Return to not printing 'zero' sigmas

Always return sigma_O
pbs-assess · Oct 23, 2023 · f58edd8 · f58edd8
1 parent 06b918a
commit f58edd8
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/R/tidy.R b/R/tidy.R
@@ -198,7 +198,7 @@ tidy.sdmTMB <- function(x, effects = c("fixed", "ran_pars", "ran_vals"), model =
       if (this == "tau_V") this <- "sigma_V"
       this_se <- as.numeric(se[[this]])
       this_est <- as.numeric(est[[this]])
-      if (length(this_est)) {
+      if (length(this_est) && !(all(this_se == 0) && all(this_est == 0))) {
         out_re[[i]] <- data.frame(
           term = i, estimate = this_est, std.error = this_se,
           conf.low = exp(.e - crit * .se),

diff --git a/src/sdmTMB.cpp b/src/sdmTMB.cpp
@@ -302,23 +302,23 @@ Type objective_function<Type>::operator()()
     if (include_spatial(m)) {
       sigma_O(0,m) = sdmTMB::calc_rf_sigma(ln_tau_O(m), ln_kappa(0,m));
       log_sigma_O(0,m) = log(sigma_O(0,m));
-      REPORT(sigma_O);
-      ADREPORT(sigma_O);
-      ADREPORT(log_sigma_O);
     }
     if (spatial_covariate) {
       for (int z = 0; z < n_z; z++) {
         sigma_Z(z,m) = sdmTMB::calc_rf_sigma(ln_tau_Z(z,m), ln_kappa(0,m));
-        REPORT(sigma_Z);
-        ADREPORT(sigma_Z);
-        ADREPORT(log_sigma_Z);
       }
     for (int z = 0; z < n_z; z++)
       for (int m = 0; m < n_m; m++)
         log_sigma_Z(z,m) = log(sigma_Z(z,m));
-        ADREPORT(log_sigma_Z);
     }
   }
+  REPORT(sigma_Z);
+  ADREPORT(sigma_Z);
+  ADREPORT(log_sigma_Z);
+  REPORT(sigma_O);
+  ADREPORT(sigma_O);
+  ADREPORT(log_sigma_O);
+  ADREPORT(log_sigma_Z);
 
   // TODO can we not always run this for speed?
   //vector<Type> sigma_E(n_m);