use foreach syntax where appropriate

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.14.8.1
+Version: 0.14.8.2
 Date: 2024-11-25
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))

src/genealogy.h

@@ -177,8 +177,7 @@ class genealogy_t : public nodeseq_t {
       sat[j] = ell[j] = 0;
       etype[j] = 0;
     }
-    for (node_it i = begin(); i != end(); i++) {
-      node_t *p = *i;
+    for (const node_t *p : *this) {
       if (tcur < p->slate) {
         tout += _ndeme; ell += _ndeme; sat += _ndeme;
         deme += _ndeme; etype += _ndeme;
@@ -310,8 +309,8 @@ class genealogy_t : public nodeseq_t {
   //! number of samples
   size_t nsample (void) const {
     size_t n = 0;
-    for (node_it k = cbegin(); k != cend(); k++) {
-      if ((*k)->holds(blue)) n++;
+    for (const node_t *p : *this) {
+      if (p->holds(blue)) n++;
     }
     return n;
   };
@@ -483,8 +482,8 @@ class genealogy_t : public nodeseq_t {
     }
     delete blacks;
     // erase deme information from nodes.
-    for (node_it i = begin(); i != end(); i++) {
-      (*i)->deme() = 0;
+    for (node_t *p : *this) {
+      p->deme() = 0;
     }
     // drop superfluous nodes (holding just one ball).
     comb();

src/inventory.h

@@ -36,8 +36,8 @@ class inventory_t {
   inventory_t (std::pair<node_it,node_it>&& I) {
     clean();
     for (node_it i = I.first; i != I.second; i++) {
-      for (ball_it j = (*i)->begin(); j != (*i)->end(); j++) {
-        insert(*j);             // 'insert' checks color
+      for (ball_t *b : *i) {
+        insert(b);              // 'insert' checks color
       }
     }
   };
@@ -49,8 +49,8 @@ class inventory_t {
   inventory_t& operator= (std::pair<node_it,node_it>&& I) {
     clean();
     for (node_it i = I.first; i != I.second; i++) {
-      for (ball_it j = (*i)->begin(); j != (*i)->end(); j++) {
-        insert(*j); // 'insert' checks color
+      for (ball_t *b : **i) {
+        insert(b);              // 'insert' checks color
       }
     }
     return *this;
@@ -150,7 +150,7 @@ class inventory_t {
         k++; j++;
       }
     } else {
-      assert(0);		// #nocov
+      assert(0);                // #nocov
     }
     return p;
   };

src/master.h

@@ -165,18 +165,18 @@ class master_t : public POPN {
   //! sample in deme i
   void sample (name_t i = 0, int n = 1) {
     pocket_t *p = inventory.random_balls(i,n);
-    for (ball_it a = p->begin(); a != p->end(); a++) {
-      geneal.sample(*a,time());
+    for (ball_t *a : *p) {
+      geneal.sample(a,time());
     }
     p->clear();
     delete p;
   };
   //! sample_death in deme i
   void sample_death (name_t i = 0, int n = 1) {
     pocket_t *p = inventory.random_balls(i,n);
-    for (ball_it a = p->begin(); a != p->end(); a++) {
-      inventory.erase(*a);
-      geneal.sample_death(*a,time());
+    for (ball_t *a : *p) {
+      inventory.erase(a);
+      geneal.sample_death(a,time());
     }
     p->clear();
     delete p;

src/node.h

@@ -130,8 +130,8 @@ class node_t : public pocket_t {
   //! number of descendants
   int nchildren (void) const {
     int n = 0;
-    for (ball_it i = begin(); i != end(); i++) {
-      switch ((*i)->color) {
+    for (ball_t *b : *this) {
+      switch (b->color) {
       case green: case black:
         n++;
         break;
@@ -151,8 +151,7 @@ class node_t : public pocket_t {
   void lineage_incr (int *incr, int *sat, int *etype) const {
     const name_t d = deme();
     incr[d]--;
-    for (ball_it i = cbegin(); i != cend(); i++) {
-      ball_t *b = *i;
+    for (ball_t *b : *this) {
       switch (b->color) {
       case green: case black:
         incr[b->deme()]++;
@@ -226,8 +225,7 @@ class node_t : public pocket_t {
       o3 += "g_";
     }
     n = 0;
-    for (ball_it i = begin(); i != end(); i++) {
-      ball_t *b = *i;
+    for (ball_t *b : *this) {
       node_t *p = 0;
       switch (b->color) {
       case green:

src/nodeseq.h

@@ -22,7 +22,7 @@ class nodeseq_t : public std::list<node_t*> {
 
   //! clean up: delete all nodes, reset globals
   void clean (void) {
-    for (node_it i = begin(); i != end(); i++) delete *i;
+    for (node_t *p : *this) delete p;
     clear();
   };
 
