Rpackage

ahomoudi · Apr 13, 2024 · 75a4d69 · 75a4d69
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diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 [![License](https://img.shields.io/badge/License-CCBY-blue)](#license)
 <!-- badges: end -->
 
-This is the official repository of the Project AquaFortR: Streamlining Atmospheric Science, Oceanography, Climate, and Water Research with Fortran-accelerated R. 
+This is the official repository of the project AquaFortR: Streamlining Atmospheric Science, Oceanography, Climate, and Water Research with Fortran-accelerated R. 
 
 The repository is structured as follows:
 
@@ -38,7 +38,7 @@ swirl::install_course_zip("path/to/AquaFortR_Swirl.zip")
 
 ### Book 
 
-Materials for the chapter 2 are available <a href="AquaFortR_Codes.zip">here</a>. Please, 
+Materials for Chapter 2 are available <a href="AquaFortR_Codes.zip">here</a>. Please, 
 revise the path to the shared libraries files in the R-Fortran functions.
 
 ## Acknowledgment

diff --git a/RPackage/NAMESPACE b/RPackage/NAMESPACE
@@ -8,5 +8,4 @@ export(mixing_ratio_from_dewpoint)
 export(saturation_vapour_pressure)
 export(xcorr2D_f)
 export(xcorr2D_r)
-useDynLib(AquaFortR)
 useDynLib(AquaFortR, .registration=TRUE)
diff --git a/RPackage/R/cape_f.R b/RPackage/R/cape_f.R
@@ -26,27 +26,26 @@
 #'   vtc = TRUE
 #' )
 #' @author Klemens Barfus (Original in Fortran), Ahmed Homoudi (Integration in R)
-#' @useDynLib AquaFortR
 #' @export
 cape_f <- function(t_parcel, dwpt_parcel, mr_parcel,
                    p_profile, t_profile, mr_profile,
                    vtc = TRUE) {
-  DIM <- c(
-    length(p_profile),
-    4,
-    as.integer(vtc)
-  )
+
+  vtc <-as.integer(vtc)
+
   result <- .Call(
     c_cape_f,
-    as.double(t_parcel),
-    as.double(dwpt_parcel),
-    as.double(mr_parcel),
-    as.double(p_profile),
-    as.double(t_profile),
-    as.double(mr_profile),
-    as.integer(DIM)
+    t_parcel,
+    dwpt_parcel,
+    mr_parcel,
+    p_profile,
+    t_profile,
+    mr_profile,
+    vtc
   )
 
   names(result) <- c("CAPE", "CIN", "p_LCL", "p_LFC")
   return(result)
 }
+
+
diff --git a/RPackage/R/cape_r.R b/RPackage/R/cape_r.R
@@ -26,7 +26,6 @@
 #'   vtc = TRUE
 #' )
 #' @author Klemens Barfus (Original in Fortran), Ahmed Homoudi (Translation to R)
-#' @useDynLib AquaFortR
 #' @export
 cape_r <- function(t_parcel, dwpt_parcel, mr_parcel,
                    p_profile, t_profile, mr_profile,

diff --git a/RPackage/R/conv2D_f.R b/RPackage/R/conv2D_f.R
@@ -12,16 +12,13 @@
 #' b <- matrix(c(5, 6, 7, 8), ncol = 2)
 #' conv2D_f(a, b)
 #' @author Ahmed Homoudi
-#' @useDynLib AquaFortR
 #' @export
 conv2D_f <- function(a, b) {
   stopifnot(length(dim(a)) == 2 | length(dim(b)) == 2)
   result <- .Call(
     c_conv2d_f,
-    as.integer(dim(a)),
-    as.double(a),
-    as.integer(dim(b)),
-    as.double(b)
+    a,
+    b
   )
   return(result)
 }
diff --git a/RPackage/R/conv2D_r.R b/RPackage/R/conv2D_r.R
@@ -12,7 +12,6 @@
 #' b <- matrix(c(5, 6, 7, 8), ncol = 2)
 #' conv2D_f(a, b)
 #' @author Ahmed Homoudi
-#' @useDynLib AquaFortR
 #' @export
 conv2D_r <- function(a, b) {
   stopifnot(length(dim(a)) == 2 | length(dim(b)) == 2)

diff --git a/RPackage/R/xcorr2D_f.R b/RPackage/R/xcorr2D_f.R
@@ -12,16 +12,13 @@
 #' b <- matrix(c(5, 6, 7, 8), ncol = 2)
 #' xcorr2D_f(a, b)
 #' @author Ahmed Homoudi
-#' @useDynLib AquaFortR
 #' @export
 xcorr2D_f <- function(a, b) {
   stopifnot(length(dim(a)) == 2 | length(dim(b)) == 2)
   result <- .Call(
     c_xcorr2d_f,
-    as.integer(dim(a)),
-    as.double(a),
-    as.integer(dim(b)),
-    as.double(b)
+    a,
+    b
   )
   return(result)
 }
diff --git a/RPackage/R/xcorr2D_r.R b/RPackage/R/xcorr2D_r.R
@@ -12,7 +12,6 @@
 #' b <- matrix(c(5, 6, 7, 8), ncol = 2)
 #' xcorr2D_f(a, b)
 #' @author Ahmed Homoudi
-#' @useDynLib AquaFortR
 #' @export
 xcorr2D_r <- function(a, b) {
   stopifnot(length(dim(a)) == 2 | length(dim(b)) == 2)

