tweak two-species filter

Author: kingaa

DESCRIPTION

@@ -2,7 +2,7 @@ Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
 Version: 0.16.0.0
-Date: 2026-01-30
+Date: 2026-02-04
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",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 +1,6 @@
 ## To-do List
 
-- ~~~curtail from the left also~~~
-- ~~~LBDP and SIRS into new format~~~
 - use integer time?
-
 - runtime yaml parser
 - trap Newick errors in `parse_newick`
 - segmented virus simulator

src/twospecies_pomp.c

@@ -119,25 +119,25 @@ static double event_rates
   // total pi = (I1-0.5*ell1)/I1
   assert(S2>=0 && I1>=ell1 && ell1>=0);
   alpha = (N1 > 0) ? Beta21*S2*I1/N1 : 0;
-  pi = (I1 > 0) ? (I1-0.5*ell1)/I1 : 0;
+  pi = (I1 > 0) ? (I1-0.5*ell1)/I1 : 1;
   event_rate += (*rate = alpha*pi); rate++;
   *logpi = log(pi); logpi++;
   assert(R_FINITE(event_rate));
   // 3: Trans_21, s = (0,1)
   // s = (0,1): pi = 1/(2*I1), m = ell1
-  pi = 1-pi;
+  pi = (I1 > 0) ? 1-pi : 1;
   event_rate += (*rate = alpha*pi); rate++;
   *logpi = log(pi)-log(ell1); logpi++;
   assert(R_FINITE(event_rate));
   // 4: Trans_12, s = (0,0),(0,1)
   assert(S1>=0 && I2>=ell2 && ell2>=0);
   alpha = (N2 > 0) ? Beta12*S1*I2/N2 : 0;
-  pi = (I2 > 0) ? (I2-ell2*0.5)/I2 : 0;
+  pi = (I2 > 0) ? (I2-ell2*0.5)/I2 : 1;
   event_rate += (*rate = alpha*pi); rate++;
   *logpi = log(pi); logpi++;
   assert(R_FINITE(event_rate));
   // 5: Trans_12, s = (1,0)
-  pi = 1-pi;
+  pi = (I2 > 0) ? 1-pi : 0;
   event_rate += (*rate = alpha*pi); rate++;
   *logpi = log(pi)-log(ell2); logpi++;
   assert(R_FINITE(event_rate));