gadget-framework / gadget3

TMB-based gadget implemtation
GNU General Public License v2.0
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Defaults for g3a_renewal_normalparam #79

Closed lentinj closed 11 months ago

lentinj commented 1 year ago
diff --git a/R/action_renewal.R b/R/action_renewal.R
index 8d6ceed..3ea0942 100644
--- a/R/action_renewal.R
+++ b/R/action_renewal.R
@@ -139,8 +139,9 @@ g3a_renewal <- function (stock, num_f, wgt_f, run_f = ~TRUE, run_at = 8) {
 # Steps to set up renewal of stocks on any stock
 g3a_renewal_normalparam <- function (
         stock,
-        factor_f,
-        mean_f,
+        factor_f = g3_parameterized('rec', by_stock = by_stock, by_year = TRUE,
+                                    scale = 'rec.scalar'),
+        mean_f = g3a_renewal_vonb(by_stock = by_stock),
         stddev_f = g3_parameterized('rec.sd', by_stock = by_stock, by_age = by_age),
         alpha_f = g3_parameterized('walpha', by_stock = wgt_by_stock),
         beta_f = g3_parameterized('wbeta', by_stock = wgt_by_stock),
diff --git a/R/step.R b/R/step.R
index 96e9e91..c1eb610 100644
--- a/R/step.R
+++ b/R/step.R
@@ -103,6 +103,7 @@ g3_step <- function(step_f, recursing = FALSE, orig_env = environment(step_f)) {
             for (var_name in all_undefined_vars(f)) {  # NB: all_undefined_vars will get rid of definitions from previous loop
                 defn <- environment(f)[[var_name]]
                 if (!is.call(defn)) next
+                # TODO: We need to select formula dependents here and consider the recursive all_undefined_vars()
                 if (!isTRUE(depend_vars) && !('stock_ss' %in% all.names(defn)) && length(intersect(all_undefined_vars(defn), depend_var
                     # There's a depend vars, but this formula doesn't depend on any of them, optionally modify and return
                     if (!is.null(filter_fn)) {
lentinj commented 11 months ago

Superseded by https://github.com/gadget-framework/gadget3/issues/118