From cheval at zaclys.net  Wed Sep  4 21:37:24 2024
From: cheval at zaclys.net (Denis Haine)
Date: Wed, 04 Sep 2024 15:37:24 -0400
Subject: [Rcpp-devel] Using formula
Message-ID: <21b7c4f776c60750f1795d42445d78f2@zaclys.net>



Hi,

Sorry for a beginner's question. I'm trying to call an R function 
(glm()) inside my cpp code. The code compiles with no problem, but when 
I'm running it, it cannot find the second element of the formula, i.e. 
the x in y~x. The error message is: Error in eval (predvars; data, env) 
: object 'e' not found.

However, if I return 'e', it is correctly calculated. I guess the 
formula is not correctly evaluated, but I haven't found any examples 
that could point me in one direction or another.

#include <Rcpp.h>
using namespace Rcpp;
// [[Rcpp::export]]
NumericVector misclass(NumericMatrix obs_mat) {
   // Obtain environment containing function
   Rcpp::Environment base("package:stats");

   // Picking up glm() and summary() function from base stats
   Rcpp::Function glm_r = base["glm"];
   Rcpp::Function sum_r = base["summary.glm"];

   Rcpp::NumericVector d = obs_mat(_, 1);
   Rcpp::NumericVector e = no_init(n);
   Rcpp::NumericVector mod_coef = no_init(n);
   // e is calculated in other section of the code
   e = as<IntegerVector>(e);
   Rcpp::List mod_pois = glm_r(_["formula"] = "d ~ e",
                     _["family"] = "poisson");
   Rcpp::List mod_sum = sum_r(mod_pois);
   Rcpp::NumericMatrix M_coef = mod_sum[12];
   mod_coef = M_coef(2, 1);

   return mod_coef;
}

I also tried providing the formula in the call, i.e. NumericVector 
misclass(NumericMatrix obs_mat, Formula f) and using it in glm_r, i.e. 
glm_r(_["formula"] = f, etc. but with the same outcome.

Thanks,

Denis
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From edd at debian.org  Wed Sep  4 22:24:48 2024
From: edd at debian.org (Dirk Eddelbuettel)
Date: Wed, 4 Sep 2024 15:24:48 -0500
Subject: [Rcpp-devel] Using formula
In-Reply-To: <21b7c4f776c60750f1795d42445d78f2@zaclys.net>
References: <21b7c4f776c60750f1795d42445d78f2@zaclys.net>
Message-ID: <26328.49680.260143.986103@rob.eddelbuettel.com>


On 4 September 2024 at 15:37, Denis Haine wrote:
| Hi,
| 
| Sorry for a beginner's question. I'm trying to call an R function (glm())
| inside my cpp code. The code compiles with no problem, but when I'm running it,
| it cannot find the second element of the formula, i.e. the x in y~x. The error
| message is: Error in eval (predvars; data, env) : object 'e' not found.
| 
| However, if I return 'e', it is correctly calculated. I guess the formula is
| not correctly evaluated, but I haven't found any examples that could point me
| in one direction or another.
| 
| #include <Rcpp.h>
| using namespace Rcpp;
| // [[Rcpp::export]]
| NumericVector misclass(NumericMatrix obs_mat) {
|   // Obtain environment containing function
|   Rcpp::Environment base("package:stats");
| 
|   // Picking up glm() and summary() function from base stats
|   Rcpp::Function glm_r = base["glm"];
|   Rcpp::Function sum_r = base["summary.glm"];

You are running glm() from base here. At the speed of glm() from base.

That you call it from C++ does not make it faster, sadly, it just creates
more work for you. Sorry to be a bearer of bad news.
 
|   Rcpp::NumericVector d = obs_mat(_, 1);
|   Rcpp::NumericVector e = no_init(n);
|   Rcpp::NumericVector mod_coef = no_init(n);
|   // e is calculated in other section of the code
|   e = as<IntegerVector>(e);
|   Rcpp::List mod_pois = glm_r(_["formula"] = "d ~ e",
|                     _["family"] = "poisson");

You need to 'work out' (ie expand) the formula on the R side. I have done
that for the lm() case of model matrices and whatnot in the fastLm()
example(s) inside eg RcppArmadillo.  Once you have done the R-level unpacking
you can call the C++ function to fit.

Big takeaway from that exercise there: the time you spent dealing with the
(convenient) formula dominates the gain from using a different, simpler,
slightly faster 'fitter' by many orders of magnitude.

