Fix #389

Author: seananderson

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9014
+Version: 0.6.0.9015
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "sean@seananderson.ca",
            role = c("aut", "cre"),

NEWS.md

@@ -1,5 +1,8 @@
 # sdmTMB (development version)
 
+* Fix bug in `est` column when predicting on new data with Poisson-link
+  delta models with `type = "link"` and `re_form = NA`. #389
+
 * Fix bug in `s95` param reporting from the `tidy()` method. `s95` is present
   in the logistic threshold models. The model itself was fine but the `s95`
   parameter was supposed to be reported by `tidy()` as a combination of two 

R/predict.R

@@ -785,14 +785,28 @@ predict.sdmTMB <- function(object, newdata = NULL,
         if (type == "response") {
           nd$est1 <- object$family[[1]]$linkinv(r$proj_fe[,1])
           nd$est2 <- object$family[[2]]$linkinv(r$proj_fe[,2])
-          nd$est <- nd$est1 * nd$est2
+          if (object$tmb_data$poisson_link_delta) {
+            .n <- nd$est1 # expected group density (already exp())
+            .p <- 1 - exp(-.n) # expected encounter rate
+            .w <- nd$est2 # expected biomass per group (already exp())
+            .r <- (.n * .w) / .p # (n * w)/p # positive expectation
+            nd$est1 <- .p # expected encounter rate
+            nd$est2 <- .r # positive expectation
+            nd$est <- .n * .w # expected combined value
+          } else {
+            nd$est <- nd$est1 * nd$est2
+          }
         } else {
           nd$est1 <- r$proj_fe[,1]
           nd$est2 <- r$proj_fe[,2]
           if (is.na(model)) {
             p1 <- object$family[[1]]$linkinv(r$proj_fe[,1])
             p2 <- object$family[[2]]$linkinv(r$proj_fe[,2])
-            nd$est <- object$family[[2]]$linkfun(p1 * p1)
+            if (object$tmb_data$poisson_link_delta) {
+              nd$est <- nd$est1 + nd$est2
+            } else {
+              nd$est <- object$family[[2]]$linkfun(p1 * p1)
+            }
             if (se_fit) {
               nd$est <- sr_est_rep$proj_rf_delta
               nd$est_se <- sr_se_rep$proj_rf_delta