DataFrames are a little different from C++ -- start by trying to
| summarize
| | in
| | just a vector, or collection of vectors.
| |
| | | What should I do to go through the "probes" and "genes" lists given
| as
| | input?
| | | Maybe more generically, how can we go through a list of lists (of
| | lists...)
| | | with Rcpp?
| | |
| | | 2nd (small) question, I don't manage to use Rprintf when using
| inline,
| | for
| | | instance Rprintf("%d\n", i);, it complains about the quotes. What
| should
| | I do
| | | to print statement from within the for loop?
| |
| | The backslashes need escaping as in
| |
| | R> printing <- cxxfunction(, plugin="Rcpp", body=' Rprintf("foo\\
| n"); ')
| | R> printing()
| | foo
| | NULL
| | R>
| |
| | | Thanks in advance. As my question is very long, I won't mind if you
| tell
| | me to
| | | find another way by myself. But maybe one of you can put me on the
| good
| | track.
| |
| | You are doing good but you have decent size problem. Try breaking
| into
| | smaller pieces and a handle on each problem in turn.
| |
| | Dirk
| |
| | |
| | | On Thu, Aug 11, 2011 at 7:00 AM, Dirk Eddelbuettel <edd at debian.org>
| | wrote:
| | |
| | |
| | | On 11 August 2011 at 03:06, Walrus Foolhill wrote:
| | | | Hello,
| | | | I need to create a list and then fill it sequentially by
| adding
| | | components in a
| | | | for loop. Here is an example that works:
| | | |
| | | | library(inline)
| | | | src <- '
| | | | Rcpp::List mylist(2);
| | | | for(int i=0; i<2; ++i)
| | | | mylist[i] = i;
| | | | mylist.names() = CharacterVector::create("a","b");
| | | | return mylist;
| | | | '
| | | | fun <- cxxfunction(body=src, plugin="Rcpp")
| | | | print(fun())
| | | |
| | | | But what I really want is to create an empty list and then
| fill it,
| | that
| | | is
| | | | without specifying its number of components before hand...
| This is
| | | because I
| | | | don't know in advance at which step of the for loop I will
| need to
| | create
| | | a new
| | | | component. Here is an example, that obviously doesn't work,
| but
| | that
| | | should
| | | | show what I am looking for:
| | | |
| | | | Rcpp::List mylist;
| | | | CharacterVector names = CharacterVector::create("a", "b");
| | |
| | | If you know how long names is, you know how long mylist going
| to be
| | ....
| | |
| | | | for(int i=0; i<2; ++i){
| | | | mylist.add(names[i], IntegerVector::create());
| | | | mylist[names[i]].push_back(i);
| | |
| | | I don't understand what that is trying to do.
| | |
| | | | }
| | | | return mylist;
| | | |
| | | | Do you know how I could achieve this? Thanks.
| | |
| | | Rcpp::List is an alias for Rcpp::GenericVector, and derives
| from
| | Vector.
| | | You
| | | can look at the public member functions -- there are things
| like
| | |
| | | push_back()
| | | push_front()
| | | insert()
| | |
| | | etc that behave like STL functions __but are inefficient as we
| | (almost
| | | always) need to copy the whole object__ so they are not
| recommended.
| | |
| | | When I had to deal with 'unknown quantities of data' returning
| I was
| | mostly
| | | able to either turn it into a 'fixed or known columns, unknow
| rows'
| | problem
| | | (easy, just grow row-wise) or I 'cached' in a C++ data
| structure
| | first
| | | before
| | | returning to R via Rcpp structures -- and then I knew the
| dimensions
| | for
| | | the
| | | to-be-created object too.
| | |
| | | Dirk
| | |
| | |
| | | --
| | | Two new Rcpp master classes for R and C++ integration scheduled
| for
| | | New York (Sep 24) and San Francisco (Oct 8), more details are
| at
| | | http://dirk.eddelbuettel.com/blog/2011/08/04#
| | | rcpp_classes_2011-09_and_2011-10
| | |
| | |
| |
| | --
| | Two new Rcpp master classes for R and C++ integration scheduled for
| | New York (Sep 24) and San Francisco (Oct 8), more details are at
| | http://dirk.eddelbuettel.com/blog/2011/08/04#
| | rcpp_classes_2011-09_and_2011-10
| | http://www.revolutionanalytics.com/products/training/public/
| | rcpp-master-class.php
| |
| |
|
| --
| Two new Rcpp master classes for R and C++ integration scheduled for
| New York (Sep 24) and San Francisco (Oct 8), more details are at
| http://dirk.eddelbuettel.com/blog/2011/08/04#
| rcpp_classes_2011-09_and_2011-10
| http://www.revolutionanalytics.com/products/training/public/
| rcpp-master-class.php
|
|
--
Two new Rcpp master classes for R and C++ integration scheduled for
New York (Sep 24) and San Francisco (Oct 8), more details are at
http://dirk.eddelbuettel.com/blog/2011/08/04#rcpp_classes_2011-09_and_2011-10
http://www.revolutionanalytics.com/products/training/public/rcpp-master-class.php
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