streamline curtail

Author: kingaa

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.14.9.0
+Version: 0.14.9.1
 Date: 2024-12-02
 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"))

TODO.md

@@ -1,9 +1,9 @@
 ## To-do List
 
-- curtail from the left also
-- LBDP and SIRS into new format
+- ~~~curtail from the left also~~~
+- ~~~LBDP and SIRS into new format~~~
 - use integer time?
 
-- trap Newick errors in `parse_newick`
 - runtime yaml parser
+- trap Newick errors in `parse_newick`
 - segmented virus simulator

src/genealogy.h

@@ -77,7 +77,7 @@ class genealogy_t : public nodeseq_t {
   //! binary serialization
   friend raw_t* operator>> (const genealogy_t& G, raw_t* o) {
     name_t A[3]; A[0] = magic; A[1] = G._unique; A[2] = name_t(G._ndeme);
-    slate_t B[2]; B[0] = G._t0; B[1] = G._time;
+    slate_t B[2]; B[0] = G.timezero(); B[1] = G.time();
     memcpy(o,A,sizeof(A)); o += sizeof(A);
     memcpy(o,B,sizeof(B)); o += sizeof(B);
     return reinterpret_cast<const nodeseq_t&>(G) >> o;
@@ -93,7 +93,7 @@ class genealogy_t : public nodeseq_t {
       err("in %s (%s line %d) corrupted genealogy serialization.",
           __func__,__FILE__,__LINE__);
     G._unique = A[1]; G._ndeme = size_t(A[2]);
-    G._t0 = B[0]; G._time = B[1];
+    G.timezero() = B[0]; G.time() = B[1];
     return o >> reinterpret_cast<nodeseq_t&>(G);
   };
 
@@ -154,6 +154,10 @@ class genealogy_t : public nodeseq_t {
   slate_t time (void) const {
     return _time;
   };
+  //! view/set zero time.
+  slate_t& timezero (void) {
+    return _t0;
+  };
   //! get zero time.
   slate_t timezero (void) const {
     return _t0;
@@ -523,7 +527,7 @@ class genealogy_t : public nodeseq_t {
         if (!empty()) p = back();
       }
     }
-    if (tnew < time()) _time = tnew;
+    time() = tnew;
     if (!empty() && troot > timezero()) {
       node_t *p = front();
       node_t *q;
@@ -563,7 +567,7 @@ class genealogy_t : public nodeseq_t {
       }
       sort();
     }
-    if (troot > timezero()) _t0 = troot;
+    if (troot > timezero()) timezero() = troot;
   };
   //! merge two genealogies:
   //! 1. the node-sequences are merged;

src/parse.cc

@@ -18,11 +18,7 @@ extern "C" {
     genealogy_t G(t0);
     G.parse(x,t0);
     if (!ISNA(tf)) {
-      if (G.time() > tf) {
-        G.curtail(tf,t0);
-      } else {
-        G.time() = tf;
-      }
+      G.curtail(tf,t0);
     }
     G.trace_lineages();
     UNPROTECT(3);

