Dot Call interface

Introduction to .Call interface

Hao Chai

Department of Statistics and Actuarial Science
The University of Iowa

Productive Seminar
March 6, 2012

Hao Chai (U of Iowa) Introduction to .Call interface 1 / 41

Outline

1 Introduction

2 C part
.C interface
.Call interface

3 R part

4 Examples

5 Other


Introduction

Outline

1 Introduction

2 C part
.C interface
.Call interface

3 R part

4 Examples

5 Other


Introduction

.C and .Call are two interfaces in R to call C routines. Similar foreign
language interface functions are .Fortran and .External.


Introduction

Advantages of R
Straight forward syntax.
Easy to learn, to use, to track the results and to debug.
Over 3,000 packages available to carry out many kinds of statistical
analysis and produce professional graphics.
Vectorized language.
...
Disadvantage of R
Loops.


Introduction

Toy example
Our goal is to generate a variance-covariance matrix Σ = (σij ), where
a · b|i−j| , if i = j;
σij =
1, if i = j.
We have at least three methods:
A simple R function matgen R:
matgen_R = function(P, a, b)
{
Covmatrix = matrix(rep(1, P * P), nrow = P)
for (i in 1 : P)
for (j in 1 : P)
if (i != j)
Covmatrix[i, j] = exp(log(a) + log(b)
* abs(i - j))
Covmatrix
}

Introduction

Toy example

An R function using matrix indexing matgen Rind:
matgen_Rind = function(P, a, b)
{
Covmatrix = matrix(rep(1, P * P), nrow = P)
for (i in 1 : (P - 1))
{Covmatrix[cbind((1 + i) : P, 1 : (P - i))] =
exp(log(a) + log(b) * abs(i))
Covmatrix[cbind(1 : (P - i), (1 + i) : P)] =
exp(log(a) + log(b) * abs(i))}
Covmatrix
}


Introduction

An R function calling C routines matgen RC:
matgen_RC = function(P, a, b)
{
.Call("matrix_gen", as.integer(P), as.double(a),
as.double(b))
}
Also we can use R compiler to compile the ﬁrst two pure R functions and
get matgen Rcmp and matgen Rindcmp.


Introduction

Toy example

Result
> P = 1000

test elapsed user.self relative
5 matgen Rindcmp(P, 0.5, 0.9) 0.80 0.75 1.00
4 matgen Rind(P, 0.5, 0.9) 0.97 0.86 1.21
1 matgen RC(P, 0.5, 0.9) 1.04 1.01 1.30
2 matgen Rcmp(P, 0.5, 0.9) 19.98 19.51 24.98
3 matgen R(P, 0.5, 0.9) 65.44 64.45 81.80


C part

Outline

1 Introduction

2 C part
.C interface
.Call interface

3 R part

4 Examples

5 Other


C part

Header ﬁles

To enable the communication between R and C, the following header ﬁles
are needed in the C code.

#include <R.h>
#include <Rinternals.h> /% For .C or .Call %/
#include <Rdefines.h> /% For .External %/
#include <R_ext/Rdynload.h>


C part .C interface

To use .C interface, main() function in C code needs to be replaced by

static void CFuncName(arg1, arg2, ...)

Arguments above have to be of pointer type. Therefore, we need to
coerce the scalar arguments to scalars in C.
C function can only return values to R through its arguments. In
other words, there are two kinds of arguments: arguments that pass
values from R to C and arguments that return values from C to R.
The C code using .C interface in the toy example is


C part .C interface

.C interface in toy example

#include <R.h>
#include <Rinternals.h>
#include <math.h>
static void matrix_gen(double *Rp, double *Ra, double *Rb,
double *Rmatrix)
{
R_len_t i, j, p = Rp[0];
double a = Ra[0], b = Rb[0];
for (i = 0; i < p; i++)
for (j = 0; j < p; j++)
if (i == j) Rmatrix[i * p + j] = 1;
else Rmatrix[i * p + j] = exp(log(a) + abs(i - j)
* log(b));
}

C part .C interface

Mapping types between R and C

Table: Comparison of R and C data types.1
R storage mode C types
logical int *
integer int *
double double *
character char **
complex Rcomplex *

1
Cited from “Writing R Extensions”

C part .Call interface

What can we expect from .Call?2

Pass R objects to C
Create R objects in C
Manipulate R objects in C
Return R objects from C
Call R functions from C

2
See Brian Caﬀo


To use .Call interface, main() function in C code needs to be replaced by

SEXP CFuncName(SEXP arg1, SEXP arg2, ...)

SEXP is a structure in C standing for S expression.
The returned value from C will also be SEXP type.
If new SEXP objects are deﬁned within the C function, use
PROTECT to protect them in the memory so that it will not be
cleaned by R as garbage.



