Clean up

pbs-assess · May 26, 2024 · a531191 · a531191
1 parent c78771b
commit a531191
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diff --git a/R/cross-val.R b/R/cross-val.R
@@ -359,9 +359,6 @@ sdmTMB_cv <- function(
         weights = weights, previous_fit = if (use_initial_fit) fit1 else NULL
       ), dot_args)
       object <- do.call(sdmTMB, args)
-      # if (max(object$gradients) > 0.01) {
-      # object <- run_extra_optimization(object, nlminb_loops = 1L, newton_loops = 0L)
-      # }
     }
 
     if (lfo) {

diff --git a/R/index.R b/R/index.R
@@ -238,8 +238,6 @@ get_generic <- function(obj, value_name, bias_correct = FALSE, level = 0.95,
   lu <- obj$fit_obj$time_lu
   tt <- lu$time_from_data[match(ii, lu$year_i)]
   d[[time_name]] <- tt
-  # d$max_gradient <- max(conv$final_grads)
-  # d$bad_eig <- conv$bad_eig
 
   # remove padded extra time fake data:
   if (!is.null(obj$fake_nd)) {

diff --git a/R/priors.R b/R/priors.R
@@ -103,7 +103,6 @@ sdmTMBpriors <- function(
 #' @examples
 #' normal(0, 1)
 normal <- function(location = 0, scale = 1) {
-  # assert_that(all(location[!is.na(location)] == 0))
   assert_that(all(scale[!is.na(scale)] > 0))
   assert_that(length(location) == length(scale))
   assert_that(sum(is.na(location)) == sum(is.na(scale)))