[ I think there are some packages dealing with glm() fits using Rcpp and
friends among the by now over 2800 CRAN packages using Rcpp -- but I can't
right now recall their names. You may find some help in those if you find
them, and if my recollection was correct in the first place ... ]

Dirk

|   Rcpp::List mod_sum = sum_r(mod_pois);
|   Rcpp::NumericMatrix M_coef = mod_sum[12];
|   mod_coef = M_coef(2, 1);
| 
|   return mod_coef;
| }
| 
| 
| I also tried providing the formula in the call, i.e. NumericVector misclass
| (NumericMatrix obs_mat, Formula f) and using it in glm_r, i.e. glm_r(_
| ["formula"] = f, etc. but with the same outcome.
| 
| Thanks,
| 
| Denis
| 
| _______________________________________________
| Rcpp-devel mailing list
| Rcpp-devel at lists.r-forge.r-project.org
| https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

From cheval at zaclys.net  Thu Sep 26 16:35:49 2024
From: cheval at zaclys.net (Denis Haine)
Date: Thu, 26 Sep 2024 10:35:49 -0400
Subject: [Rcpp-devel] Using formula
In-Reply-To: <26328.49680.260143.986103@rob.eddelbuettel.com>
References: <21b7c4f776c60750f1795d42445d78f2@zaclys.net>
 <26328.49680.260143.986103@rob.eddelbuettel.com>
Message-ID: <16ef2c101afa028fa5ad29eb84446864@zaclys.net>



Hi,

Quick follow-up and additional question.

I got it working with fastglm:

#include <Rcpp.h>
  using namespace Rcpp;
  // [[Rcpp::export]]
  NumericVector misclass(NumericMatrix obs_mat) {
    // Obtain environment containing function
    Rcpp::Environment base("package:stats");
   // Obtaining namespace of fastglm package
   Environment pkg = Environment::namespace_env("fastglm");
   Function f = pkg["fastglm"];
  ...
  mod_log = f(Named("x", ematrix), Named("y", d), Named("family", 
"binomial"));

which works fine, but I cannot figure out how to get another link than 
the default 'logit' (here for binomial()). I tried:

Named("family", "binomial(link = \"log\")")

Named("family", "binomial(link = log)")

Both gave me this error: "object of node 'function' not found.

Named("link", "log")

Named("make.link", "log")

These last two do not cause an error, but they give the default logit 
link (as if the Named was not evaluated?).

Thanks,

Denis

Le 2024-09-04 16:24, Dirk Eddelbuettel a ?crit :

> On 4 September 2024 at 15:37, Denis Haine wrote:
> | Hi,
> |
> | Sorry for a beginner's question. I'm trying to call an R function 
> (glm())
> | inside my cpp code. The code compiles with no problem, but when I'm 
> running it,
> | it cannot find the second element of the formula, i.e. the x in y~x. 
> The error
> | message is: Error in eval (predvars; data, env) : object 'e' not 
> found.
> |
> | However, if I return 'e', it is correctly calculated. I guess the 
> formula is
> | not correctly evaluated, but I haven't found any examples that could 
> point me
> | in one direction or another.
> |
> | #include <Rcpp.h>
> | using namespace Rcpp;
> | // [[Rcpp::export]]
> | NumericVector misclass(NumericMatrix obs_mat) {
> |   // Obtain environment containing function
> |   Rcpp::Environment base("package:stats");
> |
> |   // Picking up glm() and summary() function from base stats
> |   Rcpp::Function glm_r = base["glm"];
> |   Rcpp::Function sum_r = base["summary.glm"];
> 
> You are running glm() from base here. At the speed of glm() from base.
> 
> That you call it from C++ does not make it faster, sadly, it just 
> creates
> more work for you. Sorry to be a bearer of bad news.
> 
> |   Rcpp::NumericVector d = obs_mat(_, 1);
> |   Rcpp::NumericVector e = no_init(n);
> |   Rcpp::NumericVector mod_coef = no_init(n);
> |   // e is calculated in other section of the code
> |   e = as<IntegerVector>(e);
> |   Rcpp::List mod_pois = glm_r(_["formula"] = "d ~ e",
> |                     _["family"] = "poisson");
> 
> You need to 'work out' (ie expand) the formula on the R side. I have 
> done
> that for the lm() case of model matrices and whatnot in the fastLm()
> example(s) inside eg RcppArmadillo.  Once you have done the R-level 
> unpacking
> you can call the C++ function to fit.
> 
> Big takeaway from that exercise there: the time you spent dealing with 
> the
> (convenient) formula dominates the gain from using a different, 
> simpler,
> slightly faster 'fitter' by many orders of magnitude.
> 
> [ I think there are some packages dealing with glm() fits using Rcpp 
> and
> friends among the by now over 2800 CRAN packages using Rcpp -- but I 
> can't
> right now recall their names. You may find some help in those if you 
> find
> them, and if my recollection was correct in the first place ... ]
> 
> Dirk
> 
> |   Rcpp::List mod_sum = sum_r(mod_pois);
> |   Rcpp::NumericMatrix M_coef = mod_sum[12];
> |   mod_coef = M_coef(2, 1);
> |
> |   return mod_coef;
> | }
> |
> |
> | I also tried providing the formula in the call, i.e. NumericVector 
> misclass
> | (NumericMatrix obs_mat, Formula f) and using it in glm_r, i.e. 
> glm_r(_
> | ["formula"] = f, etc. but with the same outcome.
> |
> | Thanks,
> |
> | Denis
> |
> | _______________________________________________
> | Rcpp-devel mailing list
> | Rcpp-devel at lists.r-forge.r-project.org
> | 
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
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