README.Rmd

---
output: 
  html_document: 
    keep_md: yes
editor_options: 
  chunk_output_type: console
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  message = FALSE, 
  warning = FALSE,
  comment = "#>"
  #, fig.path = "man/figures/README-"
)
```

# RstoxUtils
**Utility functions for the Stox Project. R package, updated `r packageDate("RstoxUtils")`.**

This package contains utility functions for stock assessment and data flow within the Institute of Marine Research (IMR). The package has two purposes: 1) To function as a showcase and developmental platform for functions that may be included in the future releases of the Stox Project. 2) To provide a collection of functions needed in the internal workflow of the Deep-sea species group at IMR.

## Installation

The package requires the [**RstoxData**](https://github.com/StoXProject/RstoxData/releases) [Stox project](https://github.com/StoXProject) package to function. These packages can be installed by following the links for each package or using the [**devtools**](https://cran.r-project.org/web/packages/devtools/index.html) package. The **RstoxUtils** package can be installed using **devtools** once all Stox project packages are installed correctly. 

```{r eval = FALSE}
devtools::install_github("DeepWaterIMR/RstoxUtils", upgrade = "never")
```

The **RstoxUtils** uses multiple GIS packages developed for R. You may have to update these (Packages -> Update -> Select all -> Install updates in R Studio). 

```{r echo=FALSE, message=FALSE, warning=FALSE}
library(kableExtra)
library(knitr)
```

If the installation of a dependency fails, try installing those packages manually (using RStudio or `install.packages`).

## Usage

See the [website](https://deepwaterimr.github.io/RstoxUtils), [function reference](https://deepwaterimr.github.io/RstoxUtils/reference/index.html) and specific articles for the use of the package:

 1. [Sales note data](https://deepwaterimr.github.io/RstoxUtils/articles/LandingsData.html)
 2. [ERS data](https://deepwaterimr.github.io/RstoxUtils/articles/ERSdata.html)
 3. [Biotic data](https://deepwaterimr.github.io/RstoxUtils/articles/BioticData.html)

Note that the strata functions from this package have been moved to the [RstoxStrata](https://deepwaterimr.github.io/RstoxStrata/index.html) package and the entire IMR Biotic database can be accessed using the [BioticExplorerServer package](https://github.com/DeepWaterIMR/BioticExplorerServer)

## Citation

When using use the package for stock assessment or scientific articles, please cite it:

```{r}
citation("RstoxUtils")
```

## Contributions and contact information

Any contributions to the package are more than welcome. Please contact the package creator Mikko Vihtakari (<mikko.vihtakari@hi.no>) to discuss your ideas on improving the package or place a request in the issues section.