Merge pull request #205 from mbjoseph/fix-cmr-loglik

bbbales2 · web-flow · commit ffd35e915cd2 · 2021-03-01T11:34:28.000-05:00
Fix capture-recapture likelihoods
diff --git a/BPA/Ch.06/Mb.stan b/BPA/Ch.06/Mb.stan
@@ -50,7 +50,7 @@ model {
               + bernoulli_lpmf(y[i] |  p_eff[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 |  omega)   // z[i] == 1
-                            + bernoulli_lpmf(0 | p_eff[i]),
+                            + bernoulli_lpmf(y[i] | p_eff[i]),
                             bernoulli_lpmf(0 | omega));  // z[i] == 0
 }
 
diff --git a/BPA/Ch.06/Mt.stan b/BPA/Ch.06/Mt.stan
@@ -34,7 +34,7 @@ model {
               + bernoulli_lpmf(y[i] | p);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_lpmf(0 | p),
+                            + bernoulli_lpmf(y[i] | p),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
 }
 
diff --git a/BPA/Ch.06/MtX.stan b/BPA/Ch.06/MtX.stan
@@ -54,7 +54,7 @@ model {
               + bernoulli_logit_lpmf(y[i] | logit_p[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_logit_lpmf(0 | logit_p[i]),
+                            + bernoulli_logit_lpmf(y[i] | logit_p[i]),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
 }
 
diff --git a/BPA/Ch.06/Mtbh.stan b/BPA/Ch.06/Mtbh.stan
@@ -59,7 +59,7 @@ model {
               + bernoulli_logit_lpmf(y[i] | logit_p[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_logit_lpmf(0 | logit_p[i]),
+                            + bernoulli_logit_lpmf(y[i] | logit_p[i]),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
 }
 
diff --git a/BPA/Ch.06/Mth.stan b/BPA/Ch.06/Mth.stan
@@ -51,7 +51,7 @@ model {
               + bernoulli_logit_lpmf(y[i] | logit_p[i]);
     else // s[i] == 0
       target += log_sum_exp(bernoulli_lpmf(1 | omega)   // z[i] == 1
-                            + bernoulli_logit_lpmf(0 | logit_p[i]),
+                            + bernoulli_logit_lpmf(y[i] | logit_p[i]),
                             bernoulli_lpmf(0 | omega)); // z[i] == 0
   }
 }

Original file line number	Diff line number	Diff line change
`@@ -50,7 +50,7 @@ model {`
`50`	`50`	`+ bernoulli_lpmf(y[i] \| p_eff[i]);`
`51`	`51`	`else // s[i] == 0`
`52`	`52`	`target += log_sum_exp(bernoulli_lpmf(1 \| omega) // z[i] == 1`
`53`		`- + bernoulli_lpmf(0 \| p_eff[i]),`
	`53`	`+ + bernoulli_lpmf(y[i] \| p_eff[i]),`
`54`	`54`	`bernoulli_lpmf(0 \| omega)); // z[i] == 0`
`55`	`55`	`}`
`56`	`56`
Original file line number	Diff line number	Diff line change
`@@ -34,7 +34,7 @@ model {`
`34`	`34`	`+ bernoulli_lpmf(y[i] \| p);`
`35`	`35`	`else // s[i] == 0`
`36`	`36`	`target += log_sum_exp(bernoulli_lpmf(1 \| omega) // z[i] == 1`
`37`		`- + bernoulli_lpmf(0 \| p),`
	`37`	`+ + bernoulli_lpmf(y[i] \| p),`
`38`	`38`	`bernoulli_lpmf(0 \| omega)); // z[i] == 0`
`39`	`39`	`}`
`40`	`40`
Original file line number	Diff line number	Diff line change
`@@ -54,7 +54,7 @@ model {`
`54`	`54`	`+ bernoulli_logit_lpmf(y[i] \| logit_p[i]);`
`55`	`55`	`else // s[i] == 0`
`56`	`56`	`target += log_sum_exp(bernoulli_lpmf(1 \| omega) // z[i] == 1`
`57`		`- + bernoulli_logit_lpmf(0 \| logit_p[i]),`
	`57`	`+ + bernoulli_logit_lpmf(y[i] \| logit_p[i]),`
`58`	`58`	`bernoulli_lpmf(0 \| omega)); // z[i] == 0`
`59`	`59`	`}`
`60`	`60`
Original file line number	Diff line number	Diff line change
`@@ -59,7 +59,7 @@ model {`
`59`	`59`	`+ bernoulli_logit_lpmf(y[i] \| logit_p[i]);`
`60`	`60`	`else // s[i] == 0`
`61`	`61`	`target += log_sum_exp(bernoulli_lpmf(1 \| omega) // z[i] == 1`
`62`		`- + bernoulli_logit_lpmf(0 \| logit_p[i]),`
	`62`	`+ + bernoulli_logit_lpmf(y[i] \| logit_p[i]),`
`63`	`63`	`bernoulli_lpmf(0 \| omega)); // z[i] == 0`
`64`	`64`	`}`
`65`	`65`
Original file line number	Diff line number	Diff line change
`@@ -51,7 +51,7 @@ model {`
`51`	`51`	`+ bernoulli_logit_lpmf(y[i] \| logit_p[i]);`
`52`	`52`	`else // s[i] == 0`
`53`	`53`	`target += log_sum_exp(bernoulli_lpmf(1 \| omega) // z[i] == 1`
`54`		`- + bernoulli_logit_lpmf(0 \| logit_p[i]),`
	`54`	`+ + bernoulli_logit_lpmf(y[i] \| logit_p[i]),`
`55`	`55`	`bernoulli_lpmf(0 \| omega)); // z[i] == 0`
`56`	`56`	`}`
`57`	`57`	`}`