Use kvec

src/kvec.h

@@ -0,0 +1,90 @@
+/* The MIT License
+
+   Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/*
+  An example:
+
+#include "kvec.h"
+int main() {
+	kvec_t(int) array;
+	kv_init(array);
+	kv_push(int, array, 10); // append
+	kv_a(int, array, 20) = 5; // dynamic
+	kv_A(array, 20) = 4; // static
+	kv_destroy(array);
+	return 0;
+}
+*/
+
+/*
+  2008-09-22 (0.1.0):
+
+	* The initial version.
+
+*/
+
+#ifndef AC_KVEC_H
+#define AC_KVEC_H
+
+#include <stdlib.h>
+
+#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+
+#define kvec_t(type) struct { size_t n, m; type *a; }
+#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
+#define kv_destroy(v) free((v).a)
+#define kv_A(v, i) ((v).a[(i)])
+#define kv_pop(v) ((v).a[--(v).n])
+#define kv_size(v) ((v).n)
+#define kv_max(v) ((v).m)
+
+#define kv_resize(type, v, s)  ((v).m = (s), (v).a = (type*)realloc((v).a, sizeof(type) * (v).m))
+
+#define kv_copy(type, v1, v0) do {							\
+		if ((v1).m < (v0).n) kv_resize(type, v1, (v0).n);	\
+		(v1).n = (v0).n;									\
+		memcpy((v1).a, (v0).a, sizeof(type) * (v0).n);		\
+	} while (0)												\
+
+#define kv_push(type, v, x) do {									\
+		if ((v).n == (v).m) {										\
+			(v).m = (v).m? (v).m<<1 : 2;							\
+			(v).a = (type*)realloc((v).a, sizeof(type) * (v).m);	\
+		}															\
+		(v).a[(v).n++] = (x);										\
+	} while (0)
+
+#define kv_pushp(type, v) (((v).n == (v).m)?							\
+						   ((v).m = ((v).m? (v).m<<1 : 2),				\
+							(v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0)	\
+						   : 0), ((v).a + ((v).n++))
+
+#define kv_a(type, v, i) (((v).m <= (size_t)(i)? \
+						  ((v).m = (v).n = (i) + 1, kv_roundup32((v).m), \
+						   (v).a = (type*)realloc((v).a, sizeof(type) * (v).m), 0) \
+						  : (v).n <= (size_t)(i)? (v).n = (i) + 1 \
+						  : 0), (v).a[(i)])
+
+#endif

src/trace.cpp

@@ -21,6 +21,7 @@
 #define R_NO_REMAP
 #define STRICT_R_HEADERS
 
+#include "kvec.h"
 #include <algorithm>
 #include <map>
 #include <set>
@@ -605,6 +606,16 @@ SEXP networkSummary(const SEXP src,
 {
     const char *names[] = {"inDegree", "outDegree",
                            "ingoingContactChain", "outgoingContactChain", ""};
+    kvec_t(int) ingoingContactChain;
+    kvec_t(int) outgoingContactChain;
+    kvec_t(int) inDegree;
+    kvec_t(int) outDegree;
+    SEXP result, vec;
+
+    kv_init(ingoingContactChain);
+    kv_init(outgoingContactChain);
+    kv_init(inDegree);
+    kv_init(outDegree);
 
     if (check_arguments(src, dst, t, root, inBegin, inEnd,
                         outBegin, outEnd, numberOfIdentifiers))
@@ -617,11 +628,6 @@ SEXP networkSummary(const SEXP src,
                             Rf_xlength(t),
                             INTEGER(numberOfIdentifiers)[0]);
 
-    std::vector<int> ingoingContactChain;
-    std::vector<int> outgoingContactChain;
-    std::vector<int> inDegree;
-    std::vector<int> outDegree;
-
     for (R_xlen_t i = 0, end = Rf_xlength(root); i < end; ++i) {
         VisitedNodes visitedNodesIngoing(INTEGER(numberOfIdentifiers)[0]);
         VisitedNodes visitedNodesOutgoing(INTEGER(numberOfIdentifiers)[0]);
@@ -640,38 +646,42 @@ SEXP networkSummary(const SEXP src,
                      visitedNodesOutgoing,
                      false);
 
