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icesDatras

R interface to DATRAS trawl database web services

https://github.com/ices-tools-prod/icesDatras

Science Score: 26.0%

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    Scientific vocabulary similarity
    Low similarity (13.2%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

R interface to DATRAS trawl database web services

Basic Info
Statistics
  • Stars: 14
  • Watchers: 9
  • Forks: 8
  • Open Issues: 4
  • Releases: 7
Created almost 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

Build Status codecov local release CRAN Status CRAN Monthly CRAN Total License

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icesDatras

icesDatras provides R functions that access the web services of the ICES DATRAS trawl survey database.

icesDatras is implemented as an R package and available on CRAN.

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.

Feel free to open an issue 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")

Owner

  • Name: ICES tools (production)
  • Login: ices-tools-prod
  • Kind: organization
  • Email: taf@ices.dk
  • Location: Copenhagen, Denmark

Tools that are operational and maintained by the ICES Secretariat

GitHub Events

Total
  • Push event: 1
Last Year
  • Push event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 223
  • Total Committers: 11
  • Avg Commits per committer: 20.273
  • Development Distribution Score (DDS): 0.587
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Arni Magnusson a****a@h****s 92
colin millar c****r@g****m 73
Colin Millar c****r@i****k 27
Colin Millar c****r@g****m 17
Adriana Villamor a****r@i****k 5
Cecilia Kvaavik c****k@i****k 3
Scott Large s****e@u****m 2
Alban Sagouis 2****s@u****m 1
Alexandros Kokkalis a****9@g****m 1
Jeroen Ooms j****s@g****m 1
slarge l****i@g****m 1
Committer Domains (Top 20 + Academic)
ices.dk: 3 hafro.is: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 26
  • Total pull requests: 18
  • Average time to close issues: 11 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 12
  • Total pull request authors: 7
  • Average comments per issue: 2.31
  • Average comments per pull request: 0.06
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • colinpmillar (7)
  • arni-magnusson (4)
  • slarge (3)
  • James-Thorson (3)
  • hgerritsen (2)
  • afredston (1)
  • pdolder (1)
  • AndyCampbell (1)
  • einarhjorleifsson (1)
  • ClumpusJim (1)
  • davidcurrie2001 (1)
  • Franvgls (1)
Pull Request Authors
  • colinpmillar (11)
  • arni-magnusson (2)
  • alko989 (1)
  • slarge (1)
  • AlbanSagouis (1)
  • jeroen (1)
  • odontaster (1)
Top Labels
Issue Labels
bug (5) api issue (1) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 273 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: icesDatras

DATRAS Trawl Survey Database Web Services

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 273 Last month
Rankings
Forks count: 8.0%
Stargazers count: 15.1%
Dependent repos count: 19.2%
Average: 23.4%
Dependent packages count: 28.6%
Downloads: 45.9%
Maintainers (1)
colin.millar@ices.dk
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • utils * imports
  • icesVocab * suggests