Add message if limits set with optimHess #394

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: sdmTMB
 Title: Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
-Version: 0.6.0.9022
+Version: 0.6.0.9023
 Authors@R: c(
     person(c("Sean", "C."), "Anderson", , "[email protected]",
            role = c("aut", "cre"),

NEWS.md

@@ -1,5 +1,7 @@
 # sdmTMB (development version)
 
+* Warn if parameter limits are set with `newton_loops > 0`. #394
+
 * Allow for specifying only lower or upper limits. #394
 
 * Add vignette on multispecies models with sdmTMB (or any case where one wants

R/fit.R

@@ -1486,6 +1486,11 @@ sdmTMB <- function(
       tmb_opt[["evaluations"]] <- tmb_opt[["evaluations"]] + temp[["evaluations"]]
     }
   }
+  if (!is.null(control$upper) || !is.null(control$lower)) {
+    if (newton_loops > 0) {
+      cli_inform("Upper or lower limits were set. `stats::optimHess()` will ignore these limits. Set `control = sdmTMBcontrol(newton_loops = 0)` to avoid the `stats::optimHess()` optimization if desired.")
+    }
+  }
   if (newton_loops > 0) {
     if (!silent) cli_inform("attempting to improve convergence with optimHess\n")
     for (i in seq_len(newton_loops)) {

R/utils.R

@@ -47,7 +47,9 @@
 #' @param lower An optional named list of lower bounds within the optimization.
 #'   Parameter vectors with the same name (e.g., `b_j` or `ln_kappa` in some
 #'   cases) can be specified as a numeric vector. E.g.
-#'   `lower = list(b_j = c(-5, -5))`.
+#'   `lower = list(b_j = c(-5, -5))`. Note that [stats::optimHess()] does not
+#'   implement lower and upper bounds, so you must set `newton_loops = 0` if
+#'   setting limits.
 #' @param upper An optional named list of upper bounds within the optimization.
 #' @param censored_upper An optional vector of upper bounds for
 #'   [sdmTMBcontrol()]. Values of `NA` indicate an unbounded right-censored to