From 8fbcc17ff50bbd16d6c0fdd4daf06713e84aae01 Mon Sep 17 00:00:00 2001
From: Iago Mosqueira <iagomosqueira@users.noreply.github.com>
Date: Sun, 1 Dec 2024 19:54:23 +0100
Subject: [PATCH] Added full dependencies to TMB, spict and stockassessment

---
 FLfse/DESCRIPTION | 11 +++++------
 FLfse/NAMESPACE   |  3 +++
 FLfse/R/FLfse.R   | 13 +++++++++++++
 FLfse/R/sam.R     |  2 +-
 4 files changed, 22 insertions(+), 7 deletions(-)

diff --git a/FLfse/DESCRIPTION b/FLfse/DESCRIPTION
index e6daa74..e52d488 100644
--- a/FLfse/DESCRIPTION
+++ b/FLfse/DESCRIPTION
@@ -19,12 +19,11 @@ Imports:
     foreach,
     stats,
     utils,
-    FLCore (>= 2.6.5)
-Depends:
-Suggests: 
     spict (>= 1.2.1),
+    FLCore (>= 2.6.5),
     stockassessment (>= 0.9.0),
-    TMB,
-    mgcv,
+    TMB
+Depends:
+Suggests: 
     doParallel
-RoxygenNote: 7.1.1
+RoxygenNote: 7.3.2
diff --git a/FLfse/NAMESPACE b/FLfse/NAMESPACE
index e29527a..7575579 100644
--- a/FLfse/NAMESPACE
+++ b/FLfse/NAMESPACE
@@ -8,6 +8,9 @@ export(getpars)
 import(FLCore)
 import(foreach)
 import(methods)
+import(spict)
+import(stockassessment)
+importFrom(TMB,sdreport)
 importFrom(stats,complete.cases)
 importFrom(stats,plogis)
 importFrom(stats,weighted.mean)
diff --git a/FLfse/R/FLfse.R b/FLfse/R/FLfse.R
index 4cf4d55..b23ab87 100644
--- a/FLfse/R/FLfse.R
+++ b/FLfse/R/FLfse.R
@@ -18,3 +18,16 @@ NULL
 ### import functions from stats
 #' @importFrom stats complete.cases plogis weighted.mean
 NULL
+
+### import functions from TMB
+#' @importFrom TMB sdreport
+NULL
+
+### import all functionality from spict
+#' @import spict
+NULL
+
+### import all functionality from stockassessment
+#' @import stockassessment
+NULL
+
diff --git a/FLfse/R/sam.R b/FLfse/R/sam.R
index 815fa98..8e6ef14 100644
--- a/FLfse/R/sam.R
+++ b/FLfse/R/sam.R
@@ -1508,7 +1508,7 @@ setMethod(f = "SAM_uncertainty",
   ##Resample estimated values to get N, F and q
 
   ### calculate standard deviations of model parameters
-  . <- capture.output(sds <- TMB::sdreport(obj = fit$obj,
+  . <- capture.output(sds <- sdreport(obj = fit$obj,
                                            par.fixed = fit$opt$par,
                                            getJointPrecision = TRUE))
   if (isTRUE(print_screen)) cat(paste0(., sep = "\n"))