Basic structure of C functions

SEXP CFuncName(SEXP arg1, arg2, ...)
{
[arg1 = coerceVector(arg1, INTSXP)]
# Coerce the vector to the right type.
SEXP Robj, return_val; # Define new R objects.
PROTECT(return_val = allocMatrix(REALSXP, arg1, arg2))
# Protect return_val.
[body of function]
UNPROTECT(1)
return(return_val) # Return the values to R.
}



Useful data types in Rinternals.h

3
Table: SEXPTYPE and R equivalent
SEXPTYPE R equivalent
REALSXP numeric with storage mode double
INTSXP integer
LGLSXP logical
STRSXP character
VECSXP list (generic vector)
DOTSXP a ‘...’ object
ENVSXP environment

3
Cited from “Writing R Extensions”


Useful macros in Rinternals.h
There are plenty of useful functions deﬁned in Rinternals.h. Useful
functions can be found in “Writing R Extensions” or “R Internals”.

Table: List of useful functions in Rinternals.h4

Name Usage Example
coerceVector Coerce R object to SEXPTYPE arg1=..(arg1,INTSXP)
allocVector Allocate memory for R vector Robj=..(STRSXP,2)
allocMatrix Allocate memory for R matrix Robj=..(STRSXP,2,2)
nrows Get the No. of rows of a matrix ..nrow(Rmatrix)
ncols Get the No. of cols of a matrix ..ncol(Rmatrix)
PROTECT Protect an R object See examples.
UNPROTECT UNPROTECT some R objects See examples.

4
.. represents the function name in the same row.


Useful functions in Rinternals.h

Table: List of useful functions in Rinternals.h Cont.5

Name Usage Example
STRING ELT Returns the memo. add. of R string ..(Rstr, 0)
VECTOR ELT Returns the memo. add. of R list ..(Rlist, 1)
INTEGER Return the memo. add. of R int ..(Rint)
REAL Return the memo. add. of R real ..(Rdoub)
CHAR Convert a Rchar to characters ..(Rchar)
SET VECTOR ELT Assign value to an element of R list See example

5
.. represents the function name in the same row.


Special Values

There are some constants for special values in R
R NaN
R PosInf
R NegInf
R NaReal
R NilValue
There are also some macros for error checking in C ISNA, ISNAN,
R FINITE, NA INTEGER, NA LOGICAL, NA STRING, NA REAL



.Call interface in toy example

#include <R.h>
#include <Rinternals.h>
#include "math.h"
SEXP matrix_gen(SEXP RP, SEXP Ra, SEXP Rb)
{
R_len_t i, j, p = INTEGER(RP)[0];
SEXP Rmatrix;
RP = coerceVector(RP, INTSXP);
Ra = coerceVector(Ra, REALSXP);
Rb = coerceVector(Rb, REALSXP);
PROTECT(Rmatrix = allocMatrix(REALSXP, p, p));



.Call interface in toy example

double *mat, a = REAL(Ra)[0], b = REAL(Rb)[0];
mat = REAL(Rmatrix);
for (i = 0; i < p; i++)
for (j = 0; j < p; j++)
if (i == j) mat[i * p + j] = 1;
else mat[i * p + j] = exp(log(a) +
abs(i - j) * log(b));
UNPROTECT(1);
return(Rmatrix);
}


R part

Outline

1 Introduction

2 C part
.C interface
.Call interface

3 R part

4 Examples

5 Other


R part

Interfaces in R

To create a dynamic library, run the following code in the command line:

R CMD SHLIB CFileName.c

CFileName.dll or CFileName.so will be generated in the same directory.
Then load the dynamic library which is generated by C code using
> dyn.load("CFileName.so")
in Linux/MacOS, or
> dyn.load("CFileName.dll")
in Windows, or a universal solution
> dyn.load(paste("CFileName", .Platform$dynlib.ext,
+ sep = ""))


R part

There are three interfaces in R to load the dynamic library generated by C.
1 .C(”CFuncName” arg1, arg2, ...)
,
2 .Call(”CFuncName” arg1, arg2, ...)
,
3 .External(”CFuncName”, arg1, arg2, ...)

There are some options when using .C, such as NAOK and
PACKAGE. For detailed information, refer to “Writing R Extensions”.