-        ingoingContactChain.push_back(visitedNodesIngoing.N() - 1);
-        outgoingContactChain.push_back(visitedNodesOutgoing.N() - 1);
+        kv_push(int, ingoingContactChain, visitedNodesIngoing.N() - 1);
+        kv_push(int, outgoingContactChain, visitedNodesOutgoing.N() - 1);
 
-        inDegree.push_back(degree(lookup.first,
-                                  INTEGER(root)[i] - 1,
-                                  INTEGER(inBegin)[i],
-                                  INTEGER(inEnd)[i]));
+        kv_push(int, inDegree, degree(lookup.first,
+                                      INTEGER(root)[i] - 1,
+                                      INTEGER(inBegin)[i],
+                                      INTEGER(inEnd)[i]));
 
-        outDegree.push_back(degree(lookup.second,
-                                   INTEGER(root)[i] - 1,
-                                   INTEGER(outBegin)[i],
-                                   INTEGER(outEnd)[i]));
+        kv_push(int, outDegree, degree(lookup.second,
+                                       INTEGER(root)[i] - 1,
+                                       INTEGER(outBegin)[i],
+                                       INTEGER(outEnd)[i]));
     }
 
-    SEXP result, vec;
     PROTECT(result = Rf_mkNamed(VECSXP, names));
 
-    SET_VECTOR_ELT(result, 0, vec = Rf_allocVector(INTSXP, inDegree.size()));
-    for (size_t i = 0; i < inDegree.size(); ++i)
-        INTEGER(vec)[i] = inDegree[i];
+    SET_VECTOR_ELT(result, 0, vec = Rf_allocVector(INTSXP, kv_size(inDegree)));
+    for (size_t i = 0; i < kv_size(inDegree); ++i)
+        INTEGER(vec)[i] = kv_A(inDegree, i);
+
+    SET_VECTOR_ELT(result, 1, vec = Rf_allocVector(INTSXP, kv_size(outDegree)));
+    for (size_t i = 0; i < kv_size(outDegree); ++i)
+        INTEGER(vec)[i] = kv_A(outDegree, i);
 
-    SET_VECTOR_ELT(result, 1, vec = Rf_allocVector(INTSXP, outDegree.size()));
-    for (size_t i = 0; i < outDegree.size(); ++i)
-        INTEGER(vec)[i] = outDegree[i];
+    SET_VECTOR_ELT(result, 2, vec = Rf_allocVector(INTSXP, kv_size(ingoingContactChain)));
+    for (size_t i = 0; i < kv_size(ingoingContactChain); ++i)
+        INTEGER(vec)[i] = kv_A(ingoingContactChain, i);
 
-    SET_VECTOR_ELT(result, 2, vec = Rf_allocVector(INTSXP, ingoingContactChain.size()));
-    for (size_t i = 0; i < ingoingContactChain.size(); ++i)
-        INTEGER(vec)[i] = ingoingContactChain[i];
+    SET_VECTOR_ELT(result, 3, vec = Rf_allocVector(INTSXP, kv_size(outgoingContactChain)));
+    for (size_t i = 0; i < kv_size(outgoingContactChain); ++i)
+        INTEGER(vec)[i] = kv_A(outgoingContactChain, i);
 
-    SET_VECTOR_ELT(result, 3, vec = Rf_allocVector(INTSXP, outgoingContactChain.size()));
-    for (size_t i = 0; i < outgoingContactChain.size(); ++i)
-        INTEGER(vec)[i] = outgoingContactChain[i];
+    kv_destroy(ingoingContactChain);
+    kv_destroy(outgoingContactChain);
+    kv_destroy(inDegree);
+    kv_destroy(outDegree);
 
     UNPROTECT(1);