fix ll-reset error

Author: kingaa

src/lbdp_pomp.c

@@ -90,16 +90,16 @@ void lbdp_gill
   assert(parent<=nnode);
 #endif
 
+  ll = 0;
+
   // singular portion of filter equation
   switch (nodetype[parent]) {
   default:                      // non-genealogical event
     break;
   case 0:                       // root
-    ll = 0;
     ell += 1;
     break;
   case 1:                       // sample
-    ll = 0;
     assert(n >= ell);
     assert(ell >= 0);
     if (sat[parent] == 1) {     // s=1

src/seirs_pomp.c

@@ -168,12 +168,13 @@ void seirs_gill
   int parcol = color[parlin];
   assert(parlin >= 0 && parlin < nsample);
 
+  ll = 0;
+
   // singular portion of filter equation
   switch (nodetype[parent]) {
   default:                      // non-genealogical event
     break;
-  case 0:            // root
-    ll = 0;
+  case 0:                       // root
     // color lineages by sampling without replacement
     assert(sat[parent]==1);
     int c = child[index[parent]];
@@ -204,7 +205,6 @@ void seirs_gill
     }
     break;
   case 1:                       // sample
-    ll = 0;
     // If parent is not in deme I, likelihood = 0.
     if (parcol != 1) {
       ll += R_NegInf;
@@ -227,7 +227,6 @@ void seirs_gill
     color[parlin] = R_NaReal;
     break;
   case 2:                       // branch point s=(1,1)
-    ll = 0;
     // If parent is not in deme I, likelihood = 0.
     if (parcol != 1) {
       ll += R_NegInf;

src/sirs_pomp.c

@@ -110,16 +110,16 @@ void sirs_gill
   assert(parent<=nnode);
 #endif
 
+  ll = 0;
+
   // singular portion of filter equation
   switch (nodetype[parent]) {
   default:                      // non-genealogical event
     break;
   case 0:                       // root
-    ll = 0;
     ellI += 1;
     break;
   case 1:                       // sample
-    ll = 0;
     assert(I >= ellI);
     assert(ellI >= 0);
     if (sat[parent] == 1) {
@@ -133,7 +133,6 @@ void sirs_gill
     }
     break;
   case 2:                       // branch point s=(1,1)
-    ll = 0;
     assert(S >= 0);
     assert(I >= 0);
     assert(ellI > 0);

src/twospecies_pomp.c

@@ -322,12 +322,13 @@ void twospecies_gill
   assert(nearbyint(N2)==nearbyint(S2+I2+R2));
   assert(check_color(color,nsample,ell1,ell2));
 
+  ll = 0;
+
   // singular portion of filter equation
   switch (nodetype[parent]) {
   default:                      // non-genealogical event
     break;
   case 0:                       // root
-    ll = 0;
     // color lineages by sampling without replacement
     assert(sat[parent]==1);
     int c = child[index[parent]];
@@ -361,7 +362,9 @@ void twospecies_gill
     assert(check_color(color,nsample,ell1,ell2));
     break;
   case 1:                       // sample
-    ll = 0;
+    if (parcol != deme) { // parent color does not match the observed deme
+      ll += R_NegInf;
+    }
     if (sat[parent] == 0) {     // s=(0,0)
       if (parcol == host1) {
         ell1 -= 1;
@@ -404,7 +407,6 @@ void twospecies_gill
     assert(check_color(color,nsample,ell1,ell2));
     break;
   case 2:                       // branch point
-    ll = 0;
     assert(sat[parent]==2);
     if (parcol == host1) {      // parent is in I1
       assert(S1>=0 && S2 >=0 && I1>=ell1 && ell1>=0);