CalCOFI maps digitalization

• Overview
• Workflow
• Content
• Installation
• Usage
• Citation
• Contributing
• Acknowledgments
• References

Overview

This project is dedicated to digitalize pteropod abundance maps from the CalCOFI Atlas No. 6 (McGowan 1967). Species maps have been scanned, saved as TIFF images and stored in the data/ directory.

Workflow

The R function digitizer() is used to interactively extract information from maps and save data in the outputs/ directory. digitizer() works as follow:

• Import a .tiff stored in the data/ directory
• Plot the image
• Ask user to extract metadata (species, cruise, and date)
• Ask user to define the spatial axes
• Ask user to click on data points
• Convert coordinates in WGS84 system
• Ask user to extact point values
• Save data (.csv file) in the outputs/ directory

After this pipeline is completed for one image, the next image is automatically loaded until all images are processed (except if the argument image is not NULL).

When the output (.csv file) is created, the image is considered as processed and it will never be imported again by digitizer(). Thus user can digitize maps over a long period.

Content

This repository is structured as follow:

• DESCRIPTION: contains project metadata (authors, description, license, dependencies, etc.).
• R/: contains R functions developed especially for this project.
• data/: contains raw data used in this project (CalCOFI maps).
• outputs/: contains outputs of the project (one csv file per map).

Installation

To install this project:

• Fork this repository using the GitHub interface.
• Clone your fork using git clone fork-url (replace fork-url by the URL of your fork). Alternatively, open RStudio IDE and create a New Project from Version Control.

For users that are not familiar with git, Download the ZIP of the project.

Usage

Important

Do not use RStudio or Positron to run this project. It depends on the locator() function not supported by these two IDE.

• Open a Terminal (Windows user can open Git Bash)
• Launch R by typing R
• Install the devtools, cli and recolorize packages

To run the project:

• Navigate to calcofi directory by using setwd()
• Load the project by running devtools::load_all()
• Start digitalizing maps with digitizer()

You will be ask to answer some questions and to click on the map. Just follow instructions.

NB: By default, the argument day_night of the function digitizer() is set to TRUE: user will be asked to select the color the point. Otherwise, this question will be skipped. If points on the map are all black, use digitizer(day_night = FALSE). If you have two colors, use digitizer() and you will be asked to select the color of the point.

For the reporting of data values, two questions will be asked:

1. Color of the point (if digitizer(day_night = TRUE))

• Type b for black (night sampling)
• Type w for white (day sampling)

2. Abundance classe

• Type 0 for no individual per 1000m³ of water
• Type 1 for 1-49 individuals per 1000m³ of water
• Type 2 for 50-499 individuals per 1000m³ of water
• Type 3 for 500-4,999 individuals per 1000m³ of water
• Type 4 for 5,000-49,999 individuals per 1000m³ of water
• Type 5 for 50,000-499,999 individuals per 1000m³ of water
• Type 6 for > 500,000 individuals per 1000m³ of water

After digitalizing a first map, have a look at the outputs/ directory: data should have been saved as a csv file (see the example). The name of the csv will be the same as the image.

Citation

Please use the following citation:

Casajus N (2025) Digitalization of CalCOFI maps. URL: https://github.com/FRBCesab/calcofi/.

Acknowledgments

This project has been developed for the FRB-CESAB research group Dynamite that aims to synthesize and compile a unique and comprehensive database to reveal the dynamics of aragonite shell production and export in the world ocean today and over recent decades.

References

McGowan JA (1967) Distributional atlas of pelagic molluscs in the California Current region. CalCOFI Atlas No. 6. URL: https://calcofi.org/downloads/publications/atlases/CalCOFI_Atlas_06.pdf