@@ -39,16 +39,16 @@ class nodeseq_t : public std::list<node_t*> {
   //! size of serialized binary form
   size_t bytesize (void) const {
     size_t s = sizeof(size_t);
-    for (node_it i = begin(); i != end(); i++)
-      s += (*i)->bytesize();
+    for (node_t *p : *this)
+      s += p->bytesize();
     return s;
   };
   //! binary serialization
   friend raw_t* operator>> (const nodeseq_t& G, raw_t* o) {
     size_t nnode = G.size();
     memcpy(o,&nnode,sizeof(size_t)); o += sizeof(size_t);
-    for (node_it i = G.begin(); i != G.end(); i++) {
-      o = (**i >> o);
+    for (node_t *p : G) {
+      o = (*p >> o);
     }
     return o;
   };
@@ -67,8 +67,8 @@ class nodeseq_t : public std::list<node_t*> {
       G.push_back(p);
       node_names.insert({p->uniq,p});
     }
-    for (node_it i = G.begin(); i != G.end(); i++) {
-      (*i)->repair_owners(node_names,&ball_names);
+    for (node_t *q : G) {
+      q->repair_owners(node_names,&ball_names);
     }
     G.repair_owners(ball_names);
     G.trace_lineages();
@@ -81,8 +81,7 @@ class nodeseq_t : public std::list<node_t*> {
   //! This function repairs the links green balls and their names.
   void repair_owners (std::unordered_map<name_t,ball_t*>& names) {
     std::unordered_map<name_t,ball_t*>::const_iterator n;
-    for (node_it i = begin(); i != end(); i++) {
-      node_t *p = *i;
+    for (node_t *p : *this) {
       n = names.find(p->uniq);
       assert(n != names.end());
       ball_t *b = n->second;
@@ -128,29 +127,27 @@ class nodeseq_t : public std::list<node_t*> {
   //! Get all balls of a color.
   pocket_t* colored (color_t col) const {
     pocket_t *p = new pocket_t;
-    for (node_it i = begin(); i != end(); i++) {
-      for (ball_it j = (*i)->begin(); j != (*i)->end(); j++) {
-        if ((*j)->is(col)) p->insert(*j);
+    for (node_t *q : *this) {
+      for (ball_t *b : *q ) {
+        if (b->is(col)) p->insert(b);
       }
     }
     return p;
   };
   //! Number of distinct timepoints.
   size_t ntime (slate_t t) const {
     size_t count = 1;
-    for (node_it i = begin(); i != end(); i++) {
-      if (t < (*i)->slate) {
-        t = (*i)->slate;
+    for (node_t *p : *this) {
+      if (t < p->slate) {
+        t = p->slate;
         count++;
       }
     }
     return count;
   };
   //! Number of nodes in the sequence.
   size_t length (void) const {
-    size_t count = 0;
-    for (node_it i = begin(); i != end(); i++) count++;
-    return count;
+    return this->size();
   };
   //! traverse to nth node, retrieve pointer
   node_t *position (int n) {
@@ -246,10 +243,8 @@ class nodeseq_t : public std::list<node_t*> {
     // because we move from early to late,
     // the order is guaranteed to be valid.
     name_t u = 0;
-    for (node_it i = begin(); i != end(); i++) {
-      node_t *p = *i;
-      for (ball_it j = p->begin(); j != p->end(); j++) {
-        ball_t *b = *j;
+    for (node_t *p : *this ) {
+      for (ball_t *b : *p) {
         if (b->color==blue) {
           trace_lineage(b,u);
           u++;
@@ -263,17 +258,17 @@ class nodeseq_t : public std::list<node_t*> {
   //! human-readable info
   std::string describe (void) const {
     std::string o = "";
-    for (node_it p = begin(); p != end(); p++) {
-      o += (*p)->describe();
+    for (node_t *p : *this) {
+      o += p->describe();
     }
     return o;
   };
   //! human- & machine-readable info
   virtual std::string yaml (std::string tab = "") const {
     std::string o = "";
     std::string t = tab + "  ";
-    for (node_it p = begin(); p != end(); p++) {
-      o += tab + "- " + (*p)->yaml(t);
+    for (node_t *p : *this) {
+      o += tab + "- " + p->yaml(t);
     }
     return o;
   };
@@ -282,8 +277,8 @@ class nodeseq_t : public std::list<node_t*> {
     SEXP Nodes;
     PROTECT(Nodes = NEW_LIST(size()));
     int k = 0;
-    for (node_it i = begin(); i != end(); i++) {
-      SET_ELEMENT(Nodes,k++,(*i)->structure());
+    for (node_t *p : *this) {
+      SET_ELEMENT(Nodes,k++,p->structure());
     }
     UNPROTECT(1);
     return Nodes;
@@ -292,9 +287,9 @@ class nodeseq_t : public std::list<node_t*> {
   std::string newick (slate_t t) const {
     slate_t te = dawn();
     std::string o = "";
-    for (node_it i = begin(); i != end(); i++) {
-      if ((*i)->is_root()) {
-        o += (*i)->newick(t,te) + ";";
+    for (node_t *p : *this) {
+      if (p->is_root()) {
+        o += p->newick(t,te) + ";";
       }
     }
     return o;

