From d5cfce1cfdb0b1471a9035460be31091949b3148 Mon Sep 17 00:00:00 2001
From: Iago Mosqueira <iago@mosqueira.eu>
Date: Tue, 11 Oct 2022 22:59:04 +0200
Subject: [PATCH] Avoid issues with harvest iters

---
 R/flxsa.R     | 5 +++--
 R/xsa.sa.R    | 4 ++++
 man/xsa.sa.Rd | 5 +++++
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/R/flxsa.R b/R/flxsa.R
index beb3ae5..1a67c12 100644
--- a/R/flxsa.R
+++ b/R/flxsa.R
@@ -159,7 +159,8 @@ setGeneric("FLXSA", function(stock, indices, ...)
 
 setMethod("FLXSA", signature(stock="FLStock", indices="FLIndex"),
   function(stock, indices, control=FLXSA.control(), diag.flag=TRUE) {
-    FLXSA(stock=stock, indices=FLIndices(indices), control=control, diag.flag=diag.flag)
+    FLXSA(stock=stock, indices=FLIndices(indices), control=control,
+      diag.flag=diag.flag)
   }
 )
 
@@ -291,7 +292,7 @@ setMethod("FLXSA", signature(stock="FLStock", indices="FLIndices"),
         }
       }
 
-      dimnames(res@harvest)$iter <- dimnames(harvest(stock))$iter
+      dimnames(res@harvest)$iter <- dimnames(stock.n(stock))$iter
       dimnames(res@stock.n)$iter <- dimnames(stock.n(stock))$iter
 
       res@harvest@units <- "f"
diff --git a/R/xsa.sa.R b/R/xsa.sa.R
index b5dbe48..d37ebbc 100644
--- a/R/xsa.sa.R
+++ b/R/xsa.sa.R
@@ -19,6 +19,10 @@
 #' @param idx An FLIndices.
 #'
 #' @return A list containing the updated FLStock, and the tracking FLQuant.
+#' @examples
+#' data(ple4)
+#' data(ple4.index)
+#' xsa.sa(stk=ple4, idx=ple4.index, args=list(ay=2018), tracking=FLQuant())
 
 xsa.sa <- function(stk, idx, args, tracking, ...) {
 
diff --git a/man/xsa.sa.Rd b/man/xsa.sa.Rd
index ed1cc13..8e10184 100644
--- a/man/xsa.sa.Rd
+++ b/man/xsa.sa.Rd
@@ -21,3 +21,8 @@ a module for FLXSA.
 As a flag for convergence, the returned tracking FLQuant contains the number
 of maximum number of iterations (maxit).
 }
+\examples{
+data(ple4)
+data(ple4.index)
+xsa.sa(stk=ple4, idx=ple4.index, args=list(ay=2018), tracking=FLQuant())
+}