icesDatras

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R interface to DATRAS trawl database web services

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icesDatras
==========

icesDatras provides R functions that access the
[web services](https://datras.ices.dk/WebServices/Webservices.aspx) of the
[ICES](http://ices.dk) [DATRAS](http://datras.ices.dk) trawl survey database.

icesDatras is implemented as an [R](https://www.r-project.org) package and
available on [CRAN](https://cran.r-project.org/package=icesDatras).

DATRAS database support
-----------------------

If you have questions relating to the ICES DATRAS database or web services please email: DatrasAdministration@ices.dk

Installation
------------

icesDatras can be installed from CRAN using the `install.packages` command:

```R
install.packages("icesDatras")
```

Usage
-----

For a summary of the package:

```R
library(icesDatras)
?icesDatras
```
Information on available surveys in DATRAS:

```R
getSurveyList()

```

Working Examples 
-----

Extracting survey haul (HH), lenght (HL) and agebased (CA) data from a given survey, quarter and year, 
i.e. North Sea IBTS, Quarter 1, 2019:

```R
survey <- "NS-IBTS"
year <- 2019
quarter <- 1

HH <- getHHdata(survey, year, quarter) 
HL <- getHLdata(survey, year, quarter) 
CA <- getCAdata(survey, year, quarter) 
```

Extracting catch weight of cod from the Baltic Sea survey, year 2019, quarter 1.  
Note: The icesVocab package provides `findAphia`, a function to look up Aphia species codes.

```R
library(icesVocab)
aphia <- icesVocab::findAphia("cod")

survey <- "BITS"
years <- 2019
quarters <- 1
codwgt <- getCatchWgt(survey, years, quarters, aphia)

```

Get catch weight for Baltic cod from all quarters  in a small timeseries (e.g. 1991 to 2011) and plot the weight in a sipmle graph per quarter.

```R
library(icesVocab)
library(ggplot2)

aphia <- icesVocab::findAphia("cod")

survey <- "BITS"
years <- 1991:2011
quarters <- 1:4
codwgt <- getCatchWgt(survey, years, quarters, aphia)
codwgt %>% ggplot(aes(x = Year, y = CatchWgt, colour= Quarter)) + geom_point()
```

References
----------

ICES DATRAS database:
http://datras.ices.dk

ICES DATRAS web services:
https://datras.ices.dk/WebServices/Webservices.aspx

AphiaID of marine organisms: 
http://www.marinespecies.org/index.php

Development
-----------

icesDatras is developed openly on
[GitHub](https://github.com/ices-tools-prod/icesDatras).

Feel free to open an
[issue](https://github.com/ices-tools-prod/icesDatras/issues) there if you
encounter problems or have suggestions for future versions.

The current development version can be installed using:

```R
library(devtools)
install_github("ices-tools-prod/icesDatras")
```

icesDatras

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