tests/parse.Rout.save

@@ -136,7 +136,7 @@ Error : in 'scan_tree': premature end of Newick string.
 +   r"{((o_9_1:1.000000,b_3_2:0.500000,o_1_3:1.000000)m_0_0:0.000000);}" |>
 +      parse_newick()
 + )
-Error : in 'scan_label' (genealogy.h line 607): invalid Newick label: expected one of 'b','g','m', or 'o', got ';'.
+Error : in 'scan_label' (genealogy.h line 611): invalid Newick label: expected one of 'b','g','m', or 'o', got ';'.
 > 
 > try(
 +   r"{(o_9_1:1.000000,b_3_2:0.500000,o_1_3:1.000000)m_0_0:0.000000);}" |>
@@ -167,13 +167,13 @@ Error : in 'parse': invalid Newick string.
 +   r"{(o_9_1:1.000000)_g_1_3:1.000000)m_0_0:0.000000;}" |>
 +      parse_newick()
 + )
-Error : in 'scan_label' (genealogy.h line 607): invalid Newick label: expected one of 'b','g','m', or 'o', got '_'.
+Error : in 'scan_label' (genealogy.h line 611): invalid Newick label: expected one of 'b','g','m', or 'o', got '_'.
 > 
 > try(
 +   r"{(o_9_1:1.000000)z_1_3:1.000000)m_0_0:0.000000;}" |>
 +      parse_newick()
 + )
-Error : in 'scan_label' (genealogy.h line 607): invalid Newick label: expected one of 'b','g','m', or 'o', got 'z'.
+Error : in 'scan_label' (genealogy.h line 611): invalid Newick label: expected one of 'b','g','m', or 'o', got 'z'.
 > 
 > r"{((,o_9_1:1.000000,)g_1_3:1.000000)m_0_0:0.000000;}" |>
 +    parse_newick() |>
@@ -212,7 +212,7 @@ Error : in 'parse': invalid Newick string: unbalanced parentheses.
 +   r"{((((o_9_1:1.000000)g_1_3:1.000000)m_0_0:0.000000)g_3:22)()))));}" |>
 +      parse_newick()
 + )
-Error : in 'scan_label' (genealogy.h line 607): invalid Newick label: expected one of 'b','g','m', or 'o', got '('.
+Error : in 'scan_label' (genealogy.h line 611): invalid Newick label: expected one of 'b','g','m', or 'o', got '('.
 > 
 > try(
 +   r"{(o_9_1:1.000000,b_1_3)m_0_0:0.000000;}" |>
@@ -258,7 +258,7 @@ $newick
 +   r"{(o_a9_1:1.000000,b_0_0:3)m_0_0:0.000000,b_____2:17;}" |>
 +      parse_newick()
 + )
-Error : in 'scan_label' (genealogy.h line 624): invalid Newick format: deme should be indicated with an integer.
+Error : in 'scan_label' (genealogy.h line 628): invalid Newick format: deme should be indicated with an integer.
 > 
 > try(
 +   r"{(o_9_1:1.000000,b_0_0:3)m_0_0(:0.500000,b_____2:17;}" |>
@@ -270,7 +270,7 @@ Error : in 'scan_label': invalid Newick format: missing or invalid branch length
 +   r"{(o_9_1:1.000000,b_0_0:3)m_)0_0:0.500000,b_____2:17;}" |>
 +      parse_newick()
 + )
-Error : in 'scan_label' (genealogy.h line 614): invalid Newick format.
+Error : in 'scan_label' (genealogy.h line 618): invalid Newick format.
 > 
 > try(
 +   r"{(o_9_1:1.000000,b_0_0:3)m_0_0:(0.000000,b_____2:17;}" |>
@@ -321,7 +321,7 @@ $newick
 +   r"{(o_9_1:1.000000,b_0_0:3))m_0_0:0.000000,b_____2:17;}" |>
 +      parse_newick()
 + )
-Error : in 'scan_label' (genealogy.h line 607): invalid Newick label: expected one of 'b','g','m', or 'o', got ')'.
+Error : in 'scan_label' (genealogy.h line 611): invalid Newick label: expected one of 'b','g','m', or 'o', got ')'.
 > 
 > try(
 +   r"{(o_9_1:1.000000,b_0_0:3)m_0_0:0.000000,b_____2:17))));}" |>
@@ -359,7 +359,7 @@ Error : in 'scan_label': invalid Newick format: missing or invalid branch length
 +      parse_newick() |>
 +      newick(prune=FALSE,obscure=FALSE)
 + )
-Error : in 'scan_label' (genealogy.h line 593): invalid Newick format: empty label.
+Error : in 'scan_label' (genealogy.h line 597): invalid Newick format: empty label.
 > 
 > dev.off()
 null device