Examples

Outline

1 Introduction

2 C part
.C interface
.Call interface

3 R part

4 Examples

5 Other


Examples

Pass numeric values to C
func1 is a function with two arguments Rn and Rvec. It returns the largest
element of the ﬁrst Rn elements of vector Rvec.
SEXP func1(SEXP Rvec, SEXP Rn)
{
Rvec = coerceVector(Rvec, REALSXP);
R_len_t i = 0, n = INTEGER(Rn)[0];
double *vec, max = REAL(Rvec)[0];
SEXP return_val;
PROTECT(return_val = allocVector(REALSXP, 1));
vec = REAL(Rvec);
for (i = 1; i < n; i++)
if (vec[i] >= max) max = vec[i];
REAL(return_val)[0] = max;
UNPROTECT(1);
return(return_val);
}

Examples

Pass numeric values to C

In R, we do the following

a = c(7, 4, 8, 9, 2, 5)
n = 4
dyn.load("f:/presentation/intro2dotCall/illust.dll")
.Call("func1", as.double(a), as.integer(n))


Examples

Pass strings, return a list

func2 is able to calculate the quadratic form or the linear product of a
matrix and a vector. It has three arguments: Rstr, Ry and RM. Ry is a
vector, RM is a matrix. If Rstr is ”quadratic”, then t(Ry) %*% RM %*%
Ry is returned. If Rstr is ”linear”, then RM %*% Ry is returned. If Rstr is
”both” then both of the above will be returned as an R list.
,


Examples


SEXP func2(SEXP RM, SEXP Ry, SEXP Rstr)
{
Rstr = coerceVector(Rstr, STRSXP);
RM = coerceVector(RM, REALSXP);
Ry = coerceVector(Ry, REALSXP);
SEXP return_lst, vec, num;
double *M = REAL(RM), *y = REAL(Ry);
double result1 = 0, *result2;
R_len_t i, j, nr, nc, l;
const char *method;
method = CHAR(STRING_ELT(Rstr, 0));
nr = nrows(RM);
nc = ncols(RM);
l = length(Ry);


Examples

if (((strcmp(method, "both") == 0) ||
(strcmp(method,"linear") == 0)) && (nc != l))
error("The matrix and the vector need to be conformable!");
if (((strcmp(method, "both") == 0) ||
(strcmp(method, "quadratic") == 0)) &&
((nc != l) || (nr != l)))
error("The matrix and the vector need to be conformable!");
if (strcmp(method, "both") == 0)
{
PROTECT(return_lst = allocVector(VECSXP, 2));
PROTECT(vec = allocVector(REALSXP, nr));
PROTECT(num = allocVector(REALSXP, 1));
result2 = REAL(vec);
result1 = REAL(num)[0];
}
else PROTECT(return_lst = allocVector(VECSXP, 1));


Examples

if (strcmp(method, "linear") == 0)
{
PROTECT(vec = allocVector(REALSXP, nr));
result2 = REAL(vec);
}
if (strcmp(method, "quadratic") == 0)
{
PROTECT(num = allocVector(REALSXP, 1));
result1 = REAL(num)[0];
}
if ((strcmp(method, "quadratic") == 0) ||
(strcmp(method, "both") == 0))
for (i = 0; i < nr; i++)
for (j = 0; j < nc; j++)
result1 = result1 + M[i + j * nr] * y[i] * y[j];


Examples

if ((strcmp(method, "linear") == 0) ||
(strcmp(method, "both") == 0))
for (i = 0; i < nr; i++)
{
result2[i] = 0;
for (j = 0; j < nc; j++)
result2[i] = result2[i] + M[i + j * nr] * y[j];
}


Examples

if (strcmp(method, "quadratic") == 0)
SET_VECTOR_ELT(return_lst, 0, num);
if (strcmp(method, "linear") == 0)
SET_VECTOR_ELT(return_lst, 0, vec);
{
SET_VECTOR_ELT(return_lst, 0, num);
SET_VECTOR_ELT(return_lst, 1, vec);
}
UNPROTECT(2);
UNPROTECT(1);
return(return_lst);
}


Examples


The R code to call the function func2 is

dyn.load("f:/presentation/intro2dotCall/illust.dll")
M <- matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 9), nrow = 3)
y <- c(1, 0, -1)
.Call("func2", M, as.double(y), "both")


Other

Outline

1 Introduction

2 C part
.C interface
.Call interface

3 R part

4 Examples

5 Other


Other

Evaluating R expressions in C

It is also possible to evaluate R expressions in C code. The following
functions/macros are useful in this case. More details can be found in
“Writing R extensions” .
defineVar
findVar
findFun
install


Other

Some misc.
The “Writing R Extensions” manual is the main source for this talk.
More functions and macros can be found in Rinternals.h, or
alternatively Rdefines.h. Choose one and stick to it.
Several times, when ran .Call in R, R crashed. Very likely, it was
caused by the difference between number of arguments in .Call and
number of arguments in the original C functions.
Related C and R files are available at Related files.


Other

Refrences

Writing R Extensions
R Internals
Using .Call in R by Brian Caﬀo.
dot Call Interface by Gopi Goswami.
Rinternals.h


Other

Thank you!


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