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README.Rmd
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README.Rmd
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---
output:
github_document:
html_preview: false
bibliography: README.bib
---
[](https://travis-ci.org/ices-tools-prod/icesVMS)
[](https://cran.r-project.org/package=icesVMS)
[](https://cran.r-project.org/package=icesVMS)
[](https://cran.r-project.org/package=icesVMS)
[<img align="right" alt="ICES Logo" width="17%" height="17%" src="http://ices.dk/_layouts/15/1033/images/icesimg/iceslogo.png">](http://ices.dk)
```{r, setup, show = FALSE}
library(knitr)
library(icesVMS)
```
icesVMS
=======
icesVMS Functions to support the creation of ICES Fisheries Overviews, ....
icesVMS is implemented as an [R](https://www.r-project.org) package
<!-- and available on [CRAN](https://cran.r-project.org/package=icesVMS). -->
and available on GitHub and our [CRAN-like repository](https://ices-tools-prod.r-universe.dev/ui#builds)
Installation
------------
icesVMS can be installed from our CRAN-like repository using the standard `install.packages()` command
```R
install.packages("icesVMS", repos = 'https://ices-tools-prod.r-universe.dev')
```
Usage
-----
For a summary of the package:
```R
library(icesVMS)
?icesVMS
```
Examples
--------
## Download c square information
All of the VMS data submitted to ICES is at the c square level (concise spatial query and representation system, [@reese03_csquares]), and to aid in the exploration of display of data summaries extracted from the ICES VMS/Logbook database there is a service to extract information related to a C square. For example, the following code returns a table of all the c squares in the Celtic Seas ecoregion (see https://ices.dk/community/advisory-process/Pages/ICES-ecosystems-and-advisory-areas.aspx):
```{r get_csquares, eval = 3, message = FALSE}
celtic <- get_csquare(ecoregion = "Celtic Seas")
sr_32D5 <- get_csquare(stat_rec="32D5")
get_csquare(c_square = "7501:114:383:4")
```
These can be plotted by parsing the WKT (Well Known Text, https://en.wikipedia.org/wiki/Well-known_text_representation_of_geometry) field (here using the `sf` package) and then plotting using `ggplot2`, for example:
```{r plot_csquares_6a, message = FALSE}
ukwest <- get_csquare(ices_area = "6a")
ukwest <- sf::st_as_sf(ukwest, wkt = "wkt", crs = 4326)
ggplot2::ggplot() +
ggplot2::geom_sf(data = ukwest, color = "lightblue", fill = "transparent")
```
## Download bottom contact model parameters (BENTHIS)
To calculate swept area ratio by c_square, ICES uses methods developed by the BENTHIS project and within the WGSFD in which gear codes are used to imply the area swept by the gear for a given fishing speed. The parameters are available via:
```{r benthis, echo = 1, results = 'asis', message = FALSE}
benthis <- get_benthis_parameters()
kable(benthis)
```
These high level gear categories referred to as `BenthisMet` are connected to lower level metiers via a lookup table maintained by the WGSFD and available via:
```{r metier_lookup, echo = 1, results = 'asis', message = FALSE}
metiers <- get_metier_lookup()
kable(metiers[1:10,c(2,4,6,7,11)])
```
## Total landings by country
The VMS/Logbook database also gives access to total landings by country and year. This information is used in the ICES Fisheries Overviews. All data used in the Fisheries Overviews is published where possible, so this function provides open access to the aggregated landings weights.
```{r landings, echo = 1, results = 'asis', message = FALSE}
benthis <- get_benthis_parameters()
kable(benthis)
```
# References