Multiply size for binomial simulate w. no obs error #465

Author: seananderson

R/tmb-sim.R

@@ -483,14 +483,6 @@ simulate.sdmTMB <- function(object, nsim = 1L, seed = sample.int(1e6, 1L),
 
   if (!return_tmb_report) {
     if (is_delta(object)) {
-      if (object$family[[1]]$family == "binomial" &&
-          object$family$type == "standard" &&
-          !observation_error) {
-        ret <- lapply(ret, function(.x) {
-          .x[,1] <- stats::plogis(.x[,1]) # using robust dbinom in logit space
-          .x
-        })
-      }
       if (is.na(model[[1]])) {
         ret <- lapply(ret, function(.x) .x[,1] * .x[,2])
       } else if (model[[1]] == 1) {
@@ -502,13 +494,6 @@ simulate.sdmTMB <- function(object, nsim = 1L, seed = sample.int(1e6, 1L),
       }
     }
 
-    if (!is_delta(object) && !observation_error) {
-      if (object$family$family == "binomial") {
-        # using robust dbinom in logit space
-        ret <- lapply(ret, function(.x) stats::plogis(.x))
-      }
-    }
-
     ret <- do.call(cbind, ret)
 
     if (!is.null(newdata)) {

src/sdmTMB.cpp

@@ -885,7 +885,11 @@ Type objective_function<Type>::operator()()
   if (!sim_obs) {
     for (int m = 0; m < n_m; m++) {
       for (int i = 0; i < n_i; i++) {
-        y_i(i,m) = mu_i(i,m);
+        if (family(m) == binomial_family && !poisson_link_delta) {
+          y_i(i,m) = invlogit(mu_i(i,m)) * size(i); // hardcoded invlogit b/c mu_i in logit space
+        } else {
+          y_i(i,m) = mu_i(i,m);
+        }
       }
     }
   }