NEWS.Rmd

---
title: "NEWS"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Version 1.0.2

Changes to `SAM2FLStock`

* Fixed bug when observations in the SAM model fit do not include years but instead an index for the years (1, 2, 3, ...).

## Version 1.0.1

Changes to `SAM2FLStock`

* This function can now handle multi-fleet SAM model fits. An example is given in the documentation for this method (see `?SAM2FLStock`).

* Added `stock_only` argument. If set to `TRUE`, catch data (numbers, weights) are ignored and only stock data (numbers, SSB, etc.) are returned.

## Version 1.0

### Changes since version 0.x

Changes to `SAM2FLStock`

* Fix when SAM model fit included age 0 but without catches for this age.

* Fix setting of plusgroup.

* New arguments `mat_est`, `stock.wt_est`, `catch.wt_est`, `m_est` (logical `TRUE`/`FALSE`) for returning estimates of biological data from SAM, if they are estimated by SAM.

* New argument `spinoutyear` (logical `TRUE`/`FALSE`) to include/exclude estimates of biological data from SAM beyond last data year.

* Generic methods for `SAM2FLStock` updated when argument `stk` is provided as a template. In the returned output, `stk` is used as template and all slots are updated, instead of only those corresponding to catch, fishing mortality and stock size.

Changes to `SAM_uncertainty`

* Name of output list element with catch numbers including uncertainty changed from `catch_n` to `catch.n` so that it follows the same convention as `stock.n`.

General changes

* Updated help files.