---
title: "Technical Manual for the mse FLR/a4a package"
author:
  - "Iago MOSQUEIRA (WMR)"
  - "Ernesto JARDIM (MSC)"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteIndexEntry{mse}
  %\VignetteEncoding{UTF-8}
bibliography: bibliography.bib
tags: [MSE FLR]
license: Creative Commons Attribution-ShareAlike 4.0 International
---

```{r, pkgs, echo=FALSE, message=FALSE}
knitr::opts_chunk$set(collapse = T, comment = "#>",
  fig.align="center")
library(mse)
```

# Introduction

This is an introduction.

# S4 classes

## FLom

```{r FLom, echo=FALSE, out.width='50%', fig.cap="**FLom class**: Structure of the FLom class. Slot name followed by the slot class, in parenthesis."}
knitr::include_graphics('diagrams/FLom.png')
```

## FLmse

```{r FLmse, echo=FALSE, out.width='50%', fig.cap="**FLmse class**: Structure of the FLmse class. Slot name followed by the slot class, in parenthesis."}
knitr::include_graphics('diagrams/FLmse.png')
```

## FLoem

## FLiem

## mpCtrl

## mseCtrl

# Functions

## mp()

```{r mp, echo=FALSE, out.width='50%', fig.cap="Workflow of the mp() function."}
knitr::include_graphics('diagrams/mp.svg')
```

### args

The *mp()* function takes as input a named list called *args*. These are arguments of the MSE run, and determine the time frame, frequency of application and lags. Only one argument is required:

- *iy*, intermediate year. Only required element in *args*. The first year in which the procedure is applied.

For all other, default values are generated acording to the *om* object dimensions, or from internal defaults, as follows:

- *y0*, first year. Defaults to start of *om*.
- *fy*, final year. Defaults to last year of *om*.
- nsqy, number of years to use for *status quo* calculations. Defaults to 3.
- *it*, number of iterations. Defaults to iterations in *om*.
- *data_lag*, difference between final year of data and *iy*. Defaults to 1.
- *management_lag*, number of years between year of year of application and implementation.
- *frq*, frequency. How often is the procedure to be applied, and for how long is a recommendation valid. Defaults to 1.

All these values can be simply overiden by including them in the *args* argument to *mp()*. The complete list of arguments is available to every *@method* function in any element in the MSE control. In addition, these year dimension nbames vector, generated inside *mp()*, can also be used in any module function:

- *vy*, the years in which the procedure is to be applied, from *iy* to *fy*. A character vector.


## performance()

# Extending mse with your own functions

## hcr

## sa

# More information

* You can submit bug reports, questions or suggestions on `mse` at the `mse` issue page ^[<https://github.com/flr/mse/issues>], or on the *FLR* mailing list.
* Or send a pull request to <https://github.com/flr/mse/>
* For more information on the FLR Project for Quantitative Fisheries Science in R, visit the FLR webpage ^[<http://flr-project.org>].
* The latest version of `mse` can always be installed using the `devtools` package, by calling
```{r, devtools, echo=TRUE, eval=FALSE}
	library(devtools)
	install_github('flr/mse')
```

## Software Versions

* `r version$version.string`
* FLCore: `r packageVersion('FLCore')`
* mse: `r packageVersion('mse')`
* **Compiled**: `r date()`
* **Git Hash**: `r system("git log --pretty=format:'%h' -n 1", intern=TRUE)`

## Author information

**Iago MOSQUEIRA**. Wageningen Marine Research.
**Ernesto JARDIM**. Marine Stewardship Council.

# References