| cfunction {inline} | R Documentation |
Inline C, C++, Fortran function calls from R
Description
Functionality to dynamically define R functions and S4 methods with in-lined C, C++ or Fortran code supporting .C and .Call calling conventions.
Usage
cfunction(sig=character(), body=character(), includes=character(),
otherdefs=character(),
language=c("C++", "C", "Fortran", "F95", "ObjectiveC", "ObjectiveC++"),
verbose=FALSE,
convention=c(".Call", ".C", ".Fortran"),
Rcpp=FALSE,
cppargs=character(), cxxargs=character(), libargs=character(),
dim=NULL, implicit=NULL, module=NULL, name=NULL)
## S4 methods for signatures
# f='character', sig='list', body='list'
# f='character', sig='character', body='character'
setCMethod(f, sig, body, ...)
## Further arguments:
# setCMethod(f, sig, body, includes="", otherdefs="", cpp=TRUE,
# verbose=FALSE, where=topenv(.GlobalEnv), ...)
Arguments
f |
A single character value if |
sig |
A match of formal argument names for the function with the
character-string names of corresponding classes. Alternatively,
a named list of such character vectors. The names of the list elements will
be used as function names (see example). If |
body |
A character vector with C, C++ or Fortran code omitting function
declaration (only the body, i.e. in case of C starting after the function
opening curly bracket and ending before the closing curly bracket,
brackets excluded). In case of |
includes |
A character vector of additional includes and preprocessor statements etc that will be put between the R includes and the user function(s). |
otherdefs |
A characted vector with the code for any further definitions of
functions, classes, types, forward declarations, namespace usage clauses etc
which is inserted between the includes and the declarations of the functions
defined in |
language |
A character value that specifies the source language of the
inline code. The possible values for |
verbose |
If |
convention |
Which calling convention to use? See the Details section. |
Rcpp |
If |
cppargs |
Optional character vector of tokens to be passed to
the compiler via the |
cxxargs |
Optional character vector of tokens to be passed to
the compiler via the |
libargs |
Optional character vector of tokens to be passed to the
compiler via the |
dim |
Optional character vector defining the dimensionality of the
function arguments. Of same length as |
implicit |
A character vector defining the implicit declaration in
Fortran or F95; the default is to use the implicit typing rules for Fortran,
which is |
module |
Name(s) of any modules to be used in the |
name |
Function name to be used in the code. Only used if |
... |
Reserved. |
Details
To declare multiple functions in the same library one can use setCMethod
supplying lists of signatures and implementations. In this case, provide as
many method names in f as you define methods. Avoid clashes when selecting
names of the methods to declare, i.e. if you provide the same name several times
you must ensure that signatures are different but can share the same generic!
The source code in the body should not include the header or
"front-matter" of the function or the close, e.g. in C or C++ it
must start after the C-function opening curly bracket and end before
the C-function closing curly bracket, brackets should not be
included. The header will be automatically generated from the R-signature
argument. Arguments will will carry the same name as used in the signature,
so avoid variable names that are not legal in the target language
(e.g. names with dots).
C/C++: If convention == ".Call" (the default), the .Call mechanism
is used and its result is returned directly as the result of the call of the
generated function. As the last line of the generated C/C++ code a
return R_NilValue; is added in this case and a warning is generated
in case the user has forgotten to provide a return value. To suppress the
warning and still return NULL, add return R_NilValue; explicitly.
Special care is needed with types, memory allocation and protection
– exactly the same as if the code was not inline: see the
Writing R Extension manual for information on .Call.
If convention == ".C" or convention == ".Fortran", the
.C or .Fortran mechanism respectively is
used, and the return value is a list containing all arguments.
Attached R includes include R.h for ".C", and
additionally Rdefines.h and R_ext\Error.h for
".Call".
Value
If sig is a single character vector, cfunction returns a single
function; if it is a list, it returns a list of functions.
setCMethod declares new methods with given names and signatures and
returns invisible NULL.
Author(s)
Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel
See Also
Foreign Function Interface
Examples
x <- as.numeric(1:10)
n <- as.integer(10)
## Not run:
## A simple Fortran example - n and x: assumed-size vector
code <- "
integer i
do 1 i=1, n(1)
1 x(i) = x(i)**3
"
cubefn <- cfunction(signature(n="integer", x="numeric"), code, convention=".Fortran")
print(cubefn)
cubefn(n, x)$x
## Same Fortran example - now n is one number
code2 <- "
integer i
do 1 i=1, n
1 x(i) = x(i)**3
"
cubefn2 <- cfunction(signature(n="integer", x="numeric"), implicit = "none",
dim = c("", "(*)"), code2, convention=".Fortran")
cubefn2(n, x)$x
## Same in F95, now x is fixed-size vector (length = n)
code3 <- "x = x*x*x"
cubefn3 <- cfunction(sig = signature(n="integer", x="numeric"), implicit = "none",
dim = c("", "(n)"), code3, language="F95")
cubefn3(20, 1:20)
print(cubefn3)
## Same example in C
code4 <- "
int i;
for (i = 0; i < *n; i++)
x[i] = x[i]*x[i]*x[i];
"
cubefn4 <- cfunction(signature(n="integer", x="numeric"), code4, language = "C", convention = ".C")
cubefn4(20, 1:20)
## Give the function in the source code a name
cubefn5 <- cfunction(signature(n="integer", x="numeric"), code4, language = "C", convention = ".C",
name = "cubefn")
code(cubefn5)
## End(Not run)
## use of a module in F95
modct <- "module modcts
double precision, parameter :: pi = 3.14159265358979
double precision, parameter :: e = 2.71828182845905
end"
getconstants <- "x(1) = pi
x(2) = e"
cgetcts <- cfunction(getconstants, module = "modcts", implicit = "none",
includes = modct, sig = c(x = "double"), dim = c("(2)"), language = "F95")
cgetcts(x = 1:2)
print(cgetcts)
## Use of .C convention with C code
## Defining two functions, one of which calls the other
sigSq <- signature(n="integer", x="numeric")
codeSq <- "
for (int i=0; i < *n; i++) {
x[i] = x[i]*x[i];
}"
sigQd <- signature(n="integer", x="numeric")
codeQd <- "
squarefn(n, x);
squarefn(n, x);
"
fns <- cfunction( list(squarefn=sigSq, quadfn=sigQd),
list(codeSq, codeQd),
convention=".C")
squarefn <- fns[["squarefn"]]
quadfn <- fns[["quadfn"]]
squarefn(n, x)$x
quadfn(n, x)$x
## Alternative declaration using 'setCMethod'
setCMethod(c("squarefn", "quadfn"), list(sigSq, sigQd),
list(codeSq, codeQd), convention=".C")
squarefn(n, x)$x
quadfn(n, x)$x
## Use of .Call convention with C code
## Multyplying each image in a stack with a 2D Gaussian at a given position
code <- "
SEXP res;
int nprotect = 0, nx, ny, nz, x, y;
PROTECT(res = Rf_duplicate(a)); nprotect++;
nx = INTEGER(GET_DIM(a))[0];
ny = INTEGER(GET_DIM(a))[1];
nz = INTEGER(GET_DIM(a))[2];
double sigma2 = REAL(s)[0] * REAL(s)[0], d2 ;
double cx = REAL(centre)[0], cy = REAL(centre)[1], *data, *rdata;
for (int im = 0; im < nz; im++) {
data = &(REAL(a)[im*nx*ny]); rdata = &(REAL(res)[im*nx*ny]);
for (x = 0; x < nx; x++)
for (y = 0; y < ny; y++) {
d2 = (x-cx)*(x-cx) + (y-cy)*(y-cy);
rdata[x + y*nx] = data[x + y*nx] * exp(-d2/sigma2);
}
}
UNPROTECT(nprotect);
return res;
"
funx <- cfunction(signature(a="array", s="numeric", centre="numeric"), code)
x <- array(runif(50*50), c(50,50,1))
res <- funx(a=x, s=10, centre=c(25,15))
if (interactive()) image(res[,,1])
## Same but done by registering an S4 method
setCMethod("funy", signature(a="array", s="numeric", centre="numeric"), code, verbose=TRUE)
res <- funy(x, 10, c(35,35))
if (interactive()) { x11(); image(res[,,1]) }