diff --git a/RPackage/man/AquaFortR-package.Rd b/RPackage/man/AquaFortR-package.Rd
diff --git a/RPackage/man/saturation_vapour_pressure.Rd b/RPackage/man/saturation_vapour_pressure.Rd
diff --git a/RPackage/src/AquaFortRmodulec.c b/RPackage/src/AquaFortRmodulec.c
@@ -1,47 +1,45 @@
+#define R_NO_REMAP
 #include <R.h>
 #include <Rinternals.h>
 #include <stdlib.h> // for NULL
-#include <Rmath.h>
-#include <R_ext/Rdynload.h>
-#include <R_ext/Arith.h>
 
 void F77_NAME(xcorr2d_f)(int m, int n, int p, int q, int k, int l, double *a, double *b, double *cc);
 void F77_NAME(conv2d_f)(int m, int n, int p, int q, int k, int l, double *a, double *b, double *conv);
 void F77_NAME(cape_f)(double *t_parcel, double *dwpt_parcel, double *mr_parcel, int nlevels, double *p_profile,
                       double *t_profile, double *mr_profile, int vtc, int nresult, double *result);
 
-extern SEXP c_xcorr2d_f(SEXP dim_a, SEXP a, SEXP dim_b, SEXP b)
+extern SEXP c_xcorr2d_f(SEXP a, SEXP b)
 {
-    int m = INTEGER(dim_a)[0];
-    int n = INTEGER(dim_a)[1];
+    int m = Rf_nrows(a);
+    int n = Rf_ncols(a);
     //
-    int p = INTEGER(dim_b)[0];
-    int q = INTEGER(dim_b)[1];
+    int p = Rf_nrows(b);
+    int q = Rf_ncols(b);
     //
     int k = m + p - 1;
     int l = n + q - 1;
 
     SEXP ret;
-    PROTECT(ret = allocMatrix(REALSXP, k, l));
+    PROTECT(ret = Rf_allocMatrix(REALSXP, k, l));
     F77_CALL(xcorr2d_f)
     (m, n, p, q, k, l, REAL(a), REAL(b), REAL(ret));
     UNPROTECT(1);
     return (ret);
 }
 
-extern SEXP c_conv2d_f(SEXP dim_a, SEXP a, SEXP dim_b, SEXP b)
+extern SEXP c_conv2d_f(SEXP a, SEXP b)
 {
-    int m = INTEGER(dim_a)[0];
-    int n = INTEGER(dim_a)[1];
+    int m = Rf_nrows(a);
+    int n = Rf_ncols(a);
     //
-    int p = INTEGER(dim_b)[0];
-    int q = INTEGER(dim_b)[1];
+    int p = Rf_nrows(b);
+    int q = Rf_ncols(b);
     //
     int k = m + p - 1;
     int l = n + q - 1;
 
     SEXP ret;
-    PROTECT(ret = allocMatrix(REALSXP, k, l));
+    PROTECT(ret = Rf_allocMatrix(REALSXP, k, l));
     F77_CALL(conv2d_f)
     (m, n, p, q, k, l, REAL(a), REAL(b), REAL(ret));
     UNPROTECT(1);
@@ -50,34 +48,32 @@ extern SEXP c_conv2d_f(SEXP dim_a, SEXP a, SEXP dim_b, SEXP b)
 
 extern SEXP c_cape_f(SEXP t_parcel, SEXP dwpt_parcel, SEXP mr_parcel,
                      SEXP p_profile, SEXP t_profile, SEXP mr_profile,
-                     SEXP DIM)
+                     SEXP vtc)
 {
-    int nlevels = INTEGER(DIM)[0];
-    int nret = INTEGER(DIM)[1];
-    int vtc = INTEGER(DIM)[2];
+    int nlevels = Rf_length(t_profile);
+    int vtc2 = INTEGER(vtc)[0];
+    int nret = 4;
 
     SEXP ret;
     /* Order: CAPE, CIN, p_LCL, p_LFC */
-    PROTECT(ret = allocVector(REALSXP, 4));
+    PROTECT(ret = Rf_allocVector(REALSXP, 4));
     F77_CALL(cape_f)
     (REAL(t_parcel), REAL(dwpt_parcel), REAL(mr_parcel), nlevels,
-     REAL(p_profile), REAL(t_profile), REAL(mr_profile), vtc,
+     REAL(p_profile), REAL(t_profile), REAL(mr_profile), vtc2,
      nret, REAL(ret));
     UNPROTECT(1);
     return (ret);
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"c_xcorr2d_f", (DL_FUNC)&c_xcorr2d_f, 4},
-    {"c_conv2d_f", (DL_FUNC)&c_conv2d_f, 4},
+    {"c_xcorr2d_f", (DL_FUNC)&c_xcorr2d_f, 2},
+    {"c_conv2d_f", (DL_FUNC)&c_conv2d_f, 2},
     {"c_cape_f", (DL_FUNC)&c_cape_f, 7},
     {NULL, NULL, 0}};
 
-static const R_FortranMethodDef FEntries[] = {
-    {NULL, NULL, 0}};
 
 void R_init_AquaFortR(DllInfo *dll)
 {
-    R_registerRoutines(dll, NULL, CallEntries, FEntries, NULL);
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
     R_useDynamicSymbols(dll, FALSE);
 }
diff --git a/RPackage/src/AquaFortRmodulef.f90 b/RPackage/src/AquaFortRmodulef.f90
@@ -4,6 +4,7 @@ module AquaFortRmodule
 
    public :: xcorr2d_f
    public :: conv2d_f
+   public :: cape_f
 contains
 
    ! Cross-Correlation