src/pocket.h

@@ -35,7 +35,7 @@ class pocket_t : public std::set<ball_t*,ball_order> {
 
   //! delete balls and clear pocket
   void clean (void) {
-    for (ball_it i = begin(); i != end(); i++) delete *i;
+    for (ball_t *b : *this) delete b;
     clear();
   };
 
@@ -50,8 +50,8 @@ class pocket_t : public std::set<ball_t*,ball_order> {
   friend raw_t* operator>> (const pocket_t &p, raw_t *o) {
     size_t psize = p.size();
     memcpy(o,&psize,sizeof(size_t)); o += sizeof(size_t);
-    for (ball_it i = p.begin(); i != p.end(); i++)
-      o = (**i >> o);
+    for (ball_t *i : p)
+      o = (*i >> o);
     return o;
   };
   //! binary deserialization.
@@ -72,8 +72,8 @@ class pocket_t : public std::set<ball_t*,ball_order> {
   //! Needed in deserialization.
   //! Inform all balls as to their holder.
   void repair_holder (node_t* p) {
-    for (ball_it i = begin(); i != end(); i++) {
-      (*i)->holder() = p;
+    for (ball_t *b : *this) {
+      b->holder() = p;
     }
   };
 
@@ -83,8 +83,7 @@ class pocket_t : public std::set<ball_t*,ball_order> {
   void repair_owners (const std::unordered_map<name_t,node_t*>& node_name,
                       std::unordered_map<name_t,ball_t*> *ball_name) {
     std::unordered_map<name_t,node_t*>::const_iterator n;
-    for (ball_it i = begin(); i != end(); i++) {
-      ball_t *b = *i;
+    for (ball_t *b : *this) {
       if (b->is(green)) {
         n = node_name.find(b->uniq);
         if (n != node_name.end()) {
@@ -127,17 +126,17 @@ class pocket_t : public std::set<ball_t*,ball_order> {
   };
   //! retrieve the first ball of the specified color.
   ball_t* ball (const color_t c) const {
-    for (ball_it i = begin(); i != end(); i++) {
-      if ((*i)->color == c) return *i;
+    for (ball_t *b : *this) {
+      if (b->color == c) return b;
     }
     err("in '%s' (%s line %d): no ball of color %s", // # nocov
         __func__,__FILE__,__LINE__,colores[c]);      // # nocov
     return 0;
   };
   //! return a pointer to another ball
   ball_t* other (const ball_t *b) const {
-    for (ball_it i = begin(); i != end(); i++) {
-      if (*i != b) return *i;
+    for (ball_t *a : *this) {
+      if (a != b) return a;
     }
     err("error in '%s' (%s line %d): there is no other.", // # nocov
         __func__,__FILE__,__LINE__);                      // # nocov
@@ -169,8 +168,8 @@ class pocket_t : public std::set<ball_t*,ball_order> {
   std::string yaml (std::string tab = "") const {
     std::string o = "";
     std::string t = tab + "  ";
-    for (ball_it i = begin(); i != end(); i++) {
-      o += tab + "- " + (*i)->yaml(t);
+    for (ball_t *b : *this) {
+      o += tab + "- " + b->yaml(t);
     }
     return o;
   };