snakepowerpoint / compiledatras

Causal effects of population dynamics and environmental changes on spatial variability of marine fishes

This repository is an implementaion for parsing all surveys in the Database of Trawl Surveys (DATRAS) from the International Council for the Exploration of the Sea (ICES) for research work Causal effects of population dynamics and environmental changes on spatial variability of marine fishes.

• For readers who want to quickly parse surveys, please refer to Quickly Getting Started.
• For readers who want to parse surveys from scratch, please refer to Step by Step Analysis.

The repository contains:

• Source code for parsing surveys
• Raw data downloaded from DATRAS via the R-package icesDatras (https://github.com/ices-tools-prod/icesDatras) provided by ICES.
• Compiled species code defined in ICES

Requirements

R program with version 3.5.0. R is a free software and publicly available at https://www.r-project.org/. To install R, please follow procedures below:

1. Choose an CRAN Mirrors
2. Choose your operating system
3. Download binaries for base distribution
4. Install R accordingly

Previous versions are available at https://cran.r-project.org/bin/windows/base/old/. All R-packages and the corresponding versions used in this study are listed below:

• icesDatras 1.3-0

Quickly Getting Started

1. Open parse_survey.r in R, and set the working directory wd to the path where you save the repository.

2. Run code in each survey block in parse_survey.r. For example, the following code block is for parsing Baltic International Trawl Survey (BITS).

   # BITS: Baltic International Trawl Survey
   data = "BITSdata"
   survey_path = paste0(file.path(wd, "survey_outside_north_sea", data), ".RData")
   load(survey_path)
   
   years = c(1991:2018)
   quarters = c(1, 4)
   
   parse_survey(data, years, quarters)
   rm(list=c(data, data_list))
   

   After running the code, a csv file (survey_name.csv) will be generated and saved in the repository. This .csv file summarizes time series data of each species in the survey. We will then filter species and surveys based on these .csv files.

   We already provided all generated .csv file for each survey. Please check it in directory survey_stat.

Step by Step Analysis

1. Use template code in download_survey.R to overview surveys in DATRAS.

2. Use template code in download_survey.R to download age surveys data in DATRAS.

   Please save survey data in directory survey_north_sea and survey_outside_north_sea accordingly.

3. Open parse_species_code.r in R, and set the working directory wd to the path where you save the repository.

4. Run parse_species_code.R to compile species code defined by ICES in each survey.

   We have compiled a species-name chart (Species code.csv) to facilitate transformation of species code to Latin name and common name.

5. Open parse_survey.r in R, and set the working directory wd to the path where you save the repository.

6. Run code in each survey block in parse_survey.r as described in Quickly Getting Started above.

Contact

If you find any bugs or have any questions about the implementation, pelease contact